Activity
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| Clefting v4.91 | CDK13 |
Achchuthan Shanmugasundram gene: CDK13 was added gene: CDK13 was added to Clefting. Sources: Literature Mode of inheritance for gene: CDK13 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CDK13 were set to 29222009; 37010288 Review for gene: CDK13 was set to RED Added comment: PMID:29222009 - One of three patients reported with de novo heterozygous CDK13 variants had submucosal cleft palate. DECIPHER database - Only one of 42 patients reported with heterozygous sequence variants in CDK13 gene had orofacial cleft as one of the phenotypes. Sources: Literature |
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| Clefting v4.90 | NEB |
Achchuthan Shanmugasundram changed review comment from: PMID:12207937 - A 9 month-old boy from one of five families affected by nemaline myopathy and reported with NEB variants had cleft palate. This patient was homozygous for 1-bp deletion in exon 184, which was also found in the mother, whereas no DNA was available from father. PMID:21798101 - Two siblings were reported with severe arthrogryposis multiplex congenital and were identified with compound heterozygous variants in NEB gene (c.1152 + 1G > T & c.11318_11319del), of which one patient had cleft palate. PMID:33376055 - A male foetus of consanguineous parents with a severe congenital syndrome characterized by arthrogryposis detected at 13 weeks of gestation had cleft palate and was identified with homozygous splice-site NEB variant (c.19,102-1G>T). DECIPHER databse - Of 10 patients with biallelic (compound heterozygous or homozygous) sequence variants in NEB gene reported in DECIPHER database, one patient with compound heterozygous NEB variants had bifid uvula. Sources: Literature; to: PMID:12207937 - A 9 month-old boy from one of five families affected by nemaline myopathy and reported with NEB variants had cleft palate. This patient was homozygous for 1-bp deletion in exon 184, which was also found in the mother, whereas no DNA was available from father. PMID:21798101 - Two siblings were reported with severe arthrogryposis multiplex congenital and were identified with compound heterozygous variants in NEB gene (c.1152 + 1G > T & c.11318_11319del), of which one patient had cleft palate. PMID:33376055 - A male foetus of consanguineous parents with a severe congenital syndrome characterized by arthrogryposis detected at 13 weeks of gestation had cleft palate and was identified with homozygous splice-site NEB variant (c.19,102-1G>T). DECIPHER databse - Of 10 patients with biallelic (compound heterozygous or homozygous) sequence variants in NEB gene reported in DECIPHER database, one patient with compound heterozygous NEB variants had bifid uvula. Cleft palate has been associated as one of the clinical presentations of Arthrogryposis multiplex congenita 6 (MIM #619334) in OMIM. Sources: Literature |
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| Clefting v4.90 | NEB | Achchuthan Shanmugasundram Publications for gene: NEB were set to 12207937; 21798101; 33376055 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.89 | NEB | Achchuthan Shanmugasundram edited their review of gene: NEB: Changed publications to: 12207937, 21798101, 33376055, 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.89 | ECEL1 | Achchuthan Shanmugasundram Classified gene: ECEL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.89 | ECEL1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three cases reported with clefting, it is only present in a small subsection (<10%) of patients with ECEL1 biallelic variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.89 | ECEL1 | Achchuthan Shanmugasundram Gene: ecel1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.88 | NEB | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: Although there are three unrelated cases reported with cleft palate in literature and a case reported with bifid uvula in the DECIPHER project, clefting has not been consistently reported as a phenotype in patients with biallelic NEB variants and is not fully penetrant in some families .; to: Comment on list classification: Although there are three unrelated cases reported with cleft palate in literature and a case reported with bifid uvula in the DECIPHER project, clefting has not been consistently reported as a phenotype in patients with biallelic NEB variants and is not fully penetrant in at least one family with clefting. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.88 | NEB | Achchuthan Shanmugasundram Classified gene: NEB as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.88 | NEB | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are three unrelated cases reported with cleft palate in literature and a case reported with bifid uvula in the DECIPHER project, clefting has not been consistently reported as a phenotype in patients with biallelic NEB variants and is not fully penetrant in some families . | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.88 | NEB | Achchuthan Shanmugasundram Gene: neb has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.87 | NEB |
Achchuthan Shanmugasundram gene: NEB was added gene: NEB was added to Clefting. Sources: Literature Mode of inheritance for gene: NEB was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NEB were set to 12207937; 21798101; 33376055 Phenotypes for gene: NEB were set to Arthrogryposis multiplex congenita 6, OMIM:619334 Review for gene: NEB was set to AMBER Added comment: PMID:12207937 - A 9 month-old boy from one of five families affected by nemaline myopathy and reported with NEB variants had cleft palate. This patient was homozygous for 1-bp deletion in exon 184, which was also found in the mother, whereas no DNA was available from father. PMID:21798101 - Two siblings were reported with severe arthrogryposis multiplex congenital and were identified with compound heterozygous variants in NEB gene (c.1152 + 1G > T & c.11318_11319del), of which one patient had cleft palate. PMID:33376055 - A male foetus of consanguineous parents with a severe congenital syndrome characterized by arthrogryposis detected at 13 weeks of gestation had cleft palate and was identified with homozygous splice-site NEB variant (c.19,102-1G>T). DECIPHER databse - Of 10 patients with biallelic (compound heterozygous or homozygous) sequence variants in NEB gene reported in DECIPHER database, one patient with compound heterozygous NEB variants had bifid uvula. Sources: Literature |
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| Clefting v4.86 | ECEL1 |
Achchuthan Shanmugasundram changed review comment from: PMID:3013119 - Seven individuals from four unrelated families were reported with a wide phenotypic spectrum including severe congenital contractural syndromes and distal arthrogryposis type 5D and were identified with biallelic variants in ECEL1 gene. Of these two individuals from two different families presented with cleft palate. However, literature review in this publication showed only three patients from a total of 34 had cleft palate (9%). DECIPHER database - The only patient reported in DECIPHER with compound heterozygous sequence variants in ECEL1 gene had cleft soft palate. This gene was associated with distal arthrogryposis in both OMIM (MIM #615065) and Gene2Phenotype ('definitive' rating in the DD panel). OMIM recorded cleft palate as one of the clinical manifestations affecting some patients with this disorder. Sources: Literature; to: PMID:3013119 - Seven individuals from four unrelated families were reported with a wide phenotypic spectrum including severe congenital contractural syndromes and distal arthrogryposis type 5D and were identified with biallelic variants in ECEL1 gene. Of these two individuals from two different families presented with cleft palate. However, literature review in this publication showed that only three patients from a total of 34 patients with biallelic ECEL1 variants had cleft palate (9%). DECIPHER database - The only patient reported in DECIPHER with compound heterozygous sequence variants in ECEL1 gene had cleft soft palate. This gene was associated with distal arthrogryposis in both OMIM (MIM #615065) and Gene2Phenotype ('definitive' rating in the DD panel). OMIM recorded cleft palate as one of the clinical manifestations affecting some patients with this disorder. Sources: Literature |
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| Clefting v4.86 | ECEL1 |
Achchuthan Shanmugasundram gene: ECEL1 was added gene: ECEL1 was added to Clefting. Sources: Literature Mode of inheritance for gene: ECEL1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ECEL1 were set to 30131190; 37010288 Phenotypes for gene: ECEL1 were set to Arthrogryposis, distal, type 5D, OMIM:615065 Review for gene: ECEL1 was set to AMBER Added comment: PMID:3013119 - Seven individuals from four unrelated families were reported with a wide phenotypic spectrum including severe congenital contractural syndromes and distal arthrogryposis type 5D and were identified with biallelic variants in ECEL1 gene. Of these two individuals from two different families presented with cleft palate. However, literature review in this publication showed only three patients from a total of 34 had cleft palate (9%). DECIPHER database - The only patient reported in DECIPHER with compound heterozygous sequence variants in ECEL1 gene had cleft soft palate. This gene was associated with distal arthrogryposis in both OMIM (MIM #615065) and Gene2Phenotype ('definitive' rating in the DD panel). OMIM recorded cleft palate as one of the clinical manifestations affecting some patients with this disorder. Sources: Literature |
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| Short stature - SHOX deficiency v0.1 | SHOX | Achchuthan Shanmugasundram Tag Pseudoautosomal region 1 tag was added to gene: SHOX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Barth syndrome v0.1 | TAZ | Achchuthan Shanmugasundram Tag new-gene-name tag was added to gene: TAZ. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Gaucher disease v0.1 | GBA | Achchuthan Shanmugasundram Tag new-gene-name tag was added to gene: GBA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.85 | CDKL5 |
Achchuthan Shanmugasundram changed review comment from: Sources: Literature; to: Of 16 patients with sequence variants in CDKL5 in the DECIPHER database (https://www.deciphergenomics.org/), one of them had median cleft palate and another one had orofacial cleft. Sources: Literature |
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| Clefting v4.85 | CDKL5 |
Achchuthan Shanmugasundram gene: CDKL5 was added gene: CDKL5 was added to Clefting. Sources: Literature Mode of inheritance for gene: CDKL5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CDKL5 were set to 37010288 Review for gene: CDKL5 was set to RED Added comment: Sources: Literature |
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| Clefting v4.83 | CSNK2A1 |
Achchuthan Shanmugasundram gene: CSNK2A1 was added gene: CSNK2A1 was added to Clefting. Sources: Literature Mode of inheritance for gene: CSNK2A1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CSNK2A1 were set to 37010288 Review for gene: CSNK2A1 was set to RED Added comment: Of 21 patients with sequence variants in CSNK2A1 gene in the DECIPHER database (https://www.deciphergenomics.org/), two of them had cleft palate. Sources: Literature |
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| Clefting v4.82 | SOX5 |
Achchuthan Shanmugasundram gene: SOX5 was added gene: SOX5 was added to Clefting. Sources: Literature Mode of inheritance for gene: SOX5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SOX5 were set to 37010288 Review for gene: SOX5 was set to RED Added comment: Of 19 patients with sequence variants in SOX5 gene in the DECIPHER database (https://www.deciphergenomics.org/), one had cleft palate and another one had bifid uvula/ submucous cleft hard palate. Sources: Literature |
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| Clefting v4.81 | WDR26 |
Achchuthan Shanmugasundram gene: WDR26 was added gene: WDR26 was added to Clefting. Sources: Literature Mode of inheritance for gene: WDR26 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: WDR26 were set to 37010288 Review for gene: WDR26 was set to RED Added comment: Of 15 patients with sequence variants in WDR26 in the DECIPHER database (https://www.deciphergenomics.org/), two of them had (median) cleft palate. Sources: Literature |
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| Mitochondrial disorders v4.71 | MRPS23 | Achchuthan Shanmugasundram reviewed gene: MRPS23: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.12 | GIPC1 | Sarah Leigh Classified gene: GIPC1 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.12 | GIPC1 | Sarah Leigh Added comment: Comment on list classification: This gene will remain red as it is only the GIPC1_GGC expansion that has been associated with disease. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.12 | GIPC1 | Sarah Leigh Gene: gipc1 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.11 | GIPC1 | Sarah Leigh reviewed gene: GIPC1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.11 | GIPC1 | Sarah Leigh Phenotypes for gene: GIPC1 were changed from Oculopharyngodistal myopathy 2, OMIM:618940 to Oculopharyngodistal myopathy 2, OMIM:618940; oculopharyngodistal myopathy 2, MONDO:0030134 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.10 | GIPC1 | Sarah Leigh Tag STR tag was added to gene: GIPC1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.10 | GIPC1 | Sarah Leigh Classified gene: GIPC1 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.10 | GIPC1 | Sarah Leigh Gene: gipc1 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.9 | GIPC1 | Sarah Leigh Classified gene: GIPC1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.9 | GIPC1 | Sarah Leigh Gene: gipc1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.8 | SMPX |
Sarah Leigh Tag Q3_23_promote_green tag was added to gene: SMPX. Tag Q3_23_MOI tag was added to gene: SMPX. |
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| Distal myopathies v3.8 | SMPX | Sarah Leigh edited their review of gene: SMPX: Added comment: Hemizygous variants in SMPX have been associated with Myopathy, distal, 7, adult-onset, X-linked (OMIM:301075), but not been associated with phenotype in Gen2Phen. PMID: 33974137 reports four SMPX variants in seven families without shared haplotypes. In vitro studies suggested a gain-of-function action of these variants, resulting a protein that was less soluble compared to wildtype, which in some cases had a tendency to aggregate.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.38 | L2HGDH |
Achchuthan Shanmugasundram changed review comment from: PMID:15824270 - A 15 year-old boy with L-2-hydroxyglutaric aciduria was reported with early infantile-onset progressive psychomotor regression, mild choreodystonia affecting the distal part of the upper limbs, pyramidal signs, and epilepsy. PMID:18780161 - Of seven patients from three unrelated Tunisian families with L-2-hydroxyglutaric aciduria and with homozygous variants in L2HGDH gene, three patients from two different families had dystonia. PMID:24753671 - Two siblings were reported with dystonia diagnosed by classical neuroimaging findings with elevated urinary 2 hydroxyglutaric acid.; to: PMID:15824270 - A 15 year-old boy with L-2-hydroxyglutaric aciduria was reported with early infantile-onset progressive psychomotor regression, mild choreodystonia affecting the distal part of the upper limbs, pyramidal signs, and epilepsy. PMID:18780161 - Of seven patients from three unrelated Tunisian families with L-2-hydroxyglutaric aciduria and with homozygous variants in L2HGDH gene, three patients from two different families had dystonia. The age of onset of the disorder in these patients is around six years. PMID:24753671 - Two siblings (13 and 16 years of age with disease onset at 10 years of age) were reported with dystonia diagnosed by classical neuroimaging findings with elevated urinary 2 hydroxyglutaric acid. |
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| Childhood onset dystonia, chorea or related movement disorder v3.38 | SYT1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with childhood-onset dystonia as a feature of Baker-Gordon syndrome. Hence, this gene should be promoted to green rating at the next major update.; to: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated children with dystonia as a feature of Baker-Gordon syndrome. Hence, this gene should be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.38 | SYT1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with dystonia as a feature of Baker-Gordon syndrome. Hence, this gene should be promoted to green rating at the next major update.; to: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with childhood-onset dystonia as a feature of Baker-Gordon syndrome. Hence, this gene should be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.8 | SMPX | Sarah Leigh Phenotypes for gene: SMPX were changed from Distal myopathy to Myopathy, distal, 7, adult-onset, X-linked, OMIM:301075; myopathy, distal, 7, adult-onset, X-linked, MONDO:0024771 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.7 | SMPX | Sarah Leigh Publications for gene: SMPX were set to PMID: 33974137 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.6 | SMPX | Sarah Leigh Classified gene: SMPX as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.6 | SMPX | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Distal myopathies v3.6 | SMPX | Sarah Leigh Gene: smpx has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.15 | SLC12A3 | Sarah Leigh Phenotypes for gene: SLC12A3 were changed from Hypokalaemic alkalosis with hypomagnesaemia & hypocalciuria; Gitelman syndrome, 263800 to Gitelman syndrome, OMIM: 263800; Gitelman syndrome, MONDO:0009904 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.46 | SLC12A3 | Sarah Leigh Phenotypes for gene: SLC12A3 were changed from Gitelman syndrome (Disorder of magnesium metabolism); Renal tubular acidosis to Gitelman syndrome, OMIM: 263800; Gitelman syndrome, MONDO:0009904 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.38 | SLC12A3 | Sarah Leigh Phenotypes for gene: SLC12A3 were changed from to Gitelman syndrome, OMIM: 263800; Gitelman syndrome, MONDO:0009904 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.598 | SLC12A3 | Sarah Leigh Phenotypes for gene: SLC12A3 were changed from Gitelman syndrome (Disorder of magnesium metabolism); Renal tubular acidosis to Gitelman syndrome, OMIM: 263800; Gitelman syndrome, MONDO:0009904 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.27 | SLC12A3 | Sarah Leigh Phenotypes for gene: SLC12A3 were changed from Gitelman syndrome (263800) to Gitelman syndrome, OMIM: 263800; Gitelman syndrome, MONDO:0009904 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.14 | SLC12A3 |
Sarah Leigh Tag monogenic-polygenic was removed from gene: SLC12A3. Tag monogenic - polygenic tag was added to gene: SLC12A3. |
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| Childhood onset dystonia, chorea or related movement disorder v3.37 | SLC12A3 |
Sarah Leigh Tag monogenic-polygenic was removed from gene: SLC12A3. Tag monogenic - polygenic tag was added to gene: SLC12A3. |
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| Likely inborn error of metabolism v4.45 | SLC12A3 |
Sarah Leigh Tag monogenic-polygenic was removed from gene: SLC12A3. Tag monogenic - polygenic tag was added to gene: SLC12A3. |
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| Ductal plate malformation v1.26 | SLC12A3 |
Sarah Leigh Tag monogenic-polygenic was removed from gene: SLC12A3. Tag monogenic - polygenic tag was added to gene: SLC12A3. |
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| Renal tubulopathies v4.14 | SLC12A3 | Sarah Leigh Publications for gene: SLC12A3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.13 | SLC12A3 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.37 | SLC12A3 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.37 | SLC12A3 | Sarah Leigh Publications for gene: SLC12A3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.45 | SLC12A3 | Sarah Leigh Publications for gene: SLC12A3 were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.44 | SLC12A3 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.597 | SLC12A3 | Sarah Leigh Publications for gene: SLC12A3 were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.26 | SLC12A3 | Sarah Leigh Publications for gene: SLC12A3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.13 | SLC12A3 | Sarah Leigh commented on gene: SLC12A3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.36 | SLC12A3 | Sarah Leigh commented on gene: SLC12A3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.44 | SLC12A3 | Sarah Leigh commented on gene: SLC12A3: Heterozygous digenic SLC12A3 and CLCNKB variants have been associated with a variant of Gitelman syndrome (PMID: 26770037;30999883). However, the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.596 | SLC12A3 | Sarah Leigh commented on gene: SLC12A3: Heterozygous digenic SLC12A3 and CLCNKB variants have been associated with a variant of Gitelman syndrome (PMID: 26770037;30999883). However, the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.25 | SLC12A3 | Sarah Leigh commented on gene: SLC12A3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.596 | SLC12A3 | Sarah Leigh Tag monogenic - polygenic tag was added to gene: SLC12A3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neonatal diabetes - small panel v0.2 | Achchuthan Shanmugasundram List of related panels changed from R143 to R143; Neonatal diabetes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.25 | SLC12A3 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type IH or S v0.3 | Achchuthan Shanmugasundram List of related panels changed from R277 to R277; Mucopolysaccharidosis type IH/S | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucolipidosis II and III Alpha or Beta v0.3 | Achchuthan Shanmugasundram List of related panels changed from R289 to R289; Mucolipidosis II and III Alpha/Beta | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.13 | SLC12A1 | Sarah Leigh commented on gene: SLC12A1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.105 | SLC12A1 | Sarah Leigh commented on gene: SLC12A1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.9 | SLC12A1 | Sarah Leigh commented on gene: SLC12A1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.13 | SLC12A1 | Sarah Leigh Publications for gene: SLC12A1 were set to 8640224; 30999883; 32506365; 26770037; 27103762; 8640224; 9355073; 28095294; 32506365 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic nephrogenic diabetes insipidus v1.11 | SLC12A1 | Sarah Leigh commented on gene: SLC12A1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.12 | SLC12A1 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.105 | SLC12A1 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.9 | SLC12A1 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic nephrogenic diabetes insipidus v1.11 | SLC12A1 | Sarah Leigh Tag monogenic-polygenic tag was added to gene: SLC12A1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.12 | SLC12A1 | Sarah Leigh Phenotypes for gene: SLC12A1 were changed from Type 1 Bartter syndrome: infantile onset, pregnancy noted for polyhydramnios. Hyperprostagladinuria. Hypokalaemia and metabolic alkalosis +/- nephrocalcinosis; Bartter syndrome, type 1, 601678 to Bartter syndrome, type 1, OMIM:601678; Bartter disease type 1, MONDO:0100344 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.105 | SLC12A1 | Sarah Leigh Phenotypes for gene: SLC12A1 were changed from Bartter syndrome, type 1 601678 to Bartter syndrome, type 1, OMIM:601678; Bartter disease type 1, MONDO:0100344 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.9 | SLC12A1 | Sarah Leigh Phenotypes for gene: SLC12A1 were changed from Type 1 Bartter syndrome: infantile onset, pregnancy noted for polyhydramnios; Hyperprostagladinuria; Hypokalaemia and metabolic alkalosis +/- nephrocalcinosis; Antenatal Bartter Syndrome; Bartter syndrome, type 1, 601678 to Bartter syndrome, type 1, OMIM:601678; Bartter disease type 1, MONDO:0100344 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic nephrogenic diabetes insipidus v1.11 | SLC12A1 | Sarah Leigh Phenotypes for gene: SLC12A1 were changed from hyperparathyroidism, hypercalcemia, nephrogenic diabetes insipidus, and nephrocalcinosis; associated with Barter syndrome and secondary inherited NDI only to Bartter syndrome, type 1, OMIM:601678; Bartter disease type 1, MONDO:0100344 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.11 | SLC12A1 | Sarah Leigh Publications for gene: SLC12A1 were set to 8640224; 30999883; 32506365; 26770037; 27103762 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.104 | SLC12A1 | Sarah Leigh Publications for gene: SLC12A1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.8 | SLC12A1 | Sarah Leigh Publications for gene: SLC12A1 were set to PMID: 21631963; 21189980; 20219833; 19513753; 19096086; 18830715; 17998760; 16807401 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic nephrogenic diabetes insipidus v1.10 | SLC12A1 | Sarah Leigh Publications for gene: SLC12A1 were set to 28095294; 32506365 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic nephrogenic diabetes insipidus v1.9 | SLC12A1 | Sarah Leigh Publications for gene: SLC12A1 were set to 28095294 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.10 | CLCNKA | Sarah Leigh Classified gene: CLCNKA as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.10 | CLCNKA | Sarah Leigh Gene: clcnka has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.9 | CLCNKA | Sarah Leigh Classified gene: CLCNKA as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.9 | CLCNKA | Sarah Leigh Added comment: Comment on list classification: The rating of this gene is being changed to Red from Amber, to reflect that GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.9 | CLCNKA | Sarah Leigh Gene: clcnka has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.254 | CLCNKA | Sarah Leigh Phenotypes for gene: CLCNKA were changed from Bartter syndrome, type 4b, digenic, 613090; Infantile Bartter syndrome with sensorineural deafness, intellectual disability to Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.8 | CLCNKA | Sarah Leigh Phenotypes for gene: CLCNKA were changed from Bartter syndrome, type 4b, digenic, OMIM:613090 to Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.10 | CLCNKA | Sarah Leigh Phenotypes for gene: CLCNKA were changed from BARTTER SYNDROME TYPE 4B 613090 to Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.7 | CLCNKA | Sarah Leigh Phenotypes for gene: CLCNKA were changed from Bartter syndrome, type 4b, digenic, 613090 to Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.253 | CLCNKA | Sarah Leigh Publications for gene: CLCNKA were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.253 | CLCNKA | Sarah Leigh Added comment: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267;32488762). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.253 | CLCNKA | Sarah Leigh Mode of inheritance for gene: CLCNKA was changed from to Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.6 | CLCNKA | Sarah Leigh changed review comment from: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events.; to: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267;32488762). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.9 | CLCNKA | Sarah Leigh changed review comment from: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events.; to: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267;32488762). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.7 | CLCNKA | Sarah Leigh Added comment: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267;32488762). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.7 | CLCNKA | Sarah Leigh Mode of inheritance for gene: CLCNKA was changed from BIALLELIC, autosomal or pseudoautosomal to Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.6 | CLCNKA | Sarah Leigh Tag polygenic tag was added to gene: CLCNKA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.6 | CLCNKA | Sarah Leigh Publications for gene: CLCNKA were set to 18310267; 32488762 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.9 | CLCNKA | Sarah Leigh Publications for gene: CLCNKA were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.6 | CLCNKA | Sarah Leigh Publications for gene: CLCNKA were set to 15044642; 18310267 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.8 | CLCNKA | Sarah Leigh Tag polygenic tag was added to gene: CLCNKA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.8 | CLCNKA | Sarah Leigh Added comment: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.8 | CLCNKA | Sarah Leigh Mode of inheritance for gene: CLCNKA was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.5 | CLCNKA | Sarah Leigh Added comment: Comment on mode of inheritance: Digenic CLCNKA & CLCNKB variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090)(PMID: 15044642;18310267). The current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.5 | CLCNKA | Sarah Leigh Mode of inheritance for gene: CLCNKA was changed from BIALLELIC, autosomal or pseudoautosomal to Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.4 | CLCNKA | Sarah Leigh Publications for gene: CLCNKA were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.3 | CLCNKA | Sarah Leigh Tag polygenic tag was added to gene: CLCNKA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.36 | SLC18A2 | Achchuthan Shanmugasundram Classified gene: SLC18A2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.36 | SLC18A2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is sufficient evidence (at least four unrelated cases and functional evidence) available for the association of this gene to movement disorders including dystonia. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.36 | SLC18A2 | Achchuthan Shanmugasundram Gene: slc18a2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.35 | SLC18A2 | Achchuthan Shanmugasundram Phenotypes for gene: SLC18A2 were changed from Brain Dopamine Serotonin Vesicular Transport Disease (Other disorders of neurotransmitter metabolism); Vesicular monoamine transporter deficiency to ?Parkinsonism-dystonia, infantile, 2, OMIM:618049 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.34 | SLC18A2 | Achchuthan Shanmugasundram Publications for gene: SLC18A2 were set to 27830117; 28477711; 26497564; 23363473; 27520881; 24398404; 24018103; 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.33 | SLC18A2 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SLC18A2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.33 | SLC18A2 |
Achchuthan Shanmugasundram changed review comment from: PMID:23363473 - Eight children from an extended consanguineous Saudi Arabian family had a complex neurological disorder apparent since infancy. This disorder is characterised by abnormal movements, including parkinsonism, dystonia, and poor fine motor skills, as well as autonomic dysfunction, including abnormal sweating, cold extremities, and poor sleep. They were identified with a homozygous SLC18A2 variant (p.Pro387Leu). Functional evaluation showed that protein harbouring this variant has dramatically reduced activity than wild type protein, suggesting severe, but not complete loss of function as mechanism of action. PMID:26497564 - Two male siblings from a consanguineous fancy was reported with a disorder comprising truncal hypotonia, a general paucity of movements, extrapyramidal signs and cognitive delay. They were identified with a homozygous SLC18A2 variant (p.Pro237His).; to: PMID:23363473 - Eight children from an extended consanguineous Saudi Arabian family had a complex neurological disorder apparent since infancy. This disorder is characterised by abnormal movements, including parkinsonism, dystonia, and poor fine motor skills, as well as autonomic dysfunction, including abnormal sweating, cold extremities, and poor sleep. They were identified with a homozygous SLC18A2 variant (p.Pro387Leu). Functional evaluation showed that protein harbouring this variant has dramatically reduced activity than wild type protein, suggesting severe, but not complete loss of function as mechanism of action. PMID:26497564 - Two male siblings from a consanguineous family was reported with a disorder comprising truncal hypotonia, a general paucity of movements, extrapyramidal signs and cognitive delay. They were identified with a homozygous SLC18A2 variant (p.Pro237His). PMID:31240161 - A child from a consanguineous family presented with hypotonia, mental disability, epilepsy, uncontrolled movements, and gastrointestinal problems and was identified with a homozygous SLC18A2 variant (p.Pro316Ala). PMID:34078222 - A 6-month-old male infant who presented with developmental delay and suspected cerebral palsy was also diagnosed with infantile parkinsonism-dystonia-2 and was identified with the homozygous variant (p.Pro237His) reported in PMID:26497564. This gene has been associated with relevant phenotypes in OMIM (PMID:618049), but not in Gene2Phenotype. |
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| Childhood onset dystonia, chorea or related movement disorder v3.33 | SLC18A2 |
Achchuthan Shanmugasundram commented on gene: SLC18A2: PMID:23363473 - Eight children from an extended consanguineous Saudi Arabian family had a complex neurological disorder apparent since infancy. This disorder is characterised by abnormal movements, including parkinsonism, dystonia, and poor fine motor skills, as well as autonomic dysfunction, including abnormal sweating, cold extremities, and poor sleep. They were identified with a homozygous SLC18A2 variant (p.Pro387Leu). Functional evaluation showed that protein harbouring this variant has dramatically reduced activity than wild type protein, suggesting severe, but not complete loss of function as mechanism of action. PMID:26497564 - Two male siblings from a consanguineous fancy was reported with a disorder comprising truncal hypotonia, a general paucity of movements, extrapyramidal signs and cognitive delay. They were identified with a homozygous SLC18A2 variant (p.Pro237His). |
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| Early onset or syndromic epilepsy v4.84 | TMEM63B | Annalisa Vetro reviewed gene: TMEM63B: Rating: ; Mode of pathogenicity: None; Publications: 37421948; Phenotypes: abnormal myelination, developmental and epileptic encephalopathy, hemolytic anemia, infantile spasms; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.5 | CLCNKB | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.5 | CLCNKB | Sarah Leigh Mode of inheritance for gene: CLCNKB was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.4 | CLCNKB | Sarah Leigh Tag monogenic-polygenic tag was added to gene: CLCNKB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.252 | CLCNKB | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.252 | CLCNKB | Sarah Leigh Mode of inheritance for gene: CLCNKB was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.251 | CLCNKB |
Sarah Leigh Tag digenic was removed from gene: CLCNKB. Tag monogenic-polygenic tag was added to gene: CLCNKB. |
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| Fetal anomalies v3.103 | CLCNKB | Sarah Leigh Tag monogenic-polygenic tag was added to gene: CLCNKB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.103 | CLCNKB | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.103 | CLCNKB | Sarah Leigh Mode of inheritance for gene: CLCNKB was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.25 | CLCNKB | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.25 | CLCNKB | Sarah Leigh Mode of inheritance for gene: CLCNKB was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.3 | CLCNKB | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for CLCNKB should be BIALLELIC, autosomal or pseudoautosomal. Although digenic CLCNKB & CLCNKA variants are associated with Bartter syndrome, type 4b, digenic (OMIM:613090), this phenotype is not relevant to this panel and the current GMS rare disease bioinformatic pipeline does not allow for interpretation of digenic events. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.3 | CLCNKB | Sarah Leigh Mode of inheritance for gene: CLCNKB was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.24 | CLCNKB | Sarah Leigh Tag monogenic-polygenic tag was added to gene: CLCNKB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.2 | CLCNKB |
Sarah Leigh Tag monogenic-polygenic tag was added to gene: CLCNKB. Tag Q3_23_MOI tag was added to gene: CLCNKB. |
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| Ductal plate malformation v1.24 | CLCNKB | Sarah Leigh Mode of inheritance for gene: CLCNKB was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.2 | CLCNKB | Sarah Leigh reviewed gene: CLCNKB: Rating: GREEN; Mode of pathogenicity: None; Publications: 120550, 9326936, 15717167; Phenotypes: Bartter syndrome, type 3, OMIM:607364, Bartter disease type 3, MONDO:0011822; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.33 | SLC18A2 | Achchuthan Shanmugasundram reviewed gene: SLC18A2: Rating: GREEN; Mode of pathogenicity: None; Publications: 23363473, 26497564, 31240161, 34078222; Phenotypes: ?Parkinsonism-dystonia, infantile, 2, OMIM:618049; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.33 | TBC1D24 | Achchuthan Shanmugasundram Classified gene: TBC1D24 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.33 | TBC1D24 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated cases reported with dystonia as a feature of the overall phenotype. Hence, this gene can be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.33 | TBC1D24 | Achchuthan Shanmugasundram Gene: tbc1d24 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.32 | TBC1D24 | Achchuthan Shanmugasundram Phenotypes for gene: TBC1D24 were changed from Epilepsy, rolandic, with proxysmal exercise-induce dystonia and writer's cramp, MIM# 608105 to Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp, OMIM:608105; Developmental and epileptic encephalopathy 16, OMIM:615338 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.31 | TBC1D24 | Achchuthan Shanmugasundram Publications for gene: TBC1D24 were set to 31257402 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.30 | TBC1D24 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: TBC1D24. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.30 | TBC1D24 | Achchuthan Shanmugasundram reviewed gene: TBC1D24: Rating: GREEN; Mode of pathogenicity: None; Publications: 21087195, 23343562, 31257402; Phenotypes: Epilepsy, rolandic, with paroxysmal exercise-induce dystonia and writer's cramp, OMIM:608105, Developmental and epileptic encephalopathy 16, OMIM:615338; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.30 | SYT1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with dystonia as a feature of the SYT1-associated neurodevelopmental disorder. Hence, this gene should be promoted to green rating at the next major update.; to: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with dystonia as a feature of Baker-Gordon syndrome. Hence, this gene should be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.30 | SYT1 | Achchuthan Shanmugasundram Classified gene: SYT1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.30 | SYT1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with dystonia as a feature of the SYT1-associated neurodevelopmental disorder. Hence, this gene should be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.30 | SYT1 | Achchuthan Shanmugasundram Gene: syt1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.29 | SYT1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SYT1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.29 | SYT1 | Achchuthan Shanmugasundram reviewed gene: SYT1: Rating: GREEN; Mode of pathogenicity: None; Publications: 30107533; Phenotypes: Baker-Gordon syndrome, OMIM:618218; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.29 | SQSTM1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SQSTM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.29 | SQSTM1 | Achchuthan Shanmugasundram Classified gene: SQSTM1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.29 | SQSTM1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (three unrelated families) available for promoting this gene to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.29 | SQSTM1 | Achchuthan Shanmugasundram Gene: sqstm1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.28 | SQSTM1 | Achchuthan Shanmugasundram Phenotypes for gene: SQSTM1 were changed from Myopathy, distal, with rimmed vacuoles , MIM#617158 to Neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset, OMIM:617145 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.27 | SQSTM1 | Achchuthan Shanmugasundram reviewed gene: SQSTM1: Rating: GREEN; Mode of pathogenicity: None; Publications: 27545679; Phenotypes: Neurodegeneration with ataxia, dystonia, and gaze palsy, childhood-onset, OMIM:617145; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.27 | L2HGDH | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: L2HGDH. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.27 | L2HGDH | Achchuthan Shanmugasundram Classified gene: L2HGDH as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.27 | L2HGDH | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there are four unrelated cases with dystonia as a feature of the condition and hence this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.27 | L2HGDH | Achchuthan Shanmugasundram Gene: l2hgdh has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.26 | L2HGDH | Achchuthan Shanmugasundram Mode of inheritance for gene: L2HGDH was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.25 | L2HGDH | Achchuthan Shanmugasundram Phenotypes for gene: L2HGDH were changed from L-2-hydroxyglutaric aciduria, 236792 to L-2-hydroxyglutaric aciduria, OMIM:236792 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.24 | L2HGDH | Achchuthan Shanmugasundram Publications for gene: L2HGDH were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.23 | L2HGDH | Achchuthan Shanmugasundram reviewed gene: L2HGDH: Rating: GREEN; Mode of pathogenicity: None; Publications: 15824270, 18780161, 24753671; Phenotypes: L-2-hydroxyglutaric aciduria, OMIM:236792; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.251 | MKL2 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.251 | MKL2 | Achchuthan Shanmugasundram Classified gene: MKL2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.251 | MKL2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As there are only two unrelated cases reported so far, this gene should be rated amber for now. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.251 | MKL2 | Achchuthan Shanmugasundram Gene: mkl2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.250 | MKL2 | Achchuthan Shanmugasundram Phenotypes for gene: MKL2 were changed from neurodevelopmental disorder, MONDO:0700092 to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.250 | MKL2 | Achchuthan Shanmugasundram Phenotypes for gene: MKL2 were changed from neurodevelopmental disorder, MONDO:0700092 to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.250 | MKL2 | Achchuthan Shanmugasundram Phenotypes for gene: MKL2 were changed from neurodevelopmental disorder, MONDO:0700092 to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.249 | MKL2 | Achchuthan Shanmugasundram Phenotypes for gene: MKL2 were changed from neurodevelopmental disorder, MONDO:0700092 to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.249 | MKL2 | Achchuthan Shanmugasundram Phenotypes for gene: MKL2 were changed from neurodevelopmental phenotype with dysmorphic features to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.249 | MKL2 | Achchuthan Shanmugasundram Publications for gene: MKL2 were set to 37013900 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.249 | MKL2 | Achchuthan Shanmugasundram Publications for gene: MKL2 were set to 37013900 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.248 | MKL2 | Achchuthan Shanmugasundram Publications for gene: MKL2 were set to 37013900 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.248 | MKL2 | Achchuthan Shanmugasundram Publications for gene: MKL2 were set to PMID:37013900 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.247 | MKL2 | Achchuthan Shanmugasundram commented on gene: MKL2: PMID:37013900 - Two unrelated paediatric cases with de novo variants in MKL2 gene (p.Arg103Gly & p.Ala91Pro) were reported with mild dysmorphic features, severe intellectual disability, global developmental delays, speech apraxia, and impulse control issues. Functional studies in a Drosophila model suggest a gain of function disease mechanism. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.247 | MKL2 | Achchuthan Shanmugasundram reviewed gene: MKL2: Rating: AMBER; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: 37013900; Phenotypes: neurodevelopmental disorder, MONDO:0700092; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.23 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from Overgrowth syndrome (not always mosaic in this case) to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.22 | AKT3 | Arina Puzriakova Publications for gene: AKT3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.21 | AKT3 | Arina Puzriakova Mode of pathogenicity for gene: AKT3 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.20 | AKT3 | Arina Puzriakova Classified gene: AKT3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.20 | AKT3 | Arina Puzriakova Added comment: Comment on list classification: Variants in this gene cause a spectrum of megalencephaly-related disorders, which in some cases can present as megalencephaly-capillary malformation syndrome (MCAP). Both somatic and germline variants have been reported. Vascular skin anomalies have been identified in at least 2 individuals with germline variants (PMIDs: 22729224; 23745724) and 5 individuals with somatic variants (PMIDs: 25722288; 28969385; 34237354; 36695285; 37395289) meaning that AKT3 can be promoted to green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.20 | AKT3 | Arina Puzriakova Gene: akt3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.19 | AKT3 |
Arina Puzriakova Tag curated_removed was removed from gene: AKT3. Tag Q3_23_promote_green tag was added to gene: AKT3. Tag Q3_23_NHS_review tag was added to gene: AKT3. |
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| Vascular skin disorders v1.52 | AKT3 | Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: AKT3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Vascular skin disorders v1.52 | AKT3 | Arina Puzriakova Classified gene: AKT3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Vascular skin disorders v1.52 | AKT3 | Arina Puzriakova Added comment: Comment on list classification: New gene added to this panel by Zornitza Stark (Australian Genomics). Variants in this gene cause a spectrum of megalencephaly-related disorders, which in some cases can present as megalencephaly-capillary malformation syndrome (MCAP). Both somatic and germline variants have been reported. Vascular skin anomalies have been identified in at least 2 individuals germline variants (PMIDs: 22729224; 23745724) and 5 individuals with somatic variants (PMIDs: 25722288; 28969385; 34237354; 36695285; 37395289). Somatic variants may be missed but given that this panel is a possible referral route for these patients, recommending that AKT3 is promoted to green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Vascular skin disorders v1.52 | AKT3 | Arina Puzriakova Gene: akt3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.5 | FN1 | Eleanor Williams Classified gene: FN1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.5 | FN1 | Eleanor Williams Added comment: Comment on list classification: Copied this gene from the Proteinuric renal disease panel and added it to the Unexplained young onset end-stage renal disease panel. Changing it to Amber for now, until it has been completely reviewed for suitability for this panel and until the next GMS update review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.5 | FN1 | Eleanor Williams Gene: fn1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.4 | FN1 | Eleanor Williams Entity copied from Proteinuric renal disease v4.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.4 | FN1 |
Eleanor Williams gene: FN1 was added gene: FN1 was added to Unexplained young onset end-stage renal disease. Sources: Expert Review Green,Expert list Mode of inheritance for gene: FN1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: FN1 were set to 18268355; 27056061; 31419955 Phenotypes for gene: FN1 were set to Glomerulopathy with fibronectin deposits 2, OMIM:601894 |
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| Intellectual disability v5.247 | ATG4D | Achchuthan Shanmugasundram Classified gene: ATG4D as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.247 | ATG4D | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases with mild cognitive impairment and hence this gene should be rated amber with the current evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.247 | ATG4D | Achchuthan Shanmugasundram Gene: atg4d has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.246 | ATG4D |
Achchuthan Shanmugasundram changed review comment from: PMID:36765070 - Three individuals from two different families were reported with a neurodevelopmental disorder and identified with compound heterozygous variants in ATG4D gene (family 1: :c.266G>A/ p.Ser89Asn & c.839A>G/ p.Tyr280Cys; family 2: c.1310_1328del/ p.Asp437Alafs*37 & c.1066G>A/ p.Asp356Asn). Patient from family 1 and one of two patients from family 2 had mild cognitive impairment. This gene has been associated with relevant phenotypes in Gene2Phenotype (with 'limited' rating in the DD panel), but not yet in OMIM.; to: PMID:36765070 - Three individuals from two different families were reported with a neurodevelopmental disorder and identified with compound heterozygous variants in ATG4D gene (family 1: :c.266G>A/ p.Ser89Asn & c.839A>G/ p.Tyr280Cys; family 2: c.1310_1328del/ p.Asp437Alafs*37 & c.1066G>A/ p.Asp356Asn). Patient from family 1 and one of two patients from family 2 had mild cognitive impairment. Based on the clinical, bioinformatic, and functional data, the authors also concluded that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of syndromic neurodevelopmental disorder. This gene has been associated with relevant phenotypes in Gene2Phenotype (with 'limited' rating in the DD panel), but not yet in OMIM. |
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| Intellectual disability v5.246 | ATG4D |
Achchuthan Shanmugasundram changed review comment from: PMID:36765070 - Three individuals from two different families were reported with a neurodevelopmental disorder and identified with compound heterozygous variants in ATG4D gene (family 1: :c.266G>A/ p.Ser89Asn & c.839A>G/ p.Tyr280Cys; family 2: c.1310_1328del/ p.Asp437Alafs*37 & c.1066G>A/ p.Asp356Asn). Patient from family 1 and one of two patients from family 2 had cognitive impairment. This gene has been associated with relevant phenotypes in Gene2Phenotype (with 'limited' rating in the DD panel), but not yet in OMIM.; to: PMID:36765070 - Three individuals from two different families were reported with a neurodevelopmental disorder and identified with compound heterozygous variants in ATG4D gene (family 1: :c.266G>A/ p.Ser89Asn & c.839A>G/ p.Tyr280Cys; family 2: c.1310_1328del/ p.Asp437Alafs*37 & c.1066G>A/ p.Asp356Asn). Patient from family 1 and one of two patients from family 2 had mild cognitive impairment. This gene has been associated with relevant phenotypes in Gene2Phenotype (with 'limited' rating in the DD panel), but not yet in OMIM. |
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| Intellectual disability v5.246 | ATG4D | Achchuthan Shanmugasundram Phenotypes for gene: ATG4D were changed from neurodevelopmental disorder, MONDO:0700092 to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.246 | ATG4D | Achchuthan Shanmugasundram Phenotypes for gene: ATG4D were changed from neurodevelopmental disorder characterized by speech and motor impairment to neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.245 | ATG4D | Achchuthan Shanmugasundram edited their review of gene: ATG4D: Changed rating: AMBER; Changed publications to: 36765070; Changed phenotypes to: neurodevelopmental disorder, MONDO:0700092; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.84 | AKT3 | Arina Puzriakova Publications for gene: AKT3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.83 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2 615937 to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.245 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome, 603387; HEMIMEGALENCEPHALY AKT3 to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.244 | ATG4D | Achchuthan Shanmugasundram commented on gene: ATG4D | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neurological segmental overgrowth v2.7 | AKT3 | Arina Puzriakova Tag mosaicism tag was added to gene: AKT3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.102 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from HEMIMEGALENCEPHALY AKT3 to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Beckwith-Wiedemann syndrome (BWS) and other congenital overgrowth disorders v1.120 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from Human overgrowth syndrome type; Overgrowth with Intellectual disability to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Malformations of cortical development v4.4 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from Polymicrogyria, macrocephaly to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.13 | AKT3 | Arina Puzriakova Phenotypes for gene: AKT3 were changed from Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, 615937; MPPH2; Macrocephaly and Overgrowth Syndromes; Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus syndrome 2 to Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 2, OMIM:615937; Macrocephaly and Overgrowth Syndromes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Proteinuric renal disease v4.1 | FN1 |
Eleanor Williams commented on gene: FN1: Looking at reports of End-stage renal disease and the age of onset: PMID: 18268355 - Castelletti et al 2008 - 3 members of the same extended family are reported to have ESRF at ages 74, 32 and 34. PMID: 27056061- Ohtsubo et al 2016 - 1 patient with ESRD at 34 years, and one other at age 49. PMID: 31419955 - Gonçalves Dos Reis Monteiro et al 2019 - the father and son reported do not appear to have ESRD. |
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| Intellectual disability v5.244 | PSMC3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.244 | PSMC3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.244 | PSMC3 | Achchuthan Shanmugasundram Classified gene: PSMC3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.244 | PSMC3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: This gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.244 | PSMC3 | Achchuthan Shanmugasundram Gene: psmc3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.243 | PSMC3 | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: There is sufficient evidence for the association of monoallelic variants from this gene with intellectual disability. However, there is only one family reported with biallelic variants. Hence, the MOI is set as "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.243 | PSMC3 | Achchuthan Shanmugasundram Mode of inheritance for gene: PSMC3 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.243 | PSMC3 | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: There is sufficient evidence for the association of monoallelic variants from this gene with intellectual disability. However, there is only one family reported with biallelic variants. Hence, the MOI is set as "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.243 | PSMC3 | Achchuthan Shanmugasundram Mode of inheritance for gene: PSMC3 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.243 | PSMC3 | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: There is sufficient evidence for the association of monoallelic variants from this gene with intellectual disability. However, there is only one family reported with biallelic variants. Hence, the MOI is set as "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.243 | PSMC3 | Achchuthan Shanmugasundram Mode of inheritance for gene: PSMC3 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PSMC3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.242 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | PSMC3 | Achchuthan Shanmugasundram Phenotypes for gene: PSMC3 were changed from neurodevelopmental delay to ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354; neurodevelopmental disorder, MONDO:0700092 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | PSMC3 | Achchuthan Shanmugasundram Publications for gene: PSMC3 were set to 32500975; 37256937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | PSMC3 | Achchuthan Shanmugasundram Publications for gene: PSMC3 were set to 32500975; 37256937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | PSMC3 | Achchuthan Shanmugasundram Publications for gene: PSMC3 were set to 32500975; 37256937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | PSMC3 | Achchuthan Shanmugasundram Publications for gene: PSMC3 were set to 32500975; 37256937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | PSMC3 | Achchuthan Shanmugasundram Publications for gene: PSMC3 were set to PMID: 37256937 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | PSMC3 | Achchuthan Shanmugasundram reviewed gene: PSMC3: Rating: GREEN; Mode of pathogenicity: None; Publications: 32500975, 37256937; Phenotypes: ?Deafness, cataract, impaired intellectual development, and polyneuropathy, OMIM:619354, neurodevelopmental disorder, MONDO:0700092; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.12 | AKT2 | Arina Puzriakova Classified gene: AKT2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.12 | AKT2 | Arina Puzriakova Added comment: Comment on list classification: At least three unrelated families reported with the same activating mosaic c.49G>A (p.E17K) variant in the AKT2 gene. Mild asymmetric overgrowth was seen in 2/3 cases. Sibs from the third family showed early overgrowth but no signs of body asymmetry. Overall the evidence is borderline amber/green. However, as this gene has been expert reviewed as green by Tom Cullup (GOSH) and is likely to be diagnostically relevant, recommending AKT2 is promoted to green status at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.12 | AKT2 | Arina Puzriakova Gene: akt2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.11 | AKT2 | Arina Puzriakova Publications for gene: AKT2 were set to 28502730 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.10 | AKT2 | Arina Puzriakova Mode of pathogenicity for gene: AKT2 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.9 | AKT2 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: AKT2. Tag Q3_23_NHS_review tag was added to gene: AKT2. Tag recurrent-variant tag was added to gene: AKT2. |
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| Mosaic skin disorders - deep sequencing v2.19 | PIK3R1 | Arina Puzriakova Publications for gene: PIK3R1 were set to PMID: 34040190; 35964931 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.18 | PIK3R1 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: PIK3R1. Tag Q3_23_NHS_review tag was added to gene: PIK3R1. |
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| Segmental overgrowth disorders - Deep sequencing v3.9 | PIK3R1 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: PIK3R1. Tag Q3_23_NHS_review tag was added to gene: PIK3R1. |
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| Segmental overgrowth disorders - Deep sequencing v3.9 | PIK3R1 | Arina Puzriakova Publications for gene: PIK3R1 were set to PMID: 34040190; 35964931 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.18 | PIK3R1 | Arina Puzriakova Classified gene: PIK3R1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.18 | PIK3R1 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. At least 17 cases have been identified with somatic mosaic variants in PIK3R1 (PMIDs: 34040190; 35964931). Affected individuals exhibit various vascular lesions and overgrowth which were comparable to features of the PIK3CA-related overgrowth spectrum. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.18 | PIK3R1 | Arina Puzriakova Gene: pik3r1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.8 | PIK3R1 | Arina Puzriakova Classified gene: PIK3R1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.8 | PIK3R1 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. At least 17 cases have been identified with somatic mosaic variants in PIK3R1 (PMIDs: 34040190; 35964931). Affected individuals exhibit various vascular lesions and overgrowth which were comparable to features of the PIK3CA-related overgrowth spectrum. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.8 | PIK3R1 | Arina Puzriakova Gene: pik3r1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Classified gene: KCNH5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Dmitrijs Rots, there is sufficient evidence for the association of this gene to intellectual disability. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Gene: kcnh5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | KCNH5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | KCNH5 | Achchuthan Shanmugasundram Classified gene: KCNH5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | KCNH5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Dmitrijs Rots, there is sufficient evidence for the association of this gene to intellectual disability. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.241 | KCNH5 | Achchuthan Shanmugasundram Gene: kcnh5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Classified gene: KCNH5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Dmitrijs Rots, there is sufficient evidence for the association of this gene to intellectual disability. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Gene: kcnh5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.240 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from INFANTILE EPILEPTIC ENCEPHALOPATHY to developmental and epileptic encephalopathy, MONDO:0100062; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.238 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.239 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.238 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072; 35874597; 36307226; 24133262 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.238 | KCNH5 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: KCNH5 was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.238 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 23647072 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.238 | KCNH5 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: KCNH5 was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.238 | KCNH5 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: KCNH5 was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.237 | KCNH5 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: KCNH5 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.236 | KCNH5 | Achchuthan Shanmugasundram Mode of inheritance for gene: KCNH5 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.236 | KCNH5 | Achchuthan Shanmugasundram Mode of inheritance for gene: KCNH5 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.235 | KCNH5 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: KCNH5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.235 | KCNH5 | Achchuthan Shanmugasundram reviewed gene: KCNH5: Rating: GREEN; Mode of pathogenicity: None; Publications: 23647072, 35874597, 36307226, 24133262; Phenotypes: developmental and epileptic encephalopathy, MONDO:0100062, intellectual disability, MONDO:0001071; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.82 | KCNH5 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: KCNH5 was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.81 | KCNH5 | Achchuthan Shanmugasundram Publications for gene: KCNH5 were set to 24133262; 23647072 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.80 | KCNH5 | Achchuthan Shanmugasundram Phenotypes for gene: KCNH5 were changed from epilepsy to developmental and epileptic encephalopathy, MONDO:0100062; epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.79 | KCNH5 | Achchuthan Shanmugasundram Mode of inheritance for gene: KCNH5 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.78 | KCNH5 | Achchuthan Shanmugasundram Classified gene: KCNH5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.78 | KCNH5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Dmitrijs Rots, there is sufficient evidence for the association of this gene to epilepsy. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.78 | KCNH5 | Achchuthan Shanmugasundram Gene: kcnh5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.77 | KCNH5 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: KCNH5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.77 | KCNH5 | Achchuthan Shanmugasundram reviewed gene: KCNH5: Rating: GREEN; Mode of pathogenicity: None; Publications: 23647072, 35874597, 36307226, 24133262; Phenotypes: developmental and epileptic encephalopathy, MONDO:0100062, epilepsy, MONDO:0005027; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.15 | SETD5 | Achchuthan Shanmugasundram Phenotypes for gene: SETD5 were changed from Intellectual developmental disorder, autosomal dominant 23, OMIM:615761; Skeletal dysplasia; intellectual disability; developmental delay; facial dysmorphism to Intellectual developmental disorder, autosomal dominant 23, OMIM:615761; skeletal dysplasia, MONDO:0018230; facial dysmorphism | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.14 | SETD5 | Achchuthan Shanmugasundram edited their review of gene: SETD5: Changed phenotypes to: Intellectual developmental disorder, autosomal dominant 23, OMIM:615761, skeletal dysplasia, MONDO:0018230 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.14 | SETD5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.14 | SETD5 | Achchuthan Shanmugasundram Classified gene: SETD5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.14 | SETD5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Tracy Lester, the observed intellectual developmental disorder phenotype includes skeletal abnormalities ( at least 9 cases) and these might appear before ID. Hence, this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.14 | SETD5 | Achchuthan Shanmugasundram Gene: setd5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.13 | SETD5 | Achchuthan Shanmugasundram Classified gene: SETD5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.13 | SETD5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Tracy Lester, the observed intellectual developmental disorder phenotype includes skeletal abnormalities ( at least 9 cases) and these might appear before ID. Hence, this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.13 | SETD5 | Achchuthan Shanmugasundram Gene: setd5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.12 | SETD5 | Achchuthan Shanmugasundram Phenotypes for gene: SETD5 were changed from Skeletal dysplasia; intellectual disability; developmental delay; facial dysmorphism to Intellectual developmental disorder, autosomal dominant 23, OMIM:615761; Skeletal dysplasia; intellectual disability; developmental delay; facial dysmorphism | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.11 | SETD5 | Achchuthan Shanmugasundram Publications for gene: SETD5 were set to 28881385 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.10 | SETD5 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SETD5. Tag Q3_23_NHS_review tag was added to gene: SETD5. |
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| Skeletal dysplasia v4.10 | SETD5 | Achchuthan Shanmugasundram reviewed gene: SETD5: Rating: GREEN; Mode of pathogenicity: None; Publications: 24680889, 28881385; Phenotypes: Intellectual developmental disorder, autosomal dominant 23, OMIM:615761; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.28 | ELAC2 | Achchuthan Shanmugasundram Classified gene: ELAC2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.28 | ELAC2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Matthew Edwards, there is sufficient evidence for the promotion of this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.28 | ELAC2 | Achchuthan Shanmugasundram Gene: elac2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.27 | ELAC2 | Achchuthan Shanmugasundram Phenotypes for gene: ELAC2 were changed from to Combined oxidative phosphorylation deficiency 17, OMIM:615440 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.26 | ELAC2 | Achchuthan Shanmugasundram Publications for gene: ELAC2 were set to PMID: 23849775 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.25 | ELAC2 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: ELAC2. Tag Q3_23_NHS_review tag was added to gene: ELAC2. |
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| Paediatric or syndromic cardiomyopathy v3.25 | ELAC2 | Achchuthan Shanmugasundram reviewed gene: ELAC2: Rating: GREEN; Mode of pathogenicity: None; Publications: 23849775; Phenotypes: Combined oxidative phosphorylation deficiency 17, OMIM:615440; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.14 | PPA2 | Achchuthan Shanmugasundram Classified gene: PPA2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.14 | PPA2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Matthew Edwards, there is sufficient evidence for this gene to be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.14 | PPA2 | Achchuthan Shanmugasundram Gene: ppa2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.13 | PPA2 | Achchuthan Shanmugasundram Phenotypes for gene: PPA2 were changed from Sudden cardiac failure, infantile; Sudden cardiac failure, alcohol-induced to Sudden cardiac failure, infantile, OMIM:617222; ?Sudden cardiac failure, alcohol-induced, OMIM:617223 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.12 | PPA2 | Achchuthan Shanmugasundram Publications for gene: PPA2 were set to PMID: 34400813 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.11 | PPA2 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PPA2. Tag Q3_23_NHS_review tag was added to gene: PPA2. |
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| Dilated and arrhythmogenic cardiomyopathy v2.11 | PPA2 | Achchuthan Shanmugasundram reviewed gene: PPA2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34400813; Phenotypes: Sudden cardiac failure, infantile, OMIM:617222, ?Sudden cardiac failure, alcohol-induced, OMIM:617223; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.235 | CLCNKB |
Sarah Leigh Tag polygenic was removed from gene: CLCNKB. Tag digenic tag was added to gene: CLCNKB. |
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| Intellectual disability v5.235 | CLCNKB | Sarah Leigh Phenotypes for gene: CLCNKB were changed from Bartter syndrome, type 3, 607364Bartter syndrome, type 4b, digenic, 613090; BARTTER SYNDROME TYPE 4B to Bartter syndrome, type 3, OMIM:607364; Bartter disease type 3, MONDO:0011822; Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.101 | CLCNKB | Sarah Leigh Phenotypes for gene: CLCNKB were changed from BARTTER SYNDROME TYPE 4B to Bartter syndrome, type 3, OMIM:607364; Bartter disease type 3, MONDO:0011822; Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.23 | CLCNKB | Sarah Leigh Phenotypes for gene: CLCNKB were changed from Bartter syndrome, type 3 (607364); Bartter syndrome, type 4b, digenic (613090) to Bartter syndrome, type 3, OMIM:607364; Bartter disease type 3, MONDO:0011822; Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nephrocalcinosis or nephrolithiasis v4.2 | CLCNKB | Sarah Leigh Phenotypes for gene: CLCNKB were changed from Bartter syndrome, type 3, 607364; Type 3 Bartter syndrome; Bartter syndrome, type 4b, digenic, 613090; BARTTER SYNDROME TYPE 4B to Bartter syndrome, type 3, OMIM:607364; Bartter disease type 3, MONDO:0011822; Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.4 | CLCNKB | Sarah Leigh Phenotypes for gene: CLCNKB were changed from Bartter syndrome, type 3, OMIM:607364; Bartter syndrome, type 4b, digenic, OMIM:613090 to Bartter syndrome, type 3, OMIM:607364; Bartter disease type 3, MONDO:0011822; Bartter syndrome, type 4b, digenic, OMIM:613090; Bartter disease type 4B, MONDO:0000909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.3 | CLCNKB | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.16 | GCDH |
Sarah Leigh Tag Q3_23_promote_green tag was added to gene: GCDH. Tag Q3_23_MOI tag was added to gene: GCDH. |
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| Adult onset leukodystrophy v3.16 | GCDH | Sarah Leigh edited their review of gene: GCDH: Added comment: GCDH variants are associated with Glutaricaciduria, type I (OMIM:231670) and as definitive Gen2Phen gene for the same condition. Although OMIM:231670 usually manifests in infancy, four unrelated cases, including white matter involvement, have been reported with an age of onset of 16 to 35 years (15985591;12473778; https://doi.org/10.1002/mds.10442).; Changed rating: GREEN; Changed publications to: 15985591, 12473778, https://doi.org/10.1002/mds.10442; Changed phenotypes to: Glutaricaciduria, type I, OMIM:231670; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.16 | GCDH |
Sarah Leigh Added comment: Comment on publications: Publication not in PUBMED: https://doi.org/10.1002/mds.10442 "Hand tremor and orofacial dyskinesia: Clinical manifestations of glutaric aciduria type I in a young girl" Emilio Fernández-Álvarez MD, PhD, Angeles García-Cazorla MD, Anna Sans MD, Cristina Boix PhD, María Antonia Vilaseca PhD, Christianne Busquets PhD, Antonia Ribes PhD First published: 01 April 2003 |
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| Adult onset leukodystrophy v3.16 | GCDH | Sarah Leigh Publications for gene: GCDH were set to 15985591 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.17 | NEK9 | Arina Puzriakova Tag somatic tag was added to gene: NEK9. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.17 | NEK9 | Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. At least five unrelated individuals reported with nevus comedonicus due to somatic mosaic variants in the NEK9 gene. Two individuals had other syndromic features - congenital cataract was the only common finding present in both cases.; to: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. At least five unrelated individuals reported with nevus comedonicus due to somatic mosaic variants in the NEK9 gene. Two individuals had other syndromic features - congenital cataract was the only common finding present in both cases (PMIDs: 27153399; 34184242; 31961058) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.17 | NEK9 | Arina Puzriakova Publications for gene: NEK9 were set to PMID: 27153399; 34184242; 33481271 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.16 | NEK9 | Arina Puzriakova Classified gene: NEK9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.16 | NEK9 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. At least five unrelated individuals reported with nevus comedonicus due to somatic mosaic variants in the NEK9 gene. Two individuals had other syndromic features - congenital cataract was the only common finding present in both cases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.16 | NEK9 | Arina Puzriakova Gene: nek9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.47 | BLM | Achchuthan Shanmugasundram Classified gene: BLM as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.47 | BLM | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available for the association of this gene with severe insulin resistance and hence it can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.47 | BLM | Achchuthan Shanmugasundram Gene: blm has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.46 | BLM |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: BLM. Tag Q3_23_NHS_review tag was added to gene: BLM. |
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| Lipodystrophy - childhood onset v4.46 | BLM | Achchuthan Shanmugasundram Publications for gene: BLM were set to 7585968; 16763388; 21536711; 27710244; 2823277; 2947793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.45 | BLM | Achchuthan Shanmugasundram edited their review of gene: BLM: Changed publications to: 7585968, 16763388, 21536711, 27710244, 28232778, 29477938 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.45 | BLM | Achchuthan Shanmugasundram edited their review of gene: BLM: Changed publications to: 7585968, 16763388, 21536711, 27710244, 28232778, 2947793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.45 | BLM | Achchuthan Shanmugasundram Publications for gene: BLM were set to 7585968; 16763388; 2153671; 27710244; 2823277; 2947793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.44 | BLM | Achchuthan Shanmugasundram edited their review of gene: BLM: Changed publications to: 7585968, 16763388, 21536711, 27710244, 2823277, 2947793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.44 | BLM | Achchuthan Shanmugasundram Publications for gene: BLM were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.43 | BLM | Achchuthan Shanmugasundram Phenotypes for gene: BLM were changed from Bloom Syndrome, severe insulin resistance to Bloom syndrome, OMIM:210900; Insulin resistance, HP:0000855 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.15 | NEK9 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: NEK9. Tag Q3_23_NHS_review tag was added to gene: NEK9. |
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| Lipodystrophy - childhood onset v4.42 | BLM | Achchuthan Shanmugasundram edited their review of gene: BLM: Added comment: Insulin resistance was observed in six individuals and lipid profile abnormalities were reported in five of ten individuals with Bloom syndrome (PMID:16763388).; Changed rating: GREEN; Changed publications to: 7585968, 16763388, 2153671, 27710244, 2823277, 2947793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.15 | NEK9 | Arina Puzriakova Phenotypes for gene: NEK9 were changed from nevus comedonicus (NC) (MIM: 617025) to Nevus comedonicus, somatic, OMIM:617025 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.15 | GCDH | Sarah Leigh Phenotypes for gene: GCDH were changed from Glutaric aciduria, type I 231670 to Glutaricaciduria, type I, OMIM:231670; glutaryl-CoA dehydrogenase deficiency, MONDO:0009281 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.14 | GCDH | Sarah Leigh Classified gene: GCDH as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.14 | GCDH | Sarah Leigh Gene: gcdh has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.13 | RNF216 | Sarah Leigh Classified gene: RNF216 as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.13 | RNF216 | Sarah Leigh Added comment: Comment on list classification: There is not enough evidence for this gene to be rated GREEN on this panel at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.13 | RNF216 | Sarah Leigh Gene: rnf216 has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.12 | RNF216 | Sarah Leigh Tag Q3_23_demote_amber tag was added to gene: RNF216. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.12 | RNF216 |
Sarah Leigh changed review comment from: RNF216 variants are associated with Cerebellar ataxia and hypogonadotropic hypogonadism (OMIM:212840), previously known as Gordon Holmes syndrome (GDHS). No phenotype was associated with RNF216 in Gen2Phen. At least six variants have been reported in four unrelated cases of OMIM:212840. Three of these variants, in four individuals from two unrelated families, have been associated with a variant of GDHS. The variant GDHS includes Huntingtons-like features including white matter lesions (PMID: 16691578).; to: RNF216 variants are associated with Cerebellar ataxia and hypogonadotropic hypogonadism (OMIM:212840), previously known as Gordon Holmes syndrome (GDHS). No phenotype was associated with RNF216 in Gen2Phen. At least six variants have been reported in four unrelated cases of OMIM:212840. Three of these variants, in four individuals from two unrelated families, have been associated with a variant of GDHS. The variant GDHS includes Huntingtons-like features including white matter lesions (PMID: 25841028). |
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| Adult onset leukodystrophy v3.12 | RNF216 | Sarah Leigh reviewed gene: RNF216: Rating: AMBER; Mode of pathogenicity: None; Publications: 25841028; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.12 | RNF216 | Sarah Leigh Phenotypes for gene: RNF216 were changed from Cerebellar ataxia and hypogonadotropic hypogonadism, 212840 to Cerebellar ataxia and hypogonadotropic hypogonadism, OMIM:212840 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.42 | PSMA3 | Achchuthan Shanmugasundram Classified gene: PSMA3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.42 | PSMA3 | Achchuthan Shanmugasundram Gene: psma3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.41 | PSMA3 | Achchuthan Shanmugasundram Publications for gene: PSMA3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMA3 | Achchuthan Shanmugasundram Tag digenic tag was added to gene: PSMA3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMA3 |
Achchuthan Shanmugasundram changed review comment from: PMID:26524591 - Two unrelated cases with heterozygous variants in PSMA3 and PSMB8 were reported with proteasome-associated autoinflammatory syndrome (PRAAS) that includes lipodystrophy and lipid abnormalities. In addition, it was revealed from functional studies that these variants affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. This gene has not been associated with relevant phenotypes either in OMIM or in Gene2Phenotype.; to: PMID:26524591 - Two unrelated cases with heterozygous variants in PSMA3 and PSMB8 were reported with proteasome-associated autoinflammatory syndrome (PRAAS) that includes lipodystrophy and lipid abnormalities. In addition, it was revealed from functional studies that these variants affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. This gene has not been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. The 'digenic' tag has been added as both reported cases had variants in PSMB8 in addition to PSMA3 variants. |
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| Lipodystrophy - childhood onset v4.40 | PSMA3 |
Achchuthan Shanmugasundram edited their review of gene: PSMA3: Added comment: PMID:26524591 - Two unrelated cases with heterozygous variants in PSMA3 and PSMB8 were reported with proteasome-associated autoinflammatory syndrome (PRAAS) that includes lipodystrophy and lipid abnormalities. In addition, it was revealed from functional studies that these variants affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. This gene has not been associated with relevant phenotypes either in OMIM or in Gene2Phenotype.; Changed rating: AMBER; Changed publications to: 26524591 |
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| Adult onset leukodystrophy v3.11 | RNF216 | Sarah Leigh Publications for gene: RNF216 were set to 27159321; 25527826; 28334938; 20301621; 24357685 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMA3 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: These autoinflammatory syndromes include a lipodystrophy (partial and generalised have both been reported) and are caused either by biallelic loss of function mutations in PSMB4 or PSMB8 (PMID: 26524591, 34416217) or by digenic heterozygous mutations in other proteasome encoding genes (PSMB8, PMSA3 PMID: 26524591). PSMB9 has also been implicated in digenic cases but this is in a single familes and lipodystrophy is not reported in the autoinflammatory syndrome of carriers of biallelic loss of function mutations in PSMB9. Only DIGENIC cases of CANDLES involving PSMA3 have been reported.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: These autoinflammatory syndromes include a lipodystrophy (partial and generalised have both been reported) and are caused either by biallelic loss of function mutations in PSMB4 or PSMB8 (PMID: 26524591, 34416217) or by digenic heterozygous mutations in other proteasome encoding genes (PSMB8, PMSA3 PMID: 26524591). PSMB9 has also been implicated in digenic cases but this is in a single familes and lipodystrophy is not reported in the autoinflammatory syndrome of carriers of biallelic loss of function mutations in PSMB9. Only DIGENIC cases of CANDLES involving PSMA3 have been reported. |
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| Adult onset leukodystrophy v3.10 | RPS6KA3 | Sarah Leigh Classified gene: RPS6KA3 as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.10 | RPS6KA3 | Sarah Leigh Added comment: Comment on list classification: There is not enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.10 | RPS6KA3 | Sarah Leigh Gene: rps6ka3 has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.9 | RPS6KA3 | Sarah Leigh Tag Q3_23_demote_red tag was added to gene: RPS6KA3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.9 | RPS6KA3 | Sarah Leigh edited their review of gene: RPS6KA3: Changed publications to: 16691578 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.9 | RPS6KA3 | Sarah Leigh reviewed gene: RPS6KA3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMB8 | Achchuthan Shanmugasundram changed review comment from: The 'digenic' tag has been added as there are two cases reported with heterozygous variants from both PSMB4 and PSMB8 in addition to patients with homozygous PSMB8 variants.; to: The 'digenic' tag has been added as there are four digenic cases reported (two cases each with heterozygous variants in PSMA3/ PSMB8 and PSMB4/ PSMB8) in addition to patients with homozygous PSMB8 variants. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMB4 |
Achchuthan Shanmugasundram changed review comment from: PMID:26524591 - One case with compound heterozygous variants in PSMB4 (monogenic), two cases with heterozygous variants in PSMA3 and PSMB8 (digenic) and two cases with heterozygous variants in PSMB4 and PSMB8 (digenic) were reported with proteasome-associated autoinflammatory syndrome (PRAAS) that includes lipodystrophy and lipid abnormalities. In addition, it was revealed from functional studies that these variants affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. PMID:34416217 - A boy with treatment-resistant cutaneous vasculitis was identified with novel heterozygous variants in PSMB4. This patient developed mild lipodystrophy after the successful second hematopoietic stem cell transplantation (HSCT). This gene has been associated with PRAAS in OMIM and it includes lipodystrophy as one of the clinical manifestations.; to: PMID:26524591 - One case with compound heterozygous variants in PSMB4 (monogenic), two cases with heterozygous variants in PSMB4 and PSMB8 (digenic) and two cases with heterozygous variants in PSMB4 and PSMB9 (digenic) were reported with proteasome-associated autoinflammatory syndrome (PRAAS) that includes lipodystrophy and lipid abnormalities. In addition, it was revealed from functional studies that these variants affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. PMID:34416217 - A boy with treatment-resistant cutaneous vasculitis was identified with novel heterozygous variants in PSMB4. This patient developed mild lipodystrophy after the successful second hematopoietic stem cell transplantation (HSCT). This gene has been associated with PRAAS in OMIM and it includes lipodystrophy as one of the clinical manifestations. |
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| Lipodystrophy - childhood onset v4.40 | PSMB4 | Achchuthan Shanmugasundram commented on gene: PSMB4: The 'digenic' tag has been added as there are four additional cases with heterozygous PSMB4 variants and heterozygous variants in either PSMA3 and PSMB8. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMB4 | Achchuthan Shanmugasundram Classified gene: PSMB4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMB4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for the association of biallelic variants in PSMB4 with lipodystrophy (two unrelated cases and supporting functional evidence). Hence, this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.40 | PSMB4 | Achchuthan Shanmugasundram Gene: psmb4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.39 | PSMB4 |
Achchuthan Shanmugasundram Tag digenic tag was added to gene: PSMB4. Tag Q3_23_promote_green tag was added to gene: PSMB4. Tag Q3_23_NHS_review tag was added to gene: PSMB4. |
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| Lipodystrophy - childhood onset v4.39 | PSMB4 | Achchuthan Shanmugasundram Phenotypes for gene: PSMB4 were changed from Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome) to ?Proteasome-associated autoinflammatory syndrome 3 and digenic forms, OMIM:617591 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.38 | PSMB4 | Achchuthan Shanmugasundram Publications for gene: PSMB4 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.37 | PSMB4 |
Achchuthan Shanmugasundram edited their review of gene: PSMB4: Added comment: PMID:26524591 - One case with compound heterozygous variants in PSMB4 (monogenic), two cases with heterozygous variants in PSMA3 and PSMB8 (digenic) and two cases with heterozygous variants in PSMB4 and PSMB8 (digenic) were reported with proteasome-associated autoinflammatory syndrome (PRAAS) that includes lipodystrophy and lipid abnormalities. In addition, it was revealed from functional studies that these variants affect transcription, protein expression, protein folding, proteasome assembly, and, ultimately, proteasome activity. PMID:34416217 - A boy with treatment-resistant cutaneous vasculitis was identified with novel heterozygous variants in PSMB4. This patient developed mild lipodystrophy after the successful second hematopoietic stem cell transplantation (HSCT). This gene has been associated with PRAAS in OMIM and it includes lipodystrophy as one of the clinical manifestations.; Changed rating: GREEN; Changed publications to: 26524591, 34416217 |
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| Lipodystrophy - childhood onset v4.37 | PSMB4 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: These autoinflammatory syndromes include a lipodystrophy (partial and generalised have both been reported) and are caused either by biallelic loss of function mutations (PMID: 26524591, 34416217) or by digenic heterozygous mutations in other proteasome encoding genes (PSMB8, PMSA3 PMID: 26524591). See panel app reviews for autoinflammatory syndromes. PSMB9 has also been implicated in digenic cases but this is in a single familes and lipodystrophy is not reported in the autoinflammatory syndrome of carriers of biallelic loss of function mutations in PSMB9.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: These autoinflammatory syndromes include a lipodystrophy (partial and generalised have both been reported) and are caused either by biallelic loss of function mutations (PMID: 26524591, 34416217) or by digenic heterozygous mutations in other proteasome encoding genes (PSMB8, PMSA3 PMID: 26524591). See panel app reviews for autoinflammatory syndromes. PSMB9 has also been implicated in digenic cases but this is in a single familes and lipodystrophy is not reported in the autoinflammatory syndrome of carriers of biallelic loss of function mutations in PSMB9. |
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| Lipodystrophy - childhood onset v4.37 | PSMB8 | Achchuthan Shanmugasundram Classified gene: PSMB8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.37 | PSMB8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available for this gene to be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.37 | PSMB8 | Achchuthan Shanmugasundram Gene: psmb8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.36 | PSMB8 | Achchuthan Shanmugasundram commented on gene: PSMB8: The 'digenic' tag has been added as there are two cases reported with heterozygous variants from both PSMB4 and PSMB8 in addition to patients with homozygous PSMB8 variants. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.36 | PSMB8 | Achchuthan Shanmugasundram Phenotypes for gene: PSMB8 were changed from Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome) to Proteasome-associated autoinflammatory syndrome 1 and digenic forms, OMIM:256040 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.35 | PSMB8 | Achchuthan Shanmugasundram Publications for gene: PSMB8 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.34 | PSMB8 | Achchuthan Shanmugasundram edited their review of gene: PSMB8: Changed publications to: 20534754, 21129723, 21953331, 26524591 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.34 | PSMB8 |
Achchuthan Shanmugasundram Tag digenic tag was added to gene: PSMB8. Tag Q3_23_promote_green tag was added to gene: PSMB8. Tag Q3_23_NHS_review tag was added to gene: PSMB8. |
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| Lipodystrophy - childhood onset v4.34 | PSMB8 |
Achchuthan Shanmugasundram edited their review of gene: PSMB8: Added comment: PMID:21129723 - A homozygous missense variant (c.224C>T/ p.Thr75Met) in PSMB8 gene was identified in affected patients from two different families with an autosomal-recessive autoinflammatory syndrome characterised by joint contractures, muscle atrophy, microcytic anaemia, and panniculitis-induced lipodystrophy (JMP). PMID:21953331 - Of nine patients from eight families reported in this publication with chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE syndrome), four patients were homozygous and two were heterozygous for the previously reported missense variant (c.224C>T), one had no PSMB8 variant and one patient was homozygous for a novel nonsense variant (c.405C>A). This gene has been associated with relevant phenotypes in OMIM (MIM #256040) and Gene2Phenotype ('definitive' rating in the DD panel for Nakajo syndrome) and lipodystrophy has been included as a part of this phenotype in these resources.; Changed rating: GREEN; Changed publications to: 21129723, 21953331 |
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| Congenital myopathy v4.30 | LETM1 | Sarah Leigh Tag Q3_23_NHS_review was removed from gene: LETM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.30 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%), myopathy 6/12 (50%) (PMID: 36055214, figure 1c). |
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| Monogenic hearing loss v4.13 | LETM1 | Sarah Leigh Tag Q3_23_NHS_review was removed from gene: LETM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Bilateral congenital or childhood onset cataracts v4.2 | LETM1 | Sarah Leigh Tag Q3_23_NHS_review was removed from gene: LETM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.16 | LETM1 | Sarah Leigh Tag Q3_23_NHS_review was removed from gene: LETM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.16 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%), spasticity 8/15 (53%) (PMID: 36055214, figure 1c). |
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| Paediatric or syndromic cardiomyopathy v3.25 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%), cardiomyopathy (5/14, 36%)(PMID: 36055214, figure 1c). |
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| Paediatric or syndromic cardiomyopathy v3.25 | LETM1 | Sarah Leigh Tag Q3_23_NHS_review was removed from gene: LETM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.25 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.42 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.25 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Paediatric or syndromic cardiomyopathy. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_NHS_review, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Bilateral congenital or childhood onset cataracts v4.2 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.42 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Bilateral congenital or childhood onset cataracts v4.2 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Bilateral congenital or childhood onset cataracts. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_NHS_review, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Monogenic hearing loss v4.13 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.42 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.13 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Monogenic hearing loss. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_NHS_review, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Childhood onset hereditary spastic paraplegia v4.16 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.42 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.16 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Childhood onset hereditary spastic paraplegia. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_NHS_review, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Congenital myopathy v4.30 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.42 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.30 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Congenital myopathy. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_NHS_review, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Likely inborn error of metabolism v4.44 | LETM1 |
Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as moderate Gen2Phen gene. PMID: 36055214 reports 12 LETM1 variants in 11 unrelated cases of Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction (OMIM: 620089), together with supportive functional studies.; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c). |
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| Mitochondrial disorders v4.71 | LETM1 |
Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as moderate Gen2Phen gene. PMID: 36055214 reports 12 LETM1 variants in 11 unrelated cases of Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction (OMIM: 620089), together with supportive functional studies.; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c). |
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| Intellectual disability v5.234 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants has been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c). |
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| Early onset or syndromic epilepsy v4.77 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants has been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c). |
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| Possible mitochondrial disorder - nuclear genes v3.42 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants has been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c). |
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| Optic neuropathy v4.10 | LETM1 |
Sarah Leigh changed review comment from: LETM1 variants has been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; to: LETM1 variants have been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c). |
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| Acute rhabdomyolysis v1.12 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI was removed from gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.12 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.24 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.23 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.71 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI was removed from gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.71 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.234 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.7 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI was removed from gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.7 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.100 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.42 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.41 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.44 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI was removed from gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.44 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.596 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.7 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.6 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.7 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI was removed from gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.7 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.21 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.7 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.12 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.23 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.71 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.233 | SLC22A5 | Sarah Leigh changed review comment from: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.7 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.99 | SLC22A5 | Sarah Leigh changed review comment from: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.41 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.44 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.595 | SLC22A5 | Sarah Leigh changed review comment from: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.6 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.7 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.20 | SLC22A5 | Sarah Leigh changed review comment from: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; to: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.34 | PSMB8 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: These autoinflammatory syndromes include a lipodystrophy (partial and generalised have both been reported) and are caused either by biallelic loss of function mutations (PMID: 20534754, 21129723, 21953331) or by digenic heterozygous mutations in other proteasome encoding genes (PSMB4, PSMA3)(PMID: 26524591). PSMB9 has also been implicated in digenic causes but these are in single kindreds and lipodystrophy is not reported in the autoinflammatory syndrome of carriers of biallelic loss of function mutations in PSMB9.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: These autoinflammatory syndromes include a lipodystrophy (partial and generalised have both been reported) and are caused either by biallelic loss of function mutations (PMID: 20534754, 21129723, 21953331) or by digenic heterozygous mutations in other proteasome encoding genes (PSMB4, PSMA3)(PMID: 26524591). PSMB9 has also been implicated in digenic causes but these are in single kindreds and lipodystrophy is not reported in the autoinflammatory syndrome of carriers of biallelic loss of function mutations in PSMB9. |
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| Lipodystrophy - childhood onset v4.34 | EPHX1 |
Achchuthan Shanmugasundram changed review comment from: Two unrelated cases presenting with lipoatrophic diabetes were identified with de novo variants in EPHX1 gene (patient 1: p.Thr333Pro; patient 2: p.Gly430Arg). The disease was characterised by loss of adipose tissue, insulin resistance, and multiple organ dysfunction. Functional analysis showed that these variants protein aggregation within the endoplasmic reticulum and to a loss of its hydrolysis activity. In addition, CRISPR-Cas9-mediated EPHX1 knockout (KO) abolished adipocyte differentiation and decreased insulin response.; to: Two unrelated cases presenting with lipoatrophic diabetes were identified with de novo variants in EPHX1 gene (patient 1: p.Thr333Pro; patient 2: p.Gly430Arg). The disease was characterised by loss of adipose tissue, insulin resistance, and multiple organ dysfunction. Functional analysis showed that these variants protein aggregation within the endoplasmic reticulum and to a loss of its hydrolysis activity. In addition, CRISPR-Cas9-mediated EPHX1 knockout (KO) abolished adipocyte differentiation and decreased insulin response. This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype. |
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| Lipodystrophy - childhood onset v4.34 | EPHX1 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: EPHX1. Tag Q3_23_NHS_review tag was added to gene: EPHX1. |
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| Lipodystrophy - childhood onset v4.34 | EPHX1 | Achchuthan Shanmugasundram Classified gene: EPHX1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.34 | EPHX1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (two unrelated cases and functional studies) in support of the association of this gene with lipodystrophy and severe insulin resistance. Hence, this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.34 | EPHX1 | Achchuthan Shanmugasundram Gene: ephx1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.33 | EPHX1 | Achchuthan Shanmugasundram Phenotypes for gene: EPHX1 were changed from Lipodystrophy, Severe Insulin Resistance to lipodystrophy, MONDO:0006573; Insulin resistance, HP:0000855 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.32 | EPHX1 | Achchuthan Shanmugasundram Publications for gene: EPHX1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.31 | EPHX1 | Achchuthan Shanmugasundram edited their review of gene: EPHX1: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.31 | EPHX1 | Achchuthan Shanmugasundram edited their review of gene: EPHX1: Added comment: Two unrelated cases presenting with lipoatrophic diabetes were identified with de novo variants in EPHX1 gene (patient 1: p.Thr333Pro; patient 2: p.Gly430Arg). The disease was characterised by loss of adipose tissue, insulin resistance, and multiple organ dysfunction. Functional analysis showed that these variants protein aggregation within the endoplasmic reticulum and to a loss of its hydrolysis activity. In addition, CRISPR-Cas9-mediated EPHX1 knockout (KO) abolished adipocyte differentiation and decreased insulin response.; Changed publications to: 34342583 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.233 | RPS6KA3 | Arina Puzriakova Tag Q3_23_MOI tag was added to gene: RPS6KA3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.233 | RPS6KA3 | Arina Puzriakova Publications for gene: RPS6KA3 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.232 | RPS6KA3 | Arina Puzriakova Added comment: Comment on mode of inheritance: Should be updated from XLR to XLD (monoallelic variants in females may cause disease) at the next GMS panel update as several affected female carriers have been reported. ID in female carriers can range from mild to severe which is within the scope of the panel (PMIDs: 12210291; 12030896; 12558110; 17318637). This would also match the current MOI on other GMS panels and OMIM. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.232 | RPS6KA3 | Arina Puzriakova Mode of inheritance for gene: RPS6KA3 was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.99 | RPS6KA3 | Arina Puzriakova Phenotypes for gene: RPS6KA3 were changed from COFFIN-LOWRY SYNDROME to Coffin-Lowry syndrome, OMIM:303600 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.9 | RPS6KA3 | Arina Puzriakova Phenotypes for gene: RPS6KA3 were changed from Coffin-Lowry syndrome, 303600 to Coffin-Lowry syndrome, OMIM:303600 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.231 | RPS6KA3 | Arina Puzriakova Phenotypes for gene: RPS6KA3 were changed from Coffin-Lowry syndrome, 303600Mental retardation, X-linked 19, 300844; COFFIN-LOWRY SYNDROME (CLS) to Coffin-Lowry syndrome, OMIM:303600; Intellectual developmental disorder, X-linked 19, OMIM:300844 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.31 | EPHX1 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: EPHX1 is an epoxide hydroxylase, highly expressed in liver and adipose tissue. De novo missense mutations (p.Thr333Pro and p.Gly430Arg) in EPHX1 carried in heterozygosity were implicated in a lipoatrophic diabetes syndrome in two unrelated probands (PMID: 34342583). In vitro characterisation demonstrated loss of enzyme activity in these two mutants and localisation studies demonstrated aggregation of the mutant EPHX1 isoforms in the ER, suggestive of a dominant negative mechanism of action. Consistent with a causal role for EPHX1 in the affected probands' syndrome, circulating epoxy fatty acids were found to be elevated. Variants implicated in the described clinical syndrome caused EPHX1 to form oligomeric complexes and aggregate in the ER. As such it is likely that simple loss of function mutations in EPHX1 do not cause this syndrome, and a dominant negative effect of the EPHX1 mutants is likely the causal mechanism. Consistent with this EPHX1 appears to be LOF tolerant (pLI gnomad = 0, https://gnomad.broadinstitute.org/gene/ENSG00000143819); to: This gene was added on recommendation of NHSE Genomic Medicine Service: EPHX1 is an epoxide hydroxylase, highly expressed in liver and adipose tissue. De novo missense mutations (p.Thr333Pro and p.Gly430Arg) in EPHX1 carried in heterozygosity were implicated in a lipoatrophic diabetes syndrome in two unrelated probands (PMID: 34342583). In vitro characterisation demonstrated loss of enzyme activity in these two mutants and localisation studies demonstrated aggregation of the mutant EPHX1 isoforms in the ER, suggestive of a dominant negative mechanism of action. Consistent with a causal role for EPHX1 in the affected probands' syndrome, circulating epoxy fatty acids were found to be elevated. Variants implicated in the described clinical syndrome caused EPHX1 to form oligomeric complexes and aggregate in the ER. As such it is likely that simple loss of function mutations in EPHX1 do not cause this syndrome, and a dominant negative effect of the EPHX1 mutants is likely the causal mechanism. Consistent with this EPHX1 appears to be LOF tolerant (pLI gnomad = 0, https://gnomad.broadinstitute.org/gene/ENSG00000143819). |
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| Lipodystrophy - childhood onset v4.31 | MFN2 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: MFN2. Tag Q3_23_NHS_review tag was added to gene: MFN2. |
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| Lipodystrophy - childhood onset v4.31 | MFN2 | Achchuthan Shanmugasundram Classified gene: MFN2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.31 | MFN2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As recommended by NHS, there is sufficient evidence available for associating this gene with lipomatosis and severe insulin resistance and hence this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.31 | MFN2 | Achchuthan Shanmugasundram Gene: mfn2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.30 | MFN2 | Achchuthan Shanmugasundram Publications for gene: MFN2 were set to 26085578; 28414270; 3015806 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.29 | MFN2 | Achchuthan Shanmugasundram edited their review of gene: MFN2: Changed publications to: 26085578, 28414270, 30158064 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.29 | MFN2 | Achchuthan Shanmugasundram Added comment: Comment on phenotypes: Autosomal recessive variants in this gene have been associated with cephalothoracic lipodystrophy in OMIM (MIM #151800), but not in Gene2Phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.29 | MFN2 | Achchuthan Shanmugasundram Phenotypes for gene: MFN2 were changed from MFN2-associated multiple lipomatosis, lipodystrophy, severe insulin resistance, axonal sensorimotor neuropathy to Lipomatosis, multiple symmetric, with or without peripheral neuropathy, OMIM:151800 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.28 | MFN2 | Achchuthan Shanmugasundram Publications for gene: MFN2 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.27 | MFN2 | Achchuthan Shanmugasundram edited their review of gene: MFN2: Changed rating: GREEN; Changed publications to: 26085578, 28414270, 3015806 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.27 | MFN2 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Biallelic R707W mutations or R707W in compound heterozygosity with other loss of function variants cause a complex clinical syndrome consisting of multiple lipomas/upper body adipose tissue overgrowth, concomitant lipoatrophy and the development of severe insulin resistance and its metabolic complications. Affected individuals also have a paucisymptomatic axonal neuropathy. This has now been demonstrated in at least 13 patients from 10 independent families (PMID: 30158064, 28414270, 26085578). It is likely that mitochondrial dysfunction in adipose tissue is crucial to the pathogenesis of this condition but the specific cellular and molecular mechanisms remain to be elucidated.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: Biallelic R707W mutations or R707W in compound heterozygosity with other loss of function variants cause a complex clinical syndrome consisting of multiple lipomas/upper body adipose tissue overgrowth, concomitant lipoatrophy and the development of severe insulin resistance and its metabolic complications. Affected individuals also have a paucisymptomatic axonal neuropathy. This has now been demonstrated in at least 13 patients from 10 independent families (PMID: 30158064, 28414270, 26085578). It is likely that mitochondrial dysfunction in adipose tissue is crucial to the pathogenesis of this condition but the specific cellular and molecular mechanisms remain to be elucidated. |
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| Lipodystrophy - childhood onset v4.27 | POC1A |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: POC1A. Tag Q3_23_NHS_review tag was added to gene: POC1A. |
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| Lipodystrophy - childhood onset v4.27 | POC1A | Achchuthan Shanmugasundram Classified gene: POC1A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.27 | POC1A | Achchuthan Shanmugasundram Added comment: Comment on list classification: As recommended by the NHS, there is sufficient evidence (9 unrelated cases) in support of the association of this gene with severe dyslipidaemic insulin resistance. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.27 | POC1A | Achchuthan Shanmugasundram Gene: poc1a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.26 | POC1A | Achchuthan Shanmugasundram Phenotypes for gene: POC1A were changed from SOFT syndrome, Severe insulin resistance to Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis, OMIM:614813; Insulin resistance, HP:0000855 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.25 | POC1A | Achchuthan Shanmugasundram Publications for gene: POC1A were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.24 | POC1A | Achchuthan Shanmugasundram edited their review of gene: POC1A: Changed publications to: 22440536, 26336158, 28819016, 33372278, 35234134 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.24 | POC1A | Achchuthan Shanmugasundram edited their review of gene: POC1A: Changed rating: GREEN; Changed publications to: 22440536, 26336158, 28819016,33372278, 35234134 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.24 | POC1A |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: 9 unrelated probands with SHORT syndrome with severe dyslipidaemic insulin resistance are known, this represents 26% of all known cases (PMID: 35234134, 26336158, 28819016, 33372278 ,22440536 see PMID: 35234134 discussion for summary of all published and unpublished cases). Along with ALMS1 and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: 9 unrelated probands with SHORT syndrome with severe dyslipidaemic insulin resistance are known, this represents 26% of all known cases (PMID: 35234134, 26336158, 28819016, 33372278, 22440536 see PMID: 35234134 discussion for summary of all published and unpublished cases). Along with ALMS1 and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear. |
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| Lipodystrophy - childhood onset v4.24 | POC1A |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: 9 unrelated probands with SHORT syndrome with severe dyslipidaemic insulin resistance are known, this represents 26% of all known cases (PMID: 35234134, 26336158, 28819016, 33372278 ,22440536 see PMID: 35234134 discussion for summary of all published and unpublished cases). Along with ALMS1 and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: 9 unrelated probands with SHORT syndrome with severe dyslipidaemic insulin resistance are known, this represents 26% of all known cases (PMID: 35234134, 26336158, 28819016, 33372278 ,22440536 see PMID: 35234134 discussion for summary of all published and unpublished cases). Along with ALMS1 and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear. |
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| Lipodystrophy - childhood onset v4.24 | CIDEC | Achchuthan Shanmugasundram Phenotypes for gene: CIDEC were changed from Lipodystrophy, familial partial, type 5, 615238 to ?Lipodystrophy, familial partial, type 5, OMIM:615238 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.23 | CIDEC | Achchuthan Shanmugasundram Classified gene: CIDEC as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.23 | CIDEC | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is one case with partial lipodystrophy and evidence from mouse models. This gene is already reported in OMIM, but not in Gene2Phenotype. Hence, this gene can only be rated amber with current evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.23 | CIDEC | Achchuthan Shanmugasundram Gene: cidec has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.22 | CIDEC | Achchuthan Shanmugasundram Publications for gene: CIDEC were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.21 | CIDEC | Achchuthan Shanmugasundram edited their review of gene: CIDEC: Changed rating: AMBER; Changed publications to: 20049731, 25565658, 27710244; Changed phenotypes to: ?Lipodystrophy, familial partial, type 5, OMIM:615238 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.21 | PCYT1A |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Compound heterozygous loss of function mutations co-segregate with lipodystrophy and its metabolic sequelae in two independent pedigrees and PCYT1A knockdown impairs adipogenesis in vitro (PMID: 24889630). These patients did not exhibit features of spondylometaphyseal dysplasia or any retinal disesae, despite dedicated assessment. To our knowledge, the basis for the phenotypic heterogeneity in carriers of biallelic loss of function PCYT1A mutations is not understood.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: Compound heterozygous loss of function mutations co-segregate with lipodystrophy and its metabolic sequelae in two independent pedigrees and PCYT1A knockdown impairs adipogenesis in vitro (PMID: 24889630). These patients did not exhibit features of spondylometaphyseal dysplasia or any retinal disesae, despite dedicated assessment. To our knowledge, the basis for the phenotypic heterogeneity in carriers of biallelic loss of function PCYT1A mutations is not understood. |
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| Lipodystrophy - childhood onset v4.21 | PCYT1A |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PCYT1A. Tag Q3_23_NHS_review tag was added to gene: PCYT1A. |
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| Lipodystrophy - childhood onset v4.21 | PCYT1A | Achchuthan Shanmugasundram Classified gene: PCYT1A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.21 | PCYT1A | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (two unrelated cases and functional studies) for promoting this gene to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.21 | PCYT1A | Achchuthan Shanmugasundram Gene: pcyt1a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.20 | PCYT1A | Achchuthan Shanmugasundram edited their review of gene: PCYT1A: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.20 | PCYT1A | Achchuthan Shanmugasundram Phenotypes for gene: PCYT1A were changed from Spondylometaphyseal dysplasia with cone-rod dystrophy, Congenital lipodystrophy to Spondylometaphyseal dysplasia with cone-rod dystrophy, OMIM:608940; congenital generalized lipodystrophy, MONDO:0006536; Insulin resistance, HP:0000855 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.19 | PCYT1A | Achchuthan Shanmugasundram Publications for gene: PCYT1A were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.18 | PCYT1A | Achchuthan Shanmugasundram edited their review of gene: PCYT1A: Added comment: Two unrelated patients were identified with biallelic loss-of-function PCYT1A variants (patient 1: p.Glu280del/ p.Val142Met; patient 2: p.Glu280del/ p.333fs) and were reported with lipodystrophy, severe insulin resistance and diabetes. Functional studies showed that the presence of these variants result in near-total lack of PCYT1A expression and significantly reduce PC synthesis via the Kennedy pathway (PMID:24889630). Some of the phenotypes seen in patients such as severe fatty liver and low HDL cholesterol levels have also been seen in the liver-specific deletion of murine PCYT1A gene (PMID:18955728).; Changed publications to: 18955728, 24889630 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.18 | PCNT | Achchuthan Shanmugasundram Classified gene: PCNT as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.18 | PCNT | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available for promoting this gene to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.18 | PCNT | Achchuthan Shanmugasundram Gene: pcnt has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.17 | PCNT | Achchuthan Shanmugasundram Phenotypes for gene: PCNT were changed from Microcephalic osteodysplastic primordial dwarfism, type II, Severe insulin resistance to Microcephalic osteodysplastic primordial dwarfism, type II, OMIM:210720; Insulin resistance, HP:0000855 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.16 | PCNT | Achchuthan Shanmugasundram Publications for gene: PCNT were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.15 | PCNT |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PCNT. Tag Q3_23_NHS_review tag was added to gene: PCNT. |
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| Lipodystrophy - childhood onset v4.15 | PCNT | Achchuthan Shanmugasundram edited their review of gene: PCNT: Added comment: Of 21 patients with biallelic PCNT variants, 18 had insulin resistance, which was severe in the majority of patients. Ten patients had confirmed diabetes (mean age of onset 15 years), and 13 had metabolic dyslipidemia. All patients without insulin resistance were younger than 4 years old. In addition, knockdown of PCNT in adipocytes had no effect on proximal insulin signaling but produced a two-fold impairment in insulin-stimulated glucose uptake, approximately commensurate with an associated defect in cell proliferation and adipogenesis (PMID:21270239).; Changed rating: GREEN; Changed publications to: 21270239 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.230 | KCNH5 | Dmitrijs Rots reviewed gene: KCNH5: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: PMID: 36307226, 35874597; Phenotypes: Neurodevelopmental disorder and Epilepsy; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.77 | KCNH5 | Dmitrijs Rots reviewed gene: KCNH5: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: PMID: 36307226, 35874597; Phenotypes: NDD with seizures; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare genetic inflammatory skin disorders v3.1 | GNB1 |
Dmitrijs Rots gene: GNB1 was added gene: GNB1 was added to Rare genetic inflammatory skin disorders. Sources: Literature Mode of inheritance for gene: GNB1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: GNB1 were set to 35119134 Phenotypes for gene: GNB1 were set to Cutaneous mastocytosis; Intellectual developmental disorder, autosomal dominant 42 Mode of pathogenicity for gene: GNB1 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: GNB1 was set to GREEN Added comment: 5 cases reported with cutaneous mastocytosis and a de novo missense variant (mostly recurrent). Although rare feature (to date reported ~60 cases with GNB1-related disorder), enough evidence for green rating due to mastocytosis. Sources: Literature |
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| Renal tubulopathies v4.3 | RMND1 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: RMND1. Tag Q3_23_NHS_review tag was added to gene: RMND1. |
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| Renal tubulopathies v4.3 | RMND1 | Achchuthan Shanmugasundram Classified gene: RMND1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.3 | RMND1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.3 | RMND1 | Achchuthan Shanmugasundram Gene: rmnd1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.2 | RMND1 | Achchuthan Shanmugasundram Phenotypes for gene: RMND1 were changed from tubulopathy; renal tubular acidosis; interstitial nephritis; end-stage renal disease; tubular atrophy to Combined oxidative phosphorylation deficiency 11, OMIM:614922; tubulopathy; renal tubular acidosis; interstitial nephritis; end-stage renal disease; tubular atrophy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.1 | RMND1 |
Achchuthan Shanmugasundram changed review comment from: PMID:31568715 - Four patients identified with pathogenic variants in RMND1 were reported with renal disease characterised by tubulopathy (3/4), renal tubular acidosis (2/4), interstitial nephritis (1/4), and/or end-stage renal disease (4/4) necessitating renal transplantation (2/4). PMID:31889854 - A very rare homozygous pathogenic variant in RMND1 (p.Val211Met) was identified in a patient presenting with chronic kidney disease (CKD) and sensorineural hearing loss (SNHL). PMID:32911714 - Compound heterozygous missense variants in RMND1 (p.Gly195Arg & p.Tyr273Ser) was identified in female siblings presenting with severe-to-profound bilateral SNHL, ovarian dysfunction and CKD that developed in the fourth decade of life.; to: PMID:31568715 - Four patients identified with pathogenic variants in RMND1 were reported with renal disease characterised by tubulopathy (3/4), renal tubular acidosis (2/4), interstitial nephritis (1/4), and/or end-stage renal disease (4/4) necessitating renal transplantation (2/4). PMID:31889854 - A very rare homozygous pathogenic variant in RMND1 (p.Val211Met) was identified in a patient presenting with chronic kidney disease (CKD) and sensorineural hearing loss (SNHL). PMID:32911714 - Compound heterozygous missense variants in RMND1 (p.Gly195Arg & p.Tyr273Ser) was identified in female siblings presenting with severe-to-profound bilateral SNHL, ovarian dysfunction and CKD that developed in the fourth decade of life. This gene has been associated with relevant phenotypes in both OMIM (MIM #614922) and Gene2Phenotype. The clinical manifestations such as cystic kidneys, renal tubular acidosis and renal disease have been recorded as part of the OMIM phenotype. |
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| Renal tubulopathies v4.1 | RMND1 | Achchuthan Shanmugasundram reviewed gene: RMND1: Rating: GREEN; Mode of pathogenicity: None; Publications: 31568715, 31889854, 32911714; Phenotypes: Combined oxidative phosphorylation deficiency 11, OMIM:614922; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.23 | MPDZ |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: MPDZ. Tag Q3_23_NHS_review tag was added to gene: MPDZ. |
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| Retinal disorders v4.23 | MPDZ | Achchuthan Shanmugasundram Classified gene: MPDZ as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.23 | MPDZ | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated cases and supporting functional evidence available for the association of this gene with this panel and hence this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.23 | MPDZ | Achchuthan Shanmugasundram Gene: mpdz has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.22 | MPDZ | Achchuthan Shanmugasundram Phenotypes for gene: MPDZ were changed from to Hydrocephalus, congenital, 2, with or without brain or eye anomalies, OMIM:615219 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.21 | MPDZ | Achchuthan Shanmugasundram Publications for gene: MPDZ were set to PMID 28556411, 36594712, 36429029 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.20 | MPDZ | Achchuthan Shanmugasundram reviewed gene: MPDZ: Rating: GREEN; Mode of pathogenicity: None; Publications: 28556411, 36429029, 36594712; Phenotypes: Hydrocephalus, congenital, 2, with or without brain or eye anomalies, OMIM:615219; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.10 | HIKESHI |
Achchuthan Shanmugasundram Tag watchlist was removed from gene: HIKESHI. Tag Q3_23_promote_green tag was added to gene: HIKESHI. Tag Q3_23_NHS_review tag was added to gene: HIKESHI. |
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| Optic neuropathy v4.10 | HIKESHI | Achchuthan Shanmugasundram Classified gene: HIKESHI as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.10 | HIKESHI | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated cases) available now for promoting this gene to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.10 | HIKESHI | Achchuthan Shanmugasundram Gene: hikeshi has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.9 | HIKESHI | Achchuthan Shanmugasundram Publications for gene: HIKESHI were set to 26545878; 28000699 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.15 | PCNT |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Severe insulin resistance in the absence of frank lipodystrophy is a common feature of Microcephalic osteodysplastic primordial dwarfism, type II due to PCNT mutations (PMID: 21270239). Along with ALMS1 and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: Severe insulin resistance in the absence of frank lipodystrophy is a common feature of Microcephalic osteodysplastic primordial dwarfism, type II due to PCNT mutations (PMID: 21270239). Along with ALMS1 and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear. |
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| Lipodystrophy - childhood onset v4.15 | ALMS1 | Achchuthan Shanmugasundram Classified gene: ALMS1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.15 | ALMS1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available to promote this gene to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.15 | ALMS1 | Achchuthan Shanmugasundram Gene: alms1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.14 | ALMS1 | Achchuthan Shanmugasundram edited their review of gene: ALMS1: Changed phenotypes to: Alstrom syndrome, severe insulin resistance | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.14 | ALMS1 | Achchuthan Shanmugasundram Phenotypes for gene: ALMS1 were changed from BIALLELIC, autosomal or pseudoautosomal to Alstrom syndrome, OMIM:203800 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.13 | ALMS1 | Achchuthan Shanmugasundram edited their review of gene: ALMS1: Changed phenotypes to: Almstrom syndrome, severe insulin resistance | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.13 | ALMS1 | Achchuthan Shanmugasundram Publications for gene: ALMS1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.12 | ALMS1 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: ALMS1. Tag Q3_23_NHS_review tag was added to gene: ALMS1. |
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| Lipodystrophy - childhood onset v4.12 | ALMS1 |
Achchuthan Shanmugasundram edited their review of gene: ALMS1: Added comment: Among 12 unrelated cases with Alstrom syndrome, 10 were identified with ALMS1 variants, of which five had potential founder variant in exon 16. These AS patients had severe early-onset obesity, insulin resistance that increased with age, diabetes, hypertriglyceridemia, and hypertension (PMID:16720663). Evaluation of 38 patients with AS and matched controls showed that frequent abnormalities include obesity, severe insulin resistance, type 2 diabetes mellitus and adult hypogonadism (PMID:29718281). This gene has been associated with AS in both OMIM (MIM #203800) and Gene2Phenotype (definitive rating).; Changed rating: GREEN; Changed publications to: 16720663, 29718281, 32958032 |
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| Lipodystrophy - childhood onset v4.12 | ALMS1 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Severe insulin resistance and its metabolic sequalae are common in Almstrom syndrome (PMID: 32958032, 16720663) which is disproportionate to their adiposity (PMID: 29718281). Along with PCNT and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear.; to: This gene was added on recommendation of NHSE Genomic Medicine Service: Severe insulin resistance and its metabolic sequalae are common in Almstrom syndrome (PMID: 32958032, 16720663) which is disproportionate to their adiposity (PMID: 29718281). Along with PCNT and POC1A it is part of a cluster of genes that cause severe insulin resistance syndromes and affect the centrosome/primary cillium though the precise mechanistic basis for the impairment in insulin action is unclear. |
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| Lipodystrophy - childhood onset v4.12 | BLM |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/174/gene/BLM/#!details), partial lipodystrophy and insulin resistance is a recognised clinical feature of bloom syndrome (PMID: 21536711, 29477938, 16763388) and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244).; to: This gene was added on recommendation of NHSE Genomic Medicine Service: Expert Review Green (https://panelapp.genomicsengland.co.uk/panels/174/gene/BLM/#!details), partial lipodystrophy and insulin resistance is a recognised clinical feature of bloom syndrome (PMID: 21536711, 29477938, 16763388) and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). |
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| Intellectual disability v5.230 | LETM1 | Sarah Leigh Entity copied from Ataxia and cerebellar anomalies - narrow panel v4.27 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.230 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Intellectual disability - microarray and sequencing. Sources: Expert Review Amber,Expert Review Q3_23_promote_green, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Possible mitochondrial disorder - nuclear genes v3.41 | LETM1 | Sarah Leigh Tag Q3_23_NHS_review tag was added to gene: LETM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.8 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.8 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Optic neuropathy. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Ataxia and cerebellar anomalies - narrow panel v4.27 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.27 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Early onset or syndromic epilepsy v4.77 | LETM1 | Sarah Leigh Entity copied from Possible mitochondrial disorder - nuclear genes v3.41 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.77 | LETM1 |
Sarah Leigh gene: LETM1 was added gene: LETM1 was added to Early onset or syndromic epilepsy. Sources: Expert Review,Expert Review Amber Q3_23_promote_green, Q3_23_MOI tags were added to gene: LETM1. Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LETM1 were set to 36055214; 33815143 Phenotypes for gene: LETM1 were set to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 |
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| Possible mitochondrial disorder - nuclear genes v3.41 | LETM1 |
Sarah Leigh edited their review of gene: LETM1: Added comment: LETM1 variants has been associated with Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 and as moderate Gen2Phen gene for LETM1-related neurodevelopmental disorder. PMID: 36055214 reports 10 LETM1 variants in 18 patients from 11 unrelated families with childhood-onset neurodegeneration with multisystem involvement, many of whom were gathered using the GeneMatcher Program. The most common clinical features of this cohort, where an assessment could be made, were: mitochondrial respiratory complex deficiencies 11/11 (100%), global developmental delay / intellectual disability 17/18 (94%), bilateral sensorineural hearing loss 11/14 (78%) , impaired vision 10/10 (100%), cerebellar ataxia 7/9 (78%), seizures 10/15 (67%), hypotonia 11/18 (61%) (PMID: 36055214, figure 1c).; Changed rating: GREEN; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal |
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| Possible mitochondrial disorder - nuclear genes v3.41 | LETM1 |
Sarah Leigh Tag Q3_23_promote_green tag was added to gene: LETM1. Tag Q3_23_MOI tag was added to gene: LETM1. |
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| Possible mitochondrial disorder - nuclear genes v3.41 | LETM1 | Sarah Leigh Classified gene: LETM1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.41 | LETM1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.41 | LETM1 | Sarah Leigh Gene: letm1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.71 | LETM1 | Sarah Leigh Publications for gene: LETM1 were set to 36055214 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Laterality disorders and isomerism v3.4 | LETM1 | Sarah Leigh Publications for gene: LETM1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.40 | LETM1 | Sarah Leigh Publications for gene: LETM1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.12 | WRN | Achchuthan Shanmugasundram Classified gene: WRN as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.12 | WRN | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (three unrelated cases) in support of the association of this gene to severe insulin resistance/ diabetes and partial lipodystrophy and hence can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.12 | WRN | Achchuthan Shanmugasundram Gene: wrn has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.11 | WRN |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: WRN. Tag Q3_23_NHS_review tag was added to gene: WRN. |
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| Lipodystrophy - childhood onset v4.11 | WRN | Achchuthan Shanmugasundram Phenotypes for gene: WRN were changed from Werner's Syndrome, partial lipodystrophy, severe insulin resistance to Werner syndrome, OMIM:277700 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.10 | WRN | Achchuthan Shanmugasundram Publications for gene: WRN were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.9 | WRN |
Achchuthan Shanmugasundram edited their review of gene: WRN: Added comment: PMID:22654791 - A homozygous variant (p.Arg732Xaa) in WRN gene has been identified in a 16-year-old female patient with a syndrome comprising short stature, severe insulin resistance, ptosis, and microcephaly. PMID:23849162 - Biallelic WRN null variants (p.Gln748Xaa homozygous, and compound heterozygous p.Gln1257Xaa/ p.Met1329fs) were identified in two female patients who presented with a partial lipodystrophic syndrome with hypertriglyceridemia and liver steatosis. One of them also had diabetes. PMID:35780059 - Compound heterozygous variants (c.1290_1293del/ p.Asn430Lysfs*7 & c.2732+5G>A) in WRN gene was identified in a 28 year-old woman who presented with early onset diabetes associated with partial lipodystrophy, severe dyslipidaemia and rapidly progressive liver fibrosis related to non-alcoholic steatohepatitis in the absence of progeroid features. This gene has been associated with Werner syndrome in both OMIM (MIM #277700) and Gene2Phenotype.; Changed rating: GREEN; Changed publications to: 22654791, 23849162, 27710244, 35780059 |
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| Laterality disorders and isomerism v3.3 | LETM1 | Sarah Leigh Mode of inheritance for gene: LETM1 was changed from to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Laterality disorders and isomerism v3.2 | LETM1 | Sarah Leigh Phenotypes for gene: LETM1 were changed from to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.39 | LETM1 | Sarah Leigh Phenotypes for gene: LETM1 were changed from 620089 Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction to Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction, OMIM:620089 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.9 | WRN |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Premature insulin resistant diabetes is widely recognised as a complication of Werner's syndrome and lipoatrophy is commonly reported. Crucially - 3 independent pedigrees have now reported lipodystrophy and/or severe insulin resistance as presenting features of Werner's syndrome highlighting that this condition needs to be considered in the differential diagnosis of lipodystrophy (PMID: 22654791, 35780059, 23849162). It has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244).; to: This gene was added on recommendation of NHSE Genomic Medicine Service: Premature insulin resistant diabetes is widely recognised as a complication of Werner's syndrome and lipoatrophy is commonly reported. Crucially - 3 independent pedigrees have now reported lipodystrophy and/or severe insulin resistance as presenting features of Werner's syndrome highlighting that this condition needs to be considered in the differential diagnosis of lipodystrophy (PMID: 22654791, 35780059, 23849162). It has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). |
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| Lipodystrophy - childhood onset v4.9 | AKT2 | Achchuthan Shanmugasundram Classified gene: AKT2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.9 | AKT2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Two unrelated cases and supporting functional evidence from mouse models suggest that this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.9 | AKT2 | Achchuthan Shanmugasundram Gene: akt2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.8 | AKT2 | Achchuthan Shanmugasundram Publications for gene: AKT2 were set to 15166380; 17327441 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.7 | AKT2 | Achchuthan Shanmugasundram Mode of inheritance for gene: AKT2 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.6 | AKT2 |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: AKT2. Tag Q3_23_NHS_review tag was added to gene: AKT2. |
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| Lipodystrophy - childhood onset v4.6 | AKT2 |
Achchuthan Shanmugasundram edited their review of gene: AKT2: Added comment: PMID:15166380 - A missense variant (p.Arg274His) in AKT2 gene was identified in a family with autosomal dominant severe insulin resistance, diabetes mellitus and partial lipodystrophy. PMID:17327441 - Of 94 probands with severe insulin resistance (35 of which had partial lipodystrophy) that were screened for AKT2 variants, one female identified with p.Arg467Trp variant was reported with type 2 diabetes and partial lipodystrophy, while another female identified with p.Arg208Lys variant had severe insulin resistance and acanthosis nigricans. p.Arg467Trp was present in neither 47 ethnically matched control subjects nor in 2 unaffected sons of the carrier. p.Arg208Lys variant was not present in her affected son but was present in 1 of 47 white control subjects. PMID:12843127 - Functional studies in mice showed that loss of AKT2 results in severe diabetes, age-dependent lipoatrophy and mild growth deficiency.; Changed rating: GREEN; Changed publications to: 12843127, 15166380, 17327441, 27710244 |
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| Optic neuropathy v4.7 | MCAT | Hannah Knight reviewed gene: MCAT: Rating: AMBER; Mode of pathogenicity: None; Publications: 33918393; Phenotypes: Hereditary optic neuropathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.7 | MCAT | Hannah Knight Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.7 | MCAT | Hannah Knight reviewed gene: MCAT: Rating: AMBER; Mode of pathogenicity: None; Publications: 33918393; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.6 | PIK3R1 | Achchuthan Shanmugasundram Classified gene: PIK3R1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.6 | PIK3R1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available for the association of this gene with lipodystrophy and insulin resistance and hence this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.6 | PIK3R1 | Achchuthan Shanmugasundram Gene: pik3r1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.5 | PIK3R1 | Achchuthan Shanmugasundram Phenotypes for gene: PIK3R1 were changed from SHORT syndrome, partial lipodystrophy, severe insulin resistance to SHORT syndrome, OMIM:269880 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.4 | PIK3R1 | Achchuthan Shanmugasundram Publications for gene: PIK3R1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PIK3R1 | Achchuthan Shanmugasundram Tag Q3_23_NHS_review tag was added to gene: PIK3R1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PIK3R1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PIK3R1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PIK3R1 |
Achchuthan Shanmugasundram edited their review of gene: PIK3R1: Added comment: PMID:23810378 - Nine affected individuals from eight different families were identified with de novo or inherited PIK3R1 variants, including a mutational hotspot (c.1945C>T/ p.Arg649Trp) present in four families. Insulin resistance was present in seven individuals and lipoatrophy was present in 3 individuals. PMID:26497935 - Clinical reappraisal of detailed phenotypes of 32 individuals with PIK3R1-associated SHORT syndrome showed that IUGR <= 3rd percentile (19/25), postnatal growth retardation (height < -2SD, 25/31), lipoatrophy (26/29), factual dysmorphism (all 32 cases) and insulin resistance (13/17) are the main features of this disease. PMID:27766312 - Five patients were reported with SHORT syndrome and C-terminal variants in PIK3R1, of which four had extreme insulin resistance without dyslipidemia or hepatic steatosis. This gene has been associated with relevant phenotypes in both OMIM (MIM #269880) and Gene2Phenotype ('definitive' rating in the DD panel). Both lipoatrophy (lower face, upper limb, buttock) and insulin resistance diabetes has been associated as clinical manifestations of this OMIM phenotype for SHORT syndrome.; Changed rating: GREEN; Changed publications to: 23810378, 26497935, 27710244, 27766312 |
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| Lipodystrophy - childhood onset v4.3 | PIK3R1 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service. Below are the comments from NHS: PanelApp expert review green (https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!), Co-segregates with disease in multiple independent pedigrees (PMID: 27766312, 23810378, 26497935), its gene product is a member of the canonical insulin signalling cascade and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). SHORT syndrome appears to be caused by C-Terminal mutations affecting the SH2 domain, suggesting a mechanism other than simple loss of function (see Prof Rob Semple's review in Panel app @ https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!); to: This gene was added on recommendation of NHSE Genomic Medicine Service. Below are the comments from NHS: PanelApp expert review green (https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!), Co-segregates with disease in multiple independent pedigrees (PMID: 27766312, 23810378, 26497935), its gene product is a member of the canonical insulin signalling cascade and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). SHORT syndrome appears to be caused by C-Terminal mutations affecting the SH2 domain, suggesting a mechanism other than simple loss of function (see Prof Rob Semple's review in Panel app @ https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!) |
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| Lipodystrophy - childhood onset v4.3 | PIK3R1 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: PanelApp expert review green (https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!), Co-segregates with disease in multiple independent pedigrees (PMID: 27766312, 23810378, 26497935), its gene product is a member of the canonical insulin signalling cascade and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). SHORT syndrome appears to be caused by C-Terminal mutations affecting the SH2 domain, suggesting a mechanism other than simple loss of function (see Prof Rob Semple's review in Panel app @ https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!); to: This gene was added on recommendation of NHSE Genomic Medicine Service. Below are the comments from NHS: PanelApp expert review green (https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!), Co-segregates with disease in multiple independent pedigrees (PMID: 27766312, 23810378, 26497935), its gene product is a member of the canonical insulin signalling cascade and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). SHORT syndrome appears to be caused by C-Terminal mutations affecting the SH2 domain, suggesting a mechanism other than simple loss of function (see Prof Rob Semple's review in Panel app @ https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!) |
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| Lipodystrophy - childhood onset v4.3 | PIK3R1 |
Achchuthan Shanmugasundram changed review comment from: This gene was added on recommendation of NHSE Genomic Medicine Service: Panel app expert review green (https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!), Co-segregates with disease in multiple independent pedigrees (PMID: 27766312, 23810378, 26497935), its gene product is a member of the canonical insulin signalling cascade and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). SHORT syndrome appears to be caused by C-Terminal mutations affecting the SH2 domain, suggesting a mechanism other than simple loss of function (see Prof Rob Semple's review in Panel app @ https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!); to: This gene was added on recommendation of NHSE Genomic Medicine Service: PanelApp expert review green (https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!), Co-segregates with disease in multiple independent pedigrees (PMID: 27766312, 23810378, 26497935), its gene product is a member of the canonical insulin signalling cascade and has been endorsed as a cause of lipodystrophy by an international multi-society practice guideline (PMID: 27710244). SHORT syndrome appears to be caused by C-Terminal mutations affecting the SH2 domain, suggesting a mechanism other than simple loss of function (see Prof Rob Semple's review in Panel app @ https://panelapp.genomicsengland.co.uk/panels/174/gene/PIK3R1/#!) |
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| Lipodystrophy - childhood onset v4.3 | CIDEC | Achchuthan Shanmugasundram reviewed gene: CIDEC: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: Familial Partial Lipodystrophy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | AKT2 | Achchuthan Shanmugasundram reviewed gene: AKT2: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: Severe insulin resistance, familial partial lipodystrophy; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PSMA3 | Achchuthan Shanmugasundram reviewed gene: PSMA3: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PSMB4 | Achchuthan Shanmugasundram reviewed gene: PSMB4: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PSMB8 | Achchuthan Shanmugasundram reviewed gene: PSMB8: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | EPHX1 | Achchuthan Shanmugasundram reviewed gene: EPHX1: Rating: ; Mode of pathogenicity: Other; Publications: ; Phenotypes: Lipodystrophy, Severe Insulin Resistance; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | MFN2 | Achchuthan Shanmugasundram reviewed gene: MFN2: Rating: ; Mode of pathogenicity: Other; Publications: ; Phenotypes: MFN2-associated multiple lipomatosis, lipodystrophy, severe insulin resistance, axonal sensorimotor neuropathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | POC1A | Achchuthan Shanmugasundram reviewed gene: POC1A: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: SOFT syndrome, Severe insulin resistance; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PCYT1A | Achchuthan Shanmugasundram reviewed gene: PCYT1A: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Spondylometaphyseal dysplasia with cone-rod dystrophy, Congenital lipodystrophy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PCNT | Achchuthan Shanmugasundram reviewed gene: PCNT: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Microcephalic osteodysplastic primordial dwarfism, type II, Severe insulin resistance; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | ALMS1 | Achchuthan Shanmugasundram reviewed gene: ALMS1: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: BIALLELIC, autosomal or pseudoautosomal; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | BLM | Achchuthan Shanmugasundram reviewed gene: BLM: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Bloom Syndrome, severe insulin resistance; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | WRN | Achchuthan Shanmugasundram reviewed gene: WRN: Rating: ; Mode of pathogenicity: ; Publications: ; Phenotypes: Werner's Syndrome, partial lipodystrophy, severe insulin resistance; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.3 | PIK3R1 | Achchuthan Shanmugasundram reviewed gene: PIK3R1: Rating: ; Mode of pathogenicity: Other; Publications: ; Phenotypes: SHORT syndrome, partial lipodystrophy, severe insulin resistance; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lipodystrophy - childhood onset v4.2 | PSMA3 |
Achchuthan Shanmugasundram gene: PSMA3 was added gene: PSMA3 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: PSMA3 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PSMA3 were set to Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome) |
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| Lipodystrophy - childhood onset v4.2 | PSMB4 |
Achchuthan Shanmugasundram gene: PSMB4 was added gene: PSMB4 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: PSMB4 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PSMB4 were set to Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome) |
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| Lipodystrophy - childhood onset v4.2 | PSMB8 |
Achchuthan Shanmugasundram gene: PSMB8 was added gene: PSMB8 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: PSMB8 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PSMB8 were set to Proteasome associated autoinflammatory syndrome-1, CANDLES (Chronic, atypical, neutrophillic dermatosis with lipodystrophy and elevated temperature syndrome), Joint contractures, muscle atrophy, microcytic anemia, and panniculitis-induced lipodystrophy (JMP syndrome) |
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| Lipodystrophy - childhood onset v4.2 | EPHX1 |
Achchuthan Shanmugasundram gene: EPHX1 was added gene: EPHX1 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: EPHX1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: EPHX1 were set to Lipodystrophy, Severe Insulin Resistance Mode of pathogenicity for gene: EPHX1 was set to Other |
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| Lipodystrophy - childhood onset v4.2 | MFN2 |
Achchuthan Shanmugasundram gene: MFN2 was added gene: MFN2 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: MFN2 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: MFN2 were set to MFN2-associated multiple lipomatosis, lipodystrophy, severe insulin resistance, axonal sensorimotor neuropathy Mode of pathogenicity for gene: MFN2 was set to Other |
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| Lipodystrophy - childhood onset v4.2 | POC1A |
Achchuthan Shanmugasundram gene: POC1A was added gene: POC1A was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: POC1A was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: POC1A were set to SOFT syndrome, Severe insulin resistance |
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| Lipodystrophy - childhood onset v4.2 | PCYT1A |
Achchuthan Shanmugasundram gene: PCYT1A was added gene: PCYT1A was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: PCYT1A was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PCYT1A were set to Spondylometaphyseal dysplasia with cone-rod dystrophy, Congenital lipodystrophy |
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| Lipodystrophy - childhood onset v4.2 | PCNT |
Achchuthan Shanmugasundram gene: PCNT was added gene: PCNT was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: PCNT was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PCNT were set to Microcephalic osteodysplastic primordial dwarfism, type II, Severe insulin resistance |
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| Lipodystrophy - childhood onset v4.2 | ALMS1 |
Achchuthan Shanmugasundram gene: ALMS1 was added gene: ALMS1 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: ALMS1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ALMS1 were set to BIALLELIC, autosomal or pseudoautosomal |
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| Lipodystrophy - childhood onset v4.2 | BLM |
Achchuthan Shanmugasundram gene: BLM was added gene: BLM was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: BLM was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: BLM were set to Bloom Syndrome, severe insulin resistance |
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| Lipodystrophy - childhood onset v4.2 | WRN |
Achchuthan Shanmugasundram gene: WRN was added gene: WRN was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: WRN was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: WRN were set to Werner's Syndrome, partial lipodystrophy, severe insulin resistance |
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| Lipodystrophy - childhood onset v4.2 | PIK3R1 |
Achchuthan Shanmugasundram gene: PIK3R1 was added gene: PIK3R1 was added to Lipodystrophy - childhood onset. Sources: Expert list,NHS GMS Mode of inheritance for gene: PIK3R1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: PIK3R1 were set to SHORT syndrome, partial lipodystrophy, severe insulin resistance Mode of pathogenicity for gene: PIK3R1 was set to Other |
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| Insulin resistance (including lipodystrophy) v1.16 | PIK3R1 | Achchuthan Shanmugasundram Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Insulin resistance (including lipodystrophy) v1.16 | PIK3R1 | Achchuthan Shanmugasundram edited their review of gene: PIK3R1: Changed mode of pathogenicity: Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Insulin resistance (including lipodystrophy) v1.16 | PIK3R1 | Achchuthan Shanmugasundram reviewed gene: PIK3R1: Rating: ; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.38 | IDH3A | Sarah Leigh Tag Q3_23_NHS_review tag was added to gene: IDH3A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.38 | CRLS1 | Sarah Leigh Tag Q3_23_NHS_review tag was added to gene: CRLS1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.38 | C2orf69 | Sarah Leigh Phenotypes for gene: C2orf69 were changed from Combined oxidative phosphorylation deficiency 53, OMIM:619423 to Combined oxidative phosphorylation deficiency 53, OMIM:619423; combined oxidative phosphorylation deficiency 53, MONDO:0030378 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.37 | C2orf69 | Sarah Leigh Tag Q3_23_NHS_review tag was added to gene: C2orf69. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.70 | ATP5O | Sarah Leigh Phenotypes for gene: ATP5O were changed from Mitochondrial complex V (ATP synthase) deficiency to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7, OMIM:620359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.76 | ATP5O | Sarah Leigh Phenotypes for gene: ATP5O were changed from Mitochondrial complex V (ATP synthase) deficiency to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7, OMIM:620359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.44 | ATP5O | Sarah Leigh Phenotypes for gene: ATP5O were changed from Mitochondrial complex V (ATP synthase) deficiency to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7, OMIM:620359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.98 | ATP5O | Sarah Leigh Phenotypes for gene: ATP5O were changed from Mitochondrial complex V (ATP synthase) deficiency to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7, OMIM:620359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorder with complex V deficiency v2.6 | ATP5O | Sarah Leigh Phenotypes for gene: ATP5O were changed from Mitochondrial complex V (ATP synthase) deficiency to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7, OMIM:620359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.37 | ATP5O | Sarah Leigh Phenotypes for gene: ATP5O were changed from Mitochondrial complex V (ATP synthase) deficiency to Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7, OMIM:620359 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.36 | ATP5O | Sarah Leigh Tag Q3_23_NHS_review tag was added to gene: ATP5O. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.229 | SLC25A24 | Sarah Leigh Publications for gene: SLC25A24 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Structural eye disease v3.4 | SLC25A24 | Sarah Leigh Publications for gene: SLC25A24 were set to 29100093 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.172 | SLC25A24 | Sarah Leigh Publications for gene: SLC25A24 were set to 29100094; 29100093 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.97 | SLC25A24 | Sarah Leigh Publications for gene: SLC25A24 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Pneumothorax - familial v3.3 | SLC25A24 | Sarah Leigh Publications for gene: SLC25A24 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Pneumothorax - familial v3.2 | SLC25A24 | Sarah Leigh Phenotypes for gene: SLC25A24 were changed from to Fontaine progeroid syndrome, OMIM; 612289; Fontaine progeroid syndrome, MONDO:0012853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Structural eye disease v3.3 | SLC25A24 | Sarah Leigh Phenotypes for gene: SLC25A24 were changed from Gorlin-Chaudhry-Moss Syndrome, GCMS; Fontaine progeroid syndrome, 612289 to Fontaine progeroid syndrome, OMIM; 612289; Fontaine progeroid syndrome, MONDO:0012853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.228 | SLC25A24 | Sarah Leigh Phenotypes for gene: SLC25A24 were changed from to Fontaine progeroid syndrome, OMIM; 612289; Fontaine progeroid syndrome, MONDO:0012853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.171 | SLC25A24 | Sarah Leigh Phenotypes for gene: SLC25A24 were changed from Fontaine progeroid syndrome 612289; Gorlin-Chaudhry-Moss to Fontaine progeroid syndrome, OMIM; 612289; Fontaine progeroid syndrome, MONDO:0012853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.96 | SLC25A24 | Sarah Leigh Added comment: Comment on phenotypes: Gorlin-Chaudhry-Moss syndrome (GCMS);Syndrome with Hypertrichosis, Progeroid Appearance, and Mitochondrial Dysfunction | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.96 | SLC25A24 | Sarah Leigh Phenotypes for gene: SLC25A24 were changed from Gorlin-Chaudhry-Moss syndrome (GCMS); Syndrome with Hypertrichosis, Progeroid Appearance, and Mitochondrial Dysfunction to Fontaine progeroid syndrome, OMIM; 612289; Fontaine progeroid syndrome, MONDO:0012853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.69 | SLC25A24 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC25A24. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.69 | SLC25A24 | Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 2 variants reported in at least nine unrelated cases.; to: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene. At least 2 variants reported in at least nine unrelated cases, together with supportive functional studies (PMID: 29100094; 29100093). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.69 | SLC25A24 | Sarah Leigh edited their review of gene: SLC25A24: Changed rating: GREEN; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.69 | SLC25A24 | Sarah Leigh Phenotypes for gene: SLC25A24 were changed from Fontaine progeroid syndrome 612289 to Fontaine progeroid syndrome, OMIM; 612289; Fontaine progeroid syndrome, MONDO:0012853 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.68 | SLC25A24 | Sarah Leigh Classified gene: SLC25A24 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.68 | SLC25A24 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.68 | SLC25A24 | Sarah Leigh Gene: slc25a24 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.67 | SLC25A24 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: SLC25A24. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.67 | SLC25A20 | Sarah Leigh Publications for gene: SLC25A20 were set to 9399886; 31108048; 25778941 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.66 | SLC25A20 | Sarah Leigh Classified gene: SLC25A20 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.66 | SLC25A20 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.66 | SLC25A20 | Sarah Leigh Gene: slc25a20 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.65 | SLC25A20 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: SLC25A20. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.65 | SLC25A20 | Sarah Leigh edited their review of gene: SLC25A20: Added comment: SLC25A20 variants have been associated with Carnitine-acylcarnitine translocase deficiency in OMIM and as definitive Gen2Phen gene for the same condition. Numerous variants have been reported in unrelated cases.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.65 | SLC25A20 | Sarah Leigh Phenotypes for gene: SLC25A20 were changed from Carnitine-acylcarnitine translocase deficiency, 212138 to Carnitine-acylcarnitine translocase deficiency, OMIM:212138; carnitine-acylcarnitine translocase deficiency, MONDO:0008918 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.64 | SLC25A20 | Sarah Leigh Publications for gene: SLC25A20 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.63 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.63 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 9916797; 17884651; 25778941; 28857146 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.62 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Added comment: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.6 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.5 | SLC22A5 | Sarah Leigh changed review comment from: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few instances have been reported in cases carrying heterozygous SLC22A5 variants (PMID: 10545605; 11261427).; to: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.12 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 29895548 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.11 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.11 | SLC22A5 | Sarah Leigh reviewed gene: SLC22A5: Rating: ; Mode of pathogenicity: None; Publications: 10545605, 11261427; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.227 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 9916797; 10425211; 15714519; 10480371; 9700603; 2235122; 20027113; 9634512; 11058897; 3974805; 10051646 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.227 | SLC22A5 | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.227 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.7 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.7 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 9916797; 10051646; 2235122; 11058897; 20027113; 9634512; 10425211; 9700603; 15714519; 10480371; 3974805 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.6 | SLC22A5 | Sarah Leigh reviewed gene: SLC22A5: Rating: ; Mode of pathogenicity: None; Publications: 10545605, 11261427; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.95 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.94 | SLC22A5 | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.94 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.36 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.35 | SLC22A5 | Sarah Leigh reviewed gene: SLC22A5: Rating: ; Mode of pathogenicity: None; Publications: 10545605, 11261427; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.35 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.43 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 27604308; 24816252 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.42 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.42 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Added comment: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; Changed rating: GREEN; Changed publications to: 10545605, 11261427; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.23 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from DCM; Propionicacidemia; Carnitine transporter deficiency (Disorders of carnitine transport and the carnitine cycle); Arrhythmia, muscle weakness or hypotonia, liver disease, hypoketotic hypoglycaemia; HCM, mixed; Carnitine transporter deficiency (primary carnitine deficiency) to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.5 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from arrhythmia; short QT; cardiomyopathy; primary carnitine deficiency; Carnitine deficiency, systemic primary 212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.595 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.11 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary, OMIM:212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.226 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary, 212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.42 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Propionicacidemia; Carnitine transporter deficiency (Disorders of carnitine transport and the carnitine cycle) to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.93 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from SYSTEMIC PRIMARY CARNITINE DEFICIENCY to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.34 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary, 212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.594 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine transporter deficiency (Disorders of carnitine transport and the carnitine cycle); Propionicacidemia to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.593 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 27604308; 24816252 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.592 | SLC22A5 | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.592 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.20 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Propionicacidemia 606054 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.7 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary 212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.6 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.6 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 25929793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.5 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Added comment: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; Changed rating: GREEN; Changed publications to: 10545605, 11261427; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.19 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.18 | SLC22A5 | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.18 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.22 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI was removed from gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.22 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Added comment: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few individuals heterozygous for SLC22A5 variants have been seen with a milder phenotype (PMID: 10545605; 11261427).; Changed publications to: 10545605, 11261427; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.22 | SLC22A5 | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.4 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 7254270; 7131143; 26190315; 29198778 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.3 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Added comment: The mode of inheritance for SLC22A5 variants should be BOTH Monoallelic and Biallelic. Although, most of the evidence for symptoms associated SLC22A5 are seen in a patients with biallelic variants (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen), a few instances have been reported in cases carrying heterozygous SLC22A5 variants (PMID: 10545605; 11261427).; Changed publications to: 10545605, 11261427 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.3 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.3 | SLC22A5 | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.22 | SLC22A5 | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance should be change from monoallelic to biallelic at the next major review of the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.22 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.21 | SLC22A5 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.21 | SLC22A5 | Sarah Leigh reviewed gene: SLC22A5: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.3 | SLC22A5 | Sarah Leigh Added comment: Comment on mode of inheritance: The mode of inheritance is being changed from Monoallelic to Biallelic, as there is no published evidence for monoallelic inheritance of conditions associated with variants in SLC22A5 (HGNC:10969, OMIM:603377, Gen2Phen, Orphanet:118781, ClinGen). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short QT syndrome v3.3 | SLC22A5 | Sarah Leigh Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.21 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 24816252; 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.7 | LHX2 | Sarah Leigh edited their review of gene: LHX2: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.7 | LHX2 | Sarah Leigh Classified gene: LHX2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.7 | LHX2 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.7 | LHX2 | Sarah Leigh Gene: lhx2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.6 | LHX2 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: LHX2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.6 | LHX2 |
Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. PMID: 37057675 reports 17 predominantly de novo LHX2 variants in a panel of patients with a variable neurodevelopmental disorder. Haploinsufficiency and functional studies are supportive of a loss-of-function pathogenic action of the reported LHX2 variants. Seven out of the ten cases reported in table 1 (PMID: 37057675) are listed as having microcephaly, however, due to lack of clinical information, these cases cannot be classified as severe (personal communication with the author, Christiane Zweier). Sources: Literature; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. PMID: 37057675 reports 17 predominantly de novo LHX2 variants in a panel of patients with a variable neurodevelopmental disorder. Haploinsufficiency and functional studies are supportive of a loss-of-function pathogenic action of the reported LHX2 variants. Nine out of the thirteen cases reported in table 1 (PMID: 37057675) are listed as having Ophthalmologic abnormalities including macular degeneration, optic neuropathy, and esotropia. Sources: Literature |
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| Optic neuropathy v4.6 | LHX2 | Sarah Leigh Entity copied from Severe microcephaly v4.28 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.6 | LHX2 |
Sarah Leigh gene: LHX2 was added gene: LHX2 was added to Optic neuropathy. Sources: Expert Review Amber,Literature Mode of inheritance for gene: LHX2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: LHX2 were set to 37057675 Phenotypes for gene: LHX2 were set to neurodevelopmental disorder |
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| Hypogonadotropic hypogonadism (GMS) v3.4 | SOX11 | Achchuthan Shanmugasundram Classified gene: SOX11 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypogonadotropic hypogonadism (GMS) v3.4 | SOX11 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (>10 unrelated cases) to promote this gene to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypogonadotropic hypogonadism (GMS) v3.4 | SOX11 | Achchuthan Shanmugasundram Gene: sox11 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypogonadotropic hypogonadism (GMS) v3.3 | SOX11 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SOX11. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypogonadotropic hypogonadism (GMS) v3.3 | SOX11 |
Achchuthan Shanmugasundram gene: SOX11 was added gene: SOX11 was added to Hypogonadotropic hypogonadism (GMS). Sources: Literature Mode of inheritance for gene: SOX11 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SOX11 were set to 35341651 Phenotypes for gene: SOX11 were set to Intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, OMIM:615866 Review for gene: SOX11 was set to GREEN Added comment: PMID:35341651 reported 38 unrelated patients with SOX11 variants and idiopathic hypogonadotropic hypogonadism was confirmed as a feature of the intellectual developmental disorder phenotype in eight of these patients. In addition, 3 of 15 cases that were previously reported and reviewed in this publication also had hypogonadotropic hypogonadism. This gene has been associated with neurodevelopmental disorder phenotypes in both OMIM (MIM #615866) and Gene2Phenotype (with 'definitive' rating in the DD panel) and hypogonadotropic hypogonadism was reported as one of the clinical manifestations in OMIM. Sources: Literature |
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| Ataxia and cerebellar anomalies - narrow panel v4.26 | AGTPBP1 | Achchuthan Shanmugasundram Classified gene: AGTPBP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.26 | AGTPBP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.26 | AGTPBP1 | Achchuthan Shanmugasundram Gene: agtpbp1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.25 | AGTPBP1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: AGTPBP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.25 | AGTPBP1 |
Achchuthan Shanmugasundram gene: AGTPBP1 was added gene: AGTPBP1 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature Mode of inheritance for gene: AGTPBP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AGTPBP1 were set to 30420557 Phenotypes for gene: AGTPBP1 were set to Neurodegeneration, childhood-onset, with cerebellar atrophy, OMIM:618276 Review for gene: AGTPBP1 was set to GREEN Added comment: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Five unrelated patients had ataxia and all patients had cerebellar atrophy. In addition, functional studies with mouse models have recapitulated the human phenotype. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). Sources: Literature |
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| Intellectual disability v5.225 | AGTPBP1 | Achchuthan Shanmugasundram Classified gene: AGTPBP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.225 | AGTPBP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.225 | AGTPBP1 | Achchuthan Shanmugasundram Gene: agtpbp1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.224 | AGTPBP1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: AGTPBP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.224 | AGTPBP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Impaired intellectual development was severe in several patients: Two had severe cognitive delay, one had profound cognitive delay, five had no speech and four had no visual recognition. In addition, functional studies with mouse models have recapitulated the human phenotype. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). Sources: Literature; to: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Impaired intellectual development was severe in several patients: Two had severe cognitive delay, one had profound cognitive delay, five had no speech and four had no visual recognition. In addition, functional studies with mouse models have recapitulated the human phenotype. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). Sources: Literature |
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| Intellectual disability v5.224 | AGTPBP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Impaired intellectual development was severe, and several patients were unable to speak or have eye contact. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). Sources: Literature; to: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Impaired intellectual development was severe in several patients: Two had severe cognitive delay, one had profound cognitive delay, five had no speech and four had no visual recognition. In addition, functional studies with mouse models have recapitulated the human phenotype. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). Sources: Literature |
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| Hereditary neuropathy or pain disorder v3.45 | AGTPBP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Five unrelated patients had (axonal) motor neuropathy. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating).; to: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Five unrelated patients had (axonal) motor neuropathy. In addition, functional studies with mouse models have recapitulated the human phenotype. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). |
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| Intellectual disability v5.224 | AGTPBP1 |
Achchuthan Shanmugasundram gene: AGTPBP1 was added gene: AGTPBP1 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: AGTPBP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AGTPBP1 were set to 30420557 Phenotypes for gene: AGTPBP1 were set to Neurodegeneration, childhood-onset, with cerebellar atrophy, OMIM:618276 Review for gene: AGTPBP1 was set to GREEN Added comment: PMID:30420557 reported the identification of either homozygous or compound heterozygous variants in AGTPBP1 gene in 13 individuals from 10 unrelated families with infantile‐onset neurodegeneration. Impaired intellectual development was severe, and several patients were unable to speak or have eye contact. This gene has been associated with relevant phenotypes in both OMIM (MIM #618276) and Gene2Phenotype (on DD panel with 'definitive' rating). Sources: Literature |
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| Adult onset hereditary spastic paraplegia v3.15 | Eleanor Williams Panel version 3.14 has been signed off on 2023-07-31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.35 | Eleanor Williams Panel version 4.34 has been signed off on 2023-07-31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.13 | Eleanor Williams Panel version 3.12 has been signed off on 2023-07-31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.14 | ATXN10_ATTCT | Eleanor Williams commented on STR: ATXN10_ATTCT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.14 | ATXN10_ATTCT | Eleanor Williams Classified STR: ATXN10_ATTCT as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.14 | ATXN10_ATTCT | Eleanor Williams Str: atxn10_attct has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.13 | ATXN10_ATTCT |
Eleanor Williams Tag watchlist was removed from STR: ATXN10_ATTCT. Tag Q3_23_promote_green was removed from STR: ATXN10_ATTCT. |
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| Adult onset neurodegenerative disorder v4.34 | TBP_CAG | Eleanor Williams commented on STR: TBP_CAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.34 | TBP_CAG | Eleanor Williams Classified STR: TBP_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.34 | TBP_CAG | Eleanor Williams Str: tbp_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.33 | TBP_CAG |
Eleanor Williams Tag watchlist was removed from STR: TBP_CAG. Tag Q3_23_promote_green was removed from STR: TBP_CAG. |
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| Adult onset neurodegenerative disorder v4.33 | JPH3_CTG | Eleanor Williams commented on STR: JPH3_CTG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.33 | JPH3_CTG | Eleanor Williams Classified STR: JPH3_CTG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.33 | JPH3_CTG | Eleanor Williams Str: jph3_ctg has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.32 | JPH3_CTG |
Eleanor Williams Tag watchlist was removed from STR: JPH3_CTG. Tag Q3_23_promote_green was removed from STR: JPH3_CTG. |
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| Adult onset neurodegenerative disorder v4.32 | ATN1_CAG | Eleanor Williams commented on STR: ATN1_CAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.32 | ATN1_CAG | Eleanor Williams Classified STR: ATN1_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.32 | ATN1_CAG | Eleanor Williams Str: atn1_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.31 | ATN1_CAG |
Eleanor Williams Tag watchlist was removed from STR: ATN1_CAG. Tag Q3_23_promote_green was removed from STR: ATN1_CAG. |
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| Adult onset dystonia, chorea or related movement disorder v3.12 | PPP2R2B_CAG | Eleanor Williams commented on STR: PPP2R2B_CAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.12 | PPP2R2B_CAG | Eleanor Williams Classified STR: PPP2R2B_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.12 | PPP2R2B_CAG | Eleanor Williams Str: ppp2r2b_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.11 | PPP2R2B_CAG |
Eleanor Williams Tag watchlist was removed from STR: PPP2R2B_CAG. Tag Q3_23_promote_green was removed from STR: PPP2R2B_CAG. |
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| Adult onset dystonia, chorea or related movement disorder v3.11 | CSTB_CCCCGCCCCGCG | Eleanor Williams commented on STR: CSTB_CCCCGCCCCGCG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.11 | CSTB_CCCCGCCCCGCG | Eleanor Williams Classified STR: CSTB_CCCCGCCCCGCG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.11 | CSTB_CCCCGCCCCGCG | Eleanor Williams Str: cstb_ccccgccccgcg has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.10 | CSTB_CCCCGCCCCGCG |
Eleanor Williams Tag watchlist was removed from STR: CSTB_CCCCGCCCCGCG. Tag Q3_23_promote_green was removed from STR: CSTB_CCCCGCCCCGCG. |
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| Adult onset dystonia, chorea or related movement disorder v3.10 | CACNA1A_CAG | Eleanor Williams commented on STR: CACNA1A_CAG: The rating of this STR has been updated to green after review of STRs on panels that have moved to WGS in phase 2 and NHS Genomic Medicine Service approval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.10 | CACNA1A_CAG | Eleanor Williams Classified STR: CACNA1A_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.10 | CACNA1A_CAG | Eleanor Williams Str: cacna1a_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.9 | CACNA1A_CAG |
Eleanor Williams Tag watchlist was removed from STR: CACNA1A_CAG. Tag Q3_23_promote_green was removed from STR: CACNA1A_CAG. |
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| Adult onset dystonia, chorea or related movement disorder v3.9 | ATXN3_CAG | Eleanor Williams commented on STR: ATXN3_CAG: The rating of this STR has been updated to green after review of STRs on panels that have moved to WGS in phase 2 and NHS Genomic Medicine Service approval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.9 | ATXN3_CAG | Eleanor Williams Classified STR: ATXN3_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.9 | ATXN3_CAG | Eleanor Williams Str: atxn3_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.8 | ATXN3_CAG |
Eleanor Williams Tag watchlist was removed from STR: ATXN3_CAG. Tag Q3_23_promote_green was removed from STR: ATXN3_CAG. |
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| Segmental overgrowth disorders - Deep sequencing v3.7 | GJA4 |
Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. A recurrent GJA4 c.121G>T (p.Gly41Cys) somatic variant has been found in >50 individuals with cavernous venous malformation. The same somatic variant has been found in at least three unrelated cases with cutaneous lesions which plausibly could be referred via this panel. Functional studies have shown this is a GoF variant that leads to formation of a hyperactive hemichannel.; to: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. A recurrent GJA4 c.121G>T (p.Gly41Cys) somatic variant has been found in >50 individuals with cavernous venous malformation. Functional studies have shown this is a GoF variant that leads to formation of a hyperactive hemichannel. |
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| Adult onset dystonia, chorea or related movement disorder v3.8 | ATXN2_CAG | Eleanor Williams commented on STR: ATXN2_CAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.8 | ATXN2_CAG | Eleanor Williams Classified STR: ATXN2_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.8 | ATXN2_CAG | Eleanor Williams Str: atxn2_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.7 | GJA4 | Arina Puzriakova Tag Q3_23_NHS_review was removed from gene: GJA4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.7 | ATXN2_CAG |
Eleanor Williams Tag watchlist was removed from STR: ATXN2_CAG. Tag Q3_23_promote_green was removed from STR: ATXN2_CAG. |
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| Segmental overgrowth disorders - Deep sequencing v3.7 | GJA4 | Arina Puzriakova Entity copied from Mosaic skin disorders - deep sequencing v2.14 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.7 | GJA4 |
Arina Puzriakova gene: GJA4 was added gene: GJA4 was added to Segmental overgrowth disorders - Deep sequencing. Sources: Expert Review Amber,Expert list Q3_23_promote_green, Q3_23_NHS_review, recurrent-variant tags were added to gene: GJA4. Mode of inheritance for gene: GJA4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: GJA4 were set to 33912852; 35642047; 35902510; 36209871; 37072338 Phenotypes for gene: GJA4 were set to Cutaneous and hepatic vascular lesions (no OMIM phenotype) Penetrance for gene: GJA4 were set to unknown Mode of pathogenicity for gene: GJA4 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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| Mosaic skin disorders - deep sequencing v2.14 | GJA4 | Arina Puzriakova Publications for gene: GJA4 were set to 33912852 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.7 | ATXN1_CAG | Eleanor Williams commented on STR: ATXN1_CAG | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.7 | ATXN1_CAG | Eleanor Williams Classified STR: ATXN1_CAG as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.7 | ATXN1_CAG | Eleanor Williams Str: atxn1_cag has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.6 | ATXN1_CAG |
Eleanor Williams Tag watchlist was removed from STR: ATXN1_CAG. Tag Q3_23_promote_green was removed from STR: ATXN1_CAG. |
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| Mosaic skin disorders - deep sequencing v2.13 | GJA4 | Arina Puzriakova Classified gene: GJA4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.13 | GJA4 |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Tom Cullup (GOSH). There is sufficient evidence to promote this gene to green at the next GMS panel update. A recurrent GJA4 c.121G>T (p.Gly41Cys) somatic variant has been found in >50 individuals with cavernous venous malformation. The same somatic variant has been found in at least three unrelated cases with cutaneous lesions which plausibly could be referred via this panel. Functional studies have shown this is a GoF variant that leads to formation of a hyperactive hemichannel. |
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| Mosaic skin disorders - deep sequencing v2.13 | GJA4 | Arina Puzriakova Gene: gja4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.12 | GJA4 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: GJA4. Tag Q3_23_NHS_review tag was added to gene: GJA4. Tag recurrent-variant tag was added to gene: GJA4. |
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| Hereditary neuropathy or pain disorder v3.45 | AGTPBP1 | Achchuthan Shanmugasundram Classified gene: AGTPBP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.45 | AGTPBP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to green rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.45 | AGTPBP1 | Achchuthan Shanmugasundram Gene: agtpbp1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.44 | AGTPBP1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: AGTPBP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.44 | AGTPBP1 | Achchuthan Shanmugasundram reviewed gene: AGTPBP1: Rating: GREEN; Mode of pathogenicity: None; Publications: 30420557; Phenotypes: Neurodegeneration, childhood-onset, with cerebellar atrophy, OMIM:618276; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.223 | ZNF292 | Achchuthan Shanmugasundram reviewed gene: ZNF292: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Intellectual developmental disorder, autosomal dominant 64, OMIM:619188; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.75 | PIP5K1C | Achchuthan Shanmugasundram Classified gene: PIP5K1C as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.75 | PIP5K1C | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (seven unrelated cases and supporting functional evidence) for promoting this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.75 | PIP5K1C | Achchuthan Shanmugasundram Gene: pip5k1c has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.74 | PIP5K1C | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PIP5K1C. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.74 | PIP5K1C | Achchuthan Shanmugasundram Phenotypes for gene: PIP5K1C were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.73 | PIP5K1C | Achchuthan Shanmugasundram edited their review of gene: PIP5K1C: Changed phenotypes to: neurodevelopmental disorder, MONDO:0700092, epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.223 | PIP5K1C | Achchuthan Shanmugasundram Classified gene: PIP5K1C as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.223 | PIP5K1C | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (nine unrelated cases and supporting functional evidence) for promoting this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.223 | PIP5K1C | Achchuthan Shanmugasundram Gene: pip5k1c has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.222 | PIP5K1C | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PIP5K1C. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.73 | PIP5K1C |
Achchuthan Shanmugasundram gene: PIP5K1C was added gene: PIP5K1C was added to Early onset or syndromic epilepsy. Sources: Literature Mode of inheritance for gene: PIP5K1C was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PIP5K1C were set to 37451268 Phenotypes for gene: PIP5K1C were set to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 Review for gene: PIP5K1C was set to GREEN Added comment: Three de novo heterozygous missense variants in PIP5K1C (p.Glu146Lys, p.Tyr205Cys & p.Tyr221Cys) were identified in nine unrelated children exhibiting intellectual disability, developmental delay, acquired microcephaly, seizures, visual abnormalities, and dysmorphic features. Intellectual disability was reported in all nine children and seizures were present in seven children, of which three had developmental and epileptic encephalopathy. In addition, there is functional evidence available, which includes an in vivo zebrafish model that recapitulates the human phenotype (developmental defects affecting the forebrain, including the eyes, as well as craniofacial abnormalities) (PMID:37451268). This gene has been associated with another phenotype (Lethal congenital contractural syndrome 3, MIM #611369) in both OMIM and Gene2Phenotype, but not yet associated with this neurodevelopmental disorders in either databases. Sources: Literature |
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| Intellectual disability v5.222 | PIP5K1C |
Achchuthan Shanmugasundram gene: PIP5K1C was added gene: PIP5K1C was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: PIP5K1C was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PIP5K1C were set to 37451268 Phenotypes for gene: PIP5K1C were set to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 Review for gene: PIP5K1C was set to GREEN Added comment: Three de novo heterozygous missense variants in PIP5K1C (p.Glu146Lys, p.Tyr205Cys & p.Tyr221Cys) were identified in nine unrelated children exhibiting intellectual disability, developmental delay, acquired microcephaly, seizures, visual abnormalities, and dysmorphic features. Intellectual disability was reported in all nine children and seizures were present in seven children, of which three had developmental and epileptic encephalopathy. In addition, there is functional evidence available, which includes an in vivo zebrafish model that recapitulates the human phenotype (developmental defects affecting the forebrain, including the eyes, as well as craniofacial abnormalities) (PMID:37451268). This gene has been associated with another phenotype (Lethal congenital contractural syndrome 3, MIM #611369) in both OMIM and Gene2Phenotype, but not yet associated with this neurodevelopmental disorders in either databases. Sources: Literature |
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| Mosaic skin disorders - deep sequencing v2.12 | FGFR2 | Arina Puzriakova Tag somatic tag was added to gene: FGFR2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.12 | FGFR2 | Arina Puzriakova Publications for gene: FGFR2 were set to 9728990 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.11 | FGFR2 | Arina Puzriakova Mode of pathogenicity for gene: FGFR2 was changed from to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.10 | FGFR2 | Arina Puzriakova Classified gene: FGFR2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.10 | FGFR2 | Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to green at the next GMS panel update. FGFR2 is associated with multiple phenotypes but mosaic somatic variants have been found in more than 10 unrelated individuals in literature with nevoid skin disorders. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.10 | FGFR2 | Arina Puzriakova Gene: fgfr2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | LETM1 |
Carl Fratter gene: LETM1 was added gene: LETM1 was added to Possible mitochondrial disorder - nuclear genes. Sources: Expert Review Mode of inheritance for gene: LETM1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: LETM1 were set to 620089 Neurodegeneration, childhood-onset, with multisystem involvement due to mitochondrial dysfunction Review for gene: LETM1 was set to GREEN Added comment: Consensus opinion from the 3 NHSE GMS specialist mitochondrial providers. Sources: Expert Review |
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| Mosaic skin disorders - deep sequencing v2.9 | FGFR2 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: FGFR2. Tag Q3_23_NHS_review tag was added to gene: FGFR2. |
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| Paediatric or syndromic cardiomyopathy v3.20 | NAA10 | Achchuthan Shanmugasundram Classified gene: NAA10 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.20 | NAA10 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases with paediatric-onset hypertrophic cardiomyopathy. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.20 | NAA10 | Achchuthan Shanmugasundram Gene: naa10 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.19 | NAA10 |
Achchuthan Shanmugasundram gene: NAA10 was added gene: NAA10 was added to Paediatric or syndromic cardiomyopathy. Sources: Literature Mode of inheritance for gene: NAA10 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: NAA10 were set to 29748569 Phenotypes for gene: NAA10 were set to Ogden syndrome, OMIM:300855 Review for gene: NAA10 was set to AMBER Added comment: PMID:29748569 reported the identification of previously undescribed NAA10 variant (c.215T>C; p.Ile72Thr) in three boys from two unrelated families with a milder phenotypic spectrum in comparison to most of the previously described patients with NAA10 variants. These boys had developmental delay, intellectual disability, and hypertrophic cardiomyopathy. This gene has been associated with Ogden syndrome in both OMIM ands Gene2Phenotype and the OMIM record includes hypertrophic cardiomyopathy and other cardiac abnormalities as clinical manifestations of this disorder. Sources: Literature |
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| Possible mitochondrial disorder - nuclear genes v3.33 | IDH3A | Carl Fratter edited their review of gene: IDH3A: Added comment: Consensus opinion from the 3 specialist mitochondrial providers.; Changed publications to: 28412069, 28058510, 30478029; Changed phenotypes to: Infantile encephalopathy, 619007 Retinitis pigmentosa 90 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | CRLS1 | Carl Fratter reviewed gene: CRLS1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: 620167 Combined oxidative phosphorylation deficiency 57; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | C2orf69 | Carl Fratter reviewed gene: C2orf69: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: 619423 Combined oxidative phosphorylation deficiency 53; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | ATP5O | Carl Fratter edited their review of gene: ATP5O: Added comment: Consensus opinion from the 3 specialist mitochondrial providers.; Changed rating: GREEN; Changed phenotypes to: 620359 Mitochondrial complex V (ATP synthase) deficiency, nuclear type 7; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.18 | NAA15 | Achchuthan Shanmugasundram Publications for gene: NAA15 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.17 | NAA15 | Achchuthan Shanmugasundram Phenotypes for gene: NAA15 were changed from to hypertrophic cardiomyopathy, MONDO:0005045 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.16 | NAA15 | Achchuthan Shanmugasundram Mode of inheritance for gene: NAA15 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.15 | NAA15 |
Achchuthan Shanmugasundram changed review comment from: PMID:33103328 reported two unrelated individuals with paediatric hypertrophic cardiomyopathy and they were identified with de novo variants in NAA15 gene (patient 1: c.1009_1012delGAAA/ p.Glu337fs, patient 2: c.79A>G/ p.Arg27Gly). These patients presented with cardiomyopathy at 2 months and 6 years of age respectively. Although none of the patients reported with hypertrophic cardiomyopathy in PMID:29656860, 4 of 19 patients were reported with congenital cardiac defects. Although this gene has not yet been associated with cardiac abnormalities in OMIM, this gene has been associated with "Congenital heart disease and neurodevelopmental disorder" in the DD panel of Gene2Phenotype database (with 'strong' rating).; to: Comment on gene rating: The rating of this gene should remain amber in this panel, as there are only two unrelated c cases reported with paediatric hypertrophic cardiomyopathy. PMID:33103328 reported two unrelated individuals with paediatric hypertrophic cardiomyopathy and they were identified with de novo variants in NAA15 gene (patient 1: c.1009_1012delGAAA/ p.Glu337fs, patient 2: c.79A>G/ p.Arg27Gly). These patients presented with cardiomyopathy at 2 months and 6 years of age respectively. Although none of the patients reported with hypertrophic cardiomyopathy in PMID:29656860, 4 of 19 patients were reported with congenital cardiac defects. Although this gene has not yet been associated with cardiac abnormalities in OMIM, this gene has been associated with "Congenital heart disease and neurodevelopmental disorder" in the DD panel of Gene2Phenotype database (with 'strong' rating). |
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| Paediatric or syndromic cardiomyopathy v3.15 | NAA15 | Achchuthan Shanmugasundram reviewed gene: NAA15: Rating: AMBER; Mode of pathogenicity: None; Publications: 33103328; Phenotypes: hypertrophic cardiomyopathy, MONDO:0005045; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.20 | MPDZ |
Siying Lin changed review comment from: PMID 28556411: 3 families with affected individuals with biallelic MPDZ variants and congenital hydrocephalus with retinohoroidal coloboma, macular hypoplasia and foveal hypoplasia PMID 36594712: 2 siblings with biallelic MPDZ variants and macular colobomas PMID 36429029: proband with biallelic MPDZ variants and macular coloboma Sources: Literature; to: PMID 28556411: 3 families with affected individuals with biallelic MPDZ variants and congenital hydrocephalus with retinohoroidal coloboma, macular hypoplasia and foveal hypoplasia PMID 36594712: 2 siblings with biallelic MPDZ variants and macular colobomas PMID 36429029: proband with biallelic MPDZ variants and macular coloboma Sources: Literature |
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| Retinal disorders v4.20 | MPDZ |
Siying Lin gene: MPDZ was added gene: MPDZ was added to Retinal disorders. Sources: Literature Mode of inheritance for gene: MPDZ was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MPDZ were set to PMID 28556411, 36594712, 36429029 Mode of pathogenicity for gene: MPDZ was set to Other Added comment: PMID 28556411: 3 families with affected individuals with biallelic MPDZ variants and congenital hydrocephalus with retinohoroidal coloboma, macular hypoplasia and foveal hypoplasia PMID 36594712: 2 siblings with biallelic MPDZ variants and macular colobomas PMID 36429029: proband with biallelic MPDZ variants and macular coloboma Sources: Literature |
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| Early onset or syndromic epilepsy v4.72 | TMEM63B | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There is sufficient evidence available (17 unrelated cases) in support of promoting this gene to green rating in the next GMS review; to: Comment on list classification: There is sufficient evidence available (17 unrelated cases) in support of promoting this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.72 | TMEM63B | Achchuthan Shanmugasundram Classified gene: TMEM63B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.72 | TMEM63B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (17 unrelated cases) in support of promoting this gene to green rating in the next GMS review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.72 | TMEM63B | Achchuthan Shanmugasundram Gene: tmem63b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.71 | TMEM63B | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: TMEM63B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.71 | TMEM63B |
Achchuthan Shanmugasundram changed review comment from: PMID:37421948 - 17 unrelated individuals with severe early-onset developmental and epileptic encephalopathy (DEE), intellectual disability, and severe motor and cortical visual impairment were identified with ten distinct heterozygous variants inTMEM63B. The variants occurred de novo in 16/17 individuals for whom parental DNA was available and either missense or in-frame. All individuals had global developmental delay, with moderate-to-profound intellectual disability and severe motor impairment. Sources: Literature; to: PMID:37421948 - 17 unrelated individuals with severe early-onset developmental and epileptic encephalopathy (DEE), intellectual disability, and severe motor and cortical visual impairment were identified with ten distinct heterozygous variants inTMEM63B. The variants occurred de novo in 16/17 individuals for whom parental DNA was available and either missense or in-frame. All individuals had early-onset drug-resistant epilepsy, whose onset ranged from birth to 3 years but occurred within the first year in 14/17 (82%) and in the first month of life in 6/17 (35%). Sources: Literature |
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| Intellectual disability v5.221 | TMEM63B | Achchuthan Shanmugasundram Classified gene: TMEM63B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.221 | TMEM63B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (17 unrelated cases) in support of promoting this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.221 | TMEM63B | Achchuthan Shanmugasundram Gene: tmem63b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.220 | TMEM63B | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: TMEM63B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.71 | TMEM63B |
Achchuthan Shanmugasundram gene: TMEM63B was added gene: TMEM63B was added to Early onset or syndromic epilepsy. Sources: Literature Mode of inheritance for gene: TMEM63B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TMEM63B were set to 37421948 Phenotypes for gene: TMEM63B were set to developmental and epileptic encephalopathy, MONDO:0100062 Review for gene: TMEM63B was set to GREEN Added comment: PMID:37421948 - 17 unrelated individuals with severe early-onset developmental and epileptic encephalopathy (DEE), intellectual disability, and severe motor and cortical visual impairment were identified with ten distinct heterozygous variants inTMEM63B. The variants occurred de novo in 16/17 individuals for whom parental DNA was available and either missense or in-frame. All individuals had global developmental delay, with moderate-to-profound intellectual disability and severe motor impairment. Sources: Literature |
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| Intellectual disability v5.220 | TMEM63B |
Achchuthan Shanmugasundram gene: TMEM63B was added gene: TMEM63B was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: TMEM63B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TMEM63B were set to 37421948 Phenotypes for gene: TMEM63B were set to developmental and epileptic encephalopathy, MONDO:0100062 Review for gene: TMEM63B was set to GREEN Added comment: PMID:37421948 - 17 unrelated individuals with severe early-onset developmental and epileptic encephalopathy (DEE), intellectual disability, and severe motor and cortical visual impairment were identified with ten distinct heterozygous variants inTMEM63B. The variants occurred de novo in 16/17 individuals for whom parental DNA was available and either missense or in-frame. All individuals had global developmental delay, with moderate-to-profound intellectual disability and severe motor impairment. Sources: Literature |
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| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Classified gene: DHX9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (eight unrelated cases) in support of promoting this gene to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Gene: dhx9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Classified gene: DHX9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (eight unrelated cases) in support of promoting this gene to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.219 | DHX9 | Achchuthan Shanmugasundram Gene: dhx9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.218 | DHX9 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DHX9. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.218 | DHX9 |
Achchuthan Shanmugasundram gene: DHX9 was added gene: DHX9 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: DHX9 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DHX9 were set to 37467750 Phenotypes for gene: DHX9 were set to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 Review for gene: DHX9 was set to GREEN Added comment: PMID:37467750 - 17 unrelated individuals were identified with de novo, ultra-rare, heterozygous missense or loss-of-function DHX9 variants, of which 14 individuals were reported with a neurodevelopmental disorder (NDD) and three were reported with Charcot-Marie-Tooth disease (CMT). All 14 cases with NDD had developmental delay, of which eight were reported with intellectual disability (4 severe, 1 moderate, 3 mild). Two cases did not have ID, one had borderline ID and three cases were too young (0-5 years old). Sources: Literature |
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| Hereditary neuropathy or pain disorder v3.44 | DHX9 | Achchuthan Shanmugasundram Classified gene: DHX9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.44 | DHX9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available (three unrelated cases) for promoting this gene to green rating in the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.44 | DHX9 | Achchuthan Shanmugasundram Gene: dhx9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.43 | DHX9 |
Achchuthan Shanmugasundram Tag watchlist was removed from gene: DHX9. Tag Q3_23_promote_green tag was added to gene: DHX9. |
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| Hereditary neuropathy or pain disorder v3.43 | DHX9 | Achchuthan Shanmugasundram Phenotypes for gene: DHX9 were changed from Adult-onset axonal neuropathy to Adult-onset axonal neuropathy; Charcot-Marie-Tooth disease, MONDO:0015626 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.42 | DHX9 | Achchuthan Shanmugasundram Publications for gene: DHX9 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.41 | DHX9 | Achchuthan Shanmugasundram Mode of inheritance for gene: DHX9 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.40 | DHX9 | Achchuthan Shanmugasundram reviewed gene: DHX9: Rating: GREEN; Mode of pathogenicity: None; Publications: 37467750; Phenotypes: Charcot-Marie-Tooth disease, MONDO:0015626; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.24 | DNAJC3 | Achchuthan Shanmugasundram Classified gene: DNAJC3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.24 | DNAJC3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated families identified with biallelic DNAJC3 variants and reported with gait ataxia since childhood/ adolescence. Hence, this gene can be promoted to Green rating in the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.24 | DNAJC3 | Achchuthan Shanmugasundram Gene: dnajc3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.23 | DNAJC3 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DNAJC3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.23 | DNAJC3 |
Achchuthan Shanmugasundram gene: DNAJC3 was added gene: DNAJC3 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature Mode of inheritance for gene: DNAJC3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DNAJC3 were set to 25466870; 28940199; 32738013; 33486469; 34654017 Phenotypes for gene: DNAJC3 were set to Ataxia, combined cerebellar and peripheral, with hearing loss and diabetes mellitus, OMIM:616192 Review for gene: DNAJC3 was set to GREEN Added comment: PMID:25466870 - Five individuals from two different families were identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)) and reported with gait ataxia as one of the clinical manifestations. The onset of gait disturbances was during childhood/ adolescence for four of these cases. PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with gait ataxia since 15 years of age. PMID:32738013 - Two unrelated children were identified with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with gait ataxia. PMID:33486469 - Two unrelated patients were identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (patient 2: p.Arg393Ter) variants, of which patient 1 had ataxia. PMID:34654017 - Two siblings (aged 10 and 5 years) identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with gait ataxia. Sources: Literature |
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| Hereditary neuropathy v1.472 | DNAJC3 |
Achchuthan Shanmugasundram changed review comment from: PMID:25466870 - Five individuals from two different families with demyelinating sensorimotor peripheral neuropathy and identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)). PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with demyelinating sensorimotor peripheral neuropathy. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorimotor demyelinating and axonal polyneuropathy among several clinical manifestations. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, of which patient 1 had demyelinating peripheral sensorimotor neuropathy. PMID:34654017 - One of two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with demyelinating neuropathy among several other clinical manifestations.; to: PMID:25466870 - Five individuals from two different families with demyelinating sensorimotor peripheral neuropathy and identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)). PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with demyelinating sensorimotor peripheral neuropathy. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorimotor demyelinating and axonal polyneuropathy. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, of which patient 1 had demyelinating peripheral sensorimotor neuropathy. PMID:34654017 - One of two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with demyelinating neuropathy. |
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| Monogenic hearing loss v4.12 | DNAJC3 | Achchuthan Shanmugasundram Classified gene: DNAJC3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.12 | DNAJC3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are seven unrelated families with DNAJC3 biallelic variants and presenting with sensorineural hearing loss. Hence, this gene can be promoted to Green at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.12 | DNAJC3 | Achchuthan Shanmugasundram Gene: dnajc3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.11 | DNAJC3 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DNAJC3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.11 | DNAJC3 |
Achchuthan Shanmugasundram changed review comment from: PMID:25466870 - Five individuals from two different families were identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)), of which all three individuals from family 1 and one of two individuals from family 2 were reported with sensorineural hearing loss among several clinical manifestations. PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with sensorineural hearing loss. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorineural hearing loss. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, and both had sensorineural hearing loss. PMID:34654017 - Ttwo siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with sensorineural hearing loss. Sources: Literature; to: PMID:25466870 - Five individuals from two different families were identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)), of which all three individuals from family 1 and one of two individuals from family 2 were reported with sensorineural hearing loss among several clinical manifestations. PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with sensorineural hearing loss. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorineural hearing loss. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, and both had sensorineural hearing loss. PMID:34654017 - Two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with sensorineural hearing loss. Sources: Literature |
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| Monogenic hearing loss v4.11 | DNAJC3 |
Achchuthan Shanmugasundram gene: DNAJC3 was added gene: DNAJC3 was added to Monogenic hearing loss. Sources: Literature Mode of inheritance for gene: DNAJC3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DNAJC3 were set to 25466870; 28940199; 32738013; 33486469; 34654017 Phenotypes for gene: DNAJC3 were set to Ataxia, combined cerebellar and peripheral, with hearing loss and diabetes mellitus, OMIM:616192 Review for gene: DNAJC3 was set to GREEN Added comment: PMID:25466870 - Five individuals from two different families were identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)), of which all three individuals from family 1 and one of two individuals from family 2 were reported with sensorineural hearing loss among several clinical manifestations. PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with sensorineural hearing loss. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorineural hearing loss. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, and both had sensorineural hearing loss. PMID:34654017 - Ttwo siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with sensorineural hearing loss. Sources: Literature |
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| Hereditary neuropathy or pain disorder v3.40 | DNAJC3 |
Achchuthan Shanmugasundram changed review comment from: PMID:25466870 - Five individuals from two different families with demyelinating sensorimotor peripheral neuropathy and identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)). PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with demyelinating sensorimotor peripheral neuropathy. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorimotor demyelinating and axonal polyneuropathy. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, of which patient 1 had demyelinating peripheral sensorimotor neuropathy. PMID:34654017 - One of two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with demyelinating neuropathy among several other clinical manifestations.; to: PMID:25466870 - Five individuals from two different families with demyelinating sensorimotor peripheral neuropathy and identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)). PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with demyelinating sensorimotor peripheral neuropathy. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorimotor demyelinating and axonal polyneuropathy. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, of which patient 1 had demyelinating peripheral sensorimotor neuropathy. PMID:34654017 - One of two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with demyelinating neuropathy. |
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| Hereditary neuropathy or pain disorder v3.40 | DNAJC3 |
Achchuthan Shanmugasundram changed review comment from: PMID:25466870 - Five individuals from two different families with demyelinating sensorimotor peripheral neuropathy and identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)). PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with demyelinating sensorimotor peripheral neuropathy. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorimotor demyelinating and axonal polyneuropathy among several clinical manifestations. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, of which patient 1 had demyelinating peripheral sensorimotor neuropathy. PMID:34654017 - One of two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with demyelinating neuropathy among several other clinical manifestations.; to: PMID:25466870 - Five individuals from two different families with demyelinating sensorimotor peripheral neuropathy and identified with homozygous DNAJC3 variants (family 1: c.580C>T (p.Arg194Ter); family 2: 72kb del (exons 6-12)). PMID:28940199 - Cousin of family 1 from PMID:2546687 with the same variant and presented with demyelinating sensorimotor peripheral neuropathy. PMID:32738013 - Two unrelated cases with homozygous splice site variants (case 1: c.393+2T>G; case 2: c.393+2T>C) in DNAJC3 and were reported with sensorimotor demyelinating and axonal polyneuropathy. PMID:33486469 - Two unrelated patients identified with compound heterozygous (patient 1: p.Met1Val & p.Arg346Ter) or homozygous (p.Arg393Ter) variants, of which patient 1 had demyelinating peripheral sensorimotor neuropathy. PMID:34654017 - One of two siblings identified with homozygous DNAJC3 variant (c.367_1370delAGAA; p.Lys456SerfsTer85) presented with demyelinating neuropathy among several other clinical manifestations. |
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| Hereditary neuropathy v1.472 | DNAJC3 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There is sufficient evidence (six unrelated families) available for promoting this gene to green rating.; to: Comment on list classification: There is sufficient evidence (six unrelated families) available for promoting this gene to green rating in this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.472 | DNAJC3 | Achchuthan Shanmugasundram Classified gene: DNAJC3 as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.472 | DNAJC3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (six unrelated families) available for promoting this gene to green rating. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.472 | DNAJC3 | Achchuthan Shanmugasundram Gene: dnajc3 has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.471 | DNAJC3 | Achchuthan Shanmugasundram Publications for gene: DNAJC3 were set to 25466870 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.470 | DNAJC3 | Achchuthan Shanmugasundram reviewed gene: DNAJC3: Rating: GREEN; Mode of pathogenicity: None; Publications: 25466870, 28940199, 32738013, 33486469, 34654017; Phenotypes: Ataxia, combined cerebellar and peripheral, with hearing loss and diabetes mellitus, OMIM:616192; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.40 | DNAJC3 | Achchuthan Shanmugasundram edited their review of gene: DNAJC3: Changed publications to: 25466870, 28940199, 32738013, 33486469, 34654017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.40 | DNAJC3 | Achchuthan Shanmugasundram Publications for gene: DNAJC3 were set to 25466870; 28940199; 32738013; 3348646934654017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.39 | DNAJC3 | Achchuthan Shanmugasundram Classified gene: DNAJC3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.39 | DNAJC3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are six unrelated families with DNAJC3 biallelic variants and presenting with demyelinating sensorimotor peripheral neuropathy. Hence, this gene can be promoted to Green at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.39 | DNAJC3 | Achchuthan Shanmugasundram Gene: dnajc3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.38 | DNAJC3 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DNAJC3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.38 | DNAJC3 | Achchuthan Shanmugasundram Publications for gene: DNAJC3 were set to 25466870 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.37 | DNAJC3 | Achchuthan Shanmugasundram reviewed gene: DNAJC3: Rating: GREEN; Mode of pathogenicity: None; Publications: 25466870, 28940199, 32738013, 3348646934654017; Phenotypes: Ataxia, combined cerebellar and peripheral, with hearing loss and diabetes mellitus, OMIM:616192; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.5 | HIKESHI | Hannah Knight reviewed gene: HIKESHI: Rating: GREEN; Mode of pathogenicity: None; Publications: 34111619; Phenotypes: Leukodystrophy, hypomyelinating; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.20 | DYNC2H1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DYNC2H1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.20 | DYNC2H1 | Achchuthan Shanmugasundram Classified gene: DYNC2H1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.20 | DYNC2H1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated cases) in support of the association of this gene with inherited retinal disease. Hence, this gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.20 | DYNC2H1 | Achchuthan Shanmugasundram Gene: dync2h1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.19 | DYNC2H1 | Achchuthan Shanmugasundram Phenotypes for gene: DYNC2H1 were changed from to retinitis pigmentosa, MONDO:0019200 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.18 | DYNC2H1 | Achchuthan Shanmugasundram Publications for gene: DYNC2H1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.17 | DYNC2H1 | Achchuthan Shanmugasundram reviewed gene: DYNC2H1: Rating: GREEN; Mode of pathogenicity: None; Publications: 32753734; Phenotypes: retinitis pigmentosa, MONDO:0019200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.6 | UCHL1 | Sarah Leigh Mode of inheritance for gene: UCHL1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.22 | UCHL1 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: UCHL1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.22 | UCHL1 | Sarah Leigh commented on gene: UCHL1: Childhood onset cerebellar ataxia and has been reported in both Spastic paraplegia 79A, autosomal dominant, OMIM:620221 and Spastic paraplegia 79B, autosomal recessive, OMIM:615491, therefore, the mode of inheritance for this gene should be: BOTH monoallelic and biallelic, autosomal or pseudoautosomal. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.22 | UCHL1 | Sarah Leigh edited their review of gene: UCHL1: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.5 | UCHL1 | Sarah Leigh changed review comment from: In addition to previous reports of Spastic paraplegia 79, autosomal recessive (OMIM:615491), PMID: 35986737 reports a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy in cases with heterozygous UCHL1 variants. The variants included 13 heterozygous loss-of-function variants (15 families) and a heterozygous in-frame insertion (3 families). The affected individuals mainly presented with spasticity (24/31), ataxia (28/31), neuropathy (11/21), and optic atrophy (9/17), it was also noted in PMID: 35986737 that the condition onset in dominant cases was median 49 years (12-70 years) and in recessive was 7.5 years (2-10 years).; to: In addition to previous reports of Spastic paraplegia 79, autosomal recessive (OMIM:615491), PMID: 35986737 reports a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy in cases with heterozygous UCHL1 variants. The variants included 13 heterozygous loss-of-function variants (15 families) and a heterozygous in-frame insertion (3 families). The affected individuals mainly presented with spasticity (24/31), ataxia (28/31), neuropathy (11/21), and optic atrophy (9/17), it was also noted in PMID: 35986737 that the condition onset in dominant cases was median 49 years (12-70 years) and in recessive was 7.5 years (2-10 years). However, dystonia was only reported in one case in this study (Table 5S). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.17 | UCHL1 |
Sarah Leigh Tag Q3_23_promote_green tag was added to gene: UCHL1. Tag Q3_23_MOI tag was added to gene: UCHL1. |
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| Adult onset hereditary spastic paraplegia v3.13 | UCHL1 | Sarah Leigh Classified gene: UCHL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.13 | UCHL1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.13 | UCHL1 | Sarah Leigh Gene: uchl1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.17 | UCHL1 | Sarah Leigh Classified gene: UCHL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.17 | UCHL1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.17 | UCHL1 | Sarah Leigh Gene: uchl1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.16 | UCHL1 | Sarah Leigh edited their review of gene: UCHL1: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.16 | UCHL1 | Sarah Leigh changed review comment from: In addition to previous reports of Spastic paraplegia 79, autosomal recessive (OMIM:615491), PMID: 35986737 reports a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy in cases with heterozygous UCHL1 variants. The variants included 13 heterozygous loss-of-function variants (15 families) and a heterozygous in-frame insertion (3 families). The affected individuals mainly presented with spasticity (24/31), ataxia (28/31), neuropathy (11/21), and optic atrophy (9/17), it was also noted in PMID: 35986737 that the condition onset in dominant cases was median 49 years (12-70 years) and in recessive was 7.5 years (2-10 years).; to: In addition to previous reports of Spastic paraplegia 79, autosomal recessive (OMIM:615491), PMID: 35986737 reports a neurodegenerative disorder with spasticity, ataxia, neuropathy, and optic atrophy in cases with heterozygous UCHL1 variants. The variants included 13 heterozygous loss-of-function variants (15 families) and a heterozygous in-frame insertion (3 families). The affected individuals mainly presented with spasticity (24/31), ataxia (28/31), neuropathy (11/21), and optic atrophy (9/17), it was also noted in PMID: 35986737 that the condition onset in dominant cases was median 49 years (12-70 years) and in recessive was 7.5 years (2-10 years). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.12 | UCHL1 |
Sarah Leigh Tag Q3_23_promote_green tag was added to gene: UCHL1. Tag Q3_23_MOI tag was added to gene: UCHL1. |
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| Adult onset hereditary spastic paraplegia v3.12 | UCHL1 | Sarah Leigh edited their review of gene: UCHL1: Added comment: Spasticity was reported in at least six families carrying heterozygous UCHL1 variants (PMID: 35986737, figure 2 & table S5). Overall, the disease onset for Spastic paraplegia 79A, autosomal dominant, OMIM:620221 had a median of 49 years (12-70years).; Changed rating: GREEN; Changed publications to: 35986737 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.15 | UCHL1 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: UCHL1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.15 | UCHL1 | Sarah Leigh reviewed gene: UCHL1: Rating: GREEN; Mode of pathogenicity: None; Publications: 23359680, 28007905, 35986737; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.5 | UCHL1 | Sarah Leigh Tag Q3_23_MOI tag was added to gene: UCHL1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.5 | UCHL1 | Sarah Leigh reviewed gene: UCHL1: Rating: GREEN; Mode of pathogenicity: None; Publications: 23359680, 28007905, 35986737; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.331 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491 to Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.22 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209 to Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.5 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; ?{Parkinson disease 5, susceptibility to}, OMIM:613643; Parkinson disease 5, autosomal dominant, susceptibility to' MONDO:0013340 to {?Parkinson disease 5, susceptibility to}, OMIM:613643; Parkinson disease 5, autosomal dominant, susceptibility to, MONDO:0013340; Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.16 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209 to Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.31 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from {?Parkinson disease 5, susceptibility to}, OMIM:613643; Parkinson disease 5, autosomal dominant, susceptibility to, MONDO:0013340; Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 to {?Parkinson disease 5, susceptibility to}, OMIM:613643; Parkinson disease 5, autosomal dominant, susceptibility to, MONDO:0013340; Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.12 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 to Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.15 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 to Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.5 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 to Spastic paraplegia 79B, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.30 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from ?{Parkinson disease 5, susceptibility to}; Early onset ataxia and optic neuropathy to {?Parkinson disease 5, susceptibility to}, OMIM:613643; Parkinson disease 5, autosomal dominant, susceptibility to, MONDO:0013340; Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.11 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209 to Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.14 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, OMIM:615491 to Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.13 | AMFR |
Achchuthan Shanmugasundram changed review comment from: PMID:37119330 - 20 individuals from 8 unrelated consanguineous families of various origins were identified with autosomal recessive variants in AMFR gene. All patients had early disease onset (<3 years), including motor delay, lower limb hyperreflexia and spastic paraplegia that match the typical phenotypes of hereditary spastic paraplegia. Sources: Literature; to: PMID:37119330 - 20 individuals from 8 unrelated consanguineous families of various origins were identified with autosomal recessive variants in AMFR gene. All patients had early disease onset (<3 years), including motor delay, lower limb hyperreflexia and spastic paraplegia that match the typical phenotypes of hereditary spastic paraplegia. This gene has been associated with relevant phenotypes in OMIM (MIM #620379), but not in Gene2Phenotype. Sources: Literature |
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| Optic neuropathy v4.4 | UCHL1 | Sarah Leigh Phenotypes for gene: UCHL1 were changed from Spastic paraplegia 79, autosomal recessive, 615491 to Spastic paraplegia 79, autosomal recessive, OMIM:615491; early-onset progressive neurodegeneration-blindness-ataxia-spasticity syndrome, MONDO:0014209; Spastic paraplegia 79A, autosomal dominant, OMIM:620221 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.13 | AMFR | Achchuthan Shanmugasundram Classified gene: AMFR as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.13 | AMFR | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.13 | AMFR | Achchuthan Shanmugasundram Gene: amfr has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.12 | AMFR | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: AMFR. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.12 | AMFR |
Achchuthan Shanmugasundram gene: AMFR was added gene: AMFR was added to Childhood onset hereditary spastic paraplegia. Sources: Literature Mode of inheritance for gene: AMFR was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AMFR were set to 37119330 Phenotypes for gene: AMFR were set to Spastic paraplegia 89, autosomal recessive, OMIM:620379 Review for gene: AMFR was set to GREEN Added comment: PMID:37119330 - 20 individuals from 8 unrelated consanguineous families of various origins were identified with autosomal recessive variants in AMFR gene. All patients had early disease onset (<3 years), including motor delay, lower limb hyperreflexia and spastic paraplegia that match the typical phenotypes of hereditary spastic paraplegia. Sources: Literature |
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| Adult onset neurodegenerative disorder v4.29 | UCHL1 | Sarah Leigh Publications for gene: UCHL1 were set to PMID: 23359680 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.11 | UCHL1 | Sarah Leigh Publications for gene: UCHL1 were set to 23359680; 28007905; 29735986; 32656641; 11555633; 33159930 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Optic neuropathy v4.3 | UCHL1 | Sarah Leigh Publications for gene: UCHL1 were set to 29735986; 23359680; 28007905 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.70 | CNOT9 | Achchuthan Shanmugasundram Classified gene: CNOT9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.70 | CNOT9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated cases) for this gene to be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.70 | CNOT9 | Achchuthan Shanmugasundram Gene: cnot9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.69 | CNOT9 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: CNOT9. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.69 | CNOT9 | Achchuthan Shanmugasundram Phenotypes for gene: CNOT9 were changed from epilepsy, MONDO:0005027 to epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.69 | CNOT9 | Achchuthan Shanmugasundram Phenotypes for gene: CNOT9 were changed from epilepsy, MONDO:0005027 to epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.69 | CNOT9 | Achchuthan Shanmugasundram Phenotypes for gene: CNOT9 were changed from intellectual disability, MONDO:0001071 to epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.68 | CNOT9 | Achchuthan Shanmugasundram edited their review of gene: CNOT9: Changed phenotypes to: epilepsy, MONDO:0005027 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.217 | CNOT9 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: CNOT9. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.217 | CNOT9 | Achchuthan Shanmugasundram Classified gene: CNOT9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.217 | CNOT9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (seven unrelated cases) for this gene to be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.217 | CNOT9 | Achchuthan Shanmugasundram Gene: cnot9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.68 | CNOT9 |
Achchuthan Shanmugasundram gene: CNOT9 was added gene: CNOT9 was added to Early onset or syndromic epilepsy. Sources: Literature Mode of inheritance for gene: CNOT9 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CNOT9 were set to 37092538 Phenotypes for gene: CNOT9 were set to intellectual disability, MONDO:0001071 Review for gene: CNOT9 was set to GREEN Added comment: PMID:37092538 - Seven unrelated individuals with de novo variants in CNOT9 gene (one individual each with variants p.Arg46Gly, p.Pro131Leu and p.Arg227His and four individuals with p.Arg292Trp) were reported with a neurodevelopmental disorder. All affected persons have intellectual disability (three severe, three mild and one unclassified) and five of them have seizures. This gene has not yet been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.216 | CNOT9 |
Achchuthan Shanmugasundram gene: CNOT9 was added gene: CNOT9 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: CNOT9 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CNOT9 were set to 37092538 Phenotypes for gene: CNOT9 were set to intellectual disability, MONDO:0001071 Review for gene: CNOT9 was set to GREEN Added comment: PMID:37092538 - Seven unrelated individuals with de novo variants in CNOT9 gene (one individual each with variants p.Arg46Gly, p.Pro131Leu and p.Arg227His and four individuals with p.Arg292Trp) were reported with a neurodevelopmental disorder. All affected persons have intellectual disability (three severe, three mild and one unclassified) and five of them have seizures. This gene has not yet been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. Sources: Literature |
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| Childhood onset dystonia, chorea or related movement disorder v3.23 | SLC30A9 | Achchuthan Shanmugasundram Classified gene: SLC30A9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.23 | SLC30A9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are six unrelated families with childhood onset dystonia or choreoathetosis reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.23 | SLC30A9 | Achchuthan Shanmugasundram Gene: slc30a9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.22 | SLC30A9 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SLC30A9. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.22 | SLC30A9 |
Achchuthan Shanmugasundram gene: SLC30A9 was added gene: SLC30A9 was added to Childhood onset dystonia, chorea or related movement disorder. Sources: Literature Mode of inheritance for gene: SLC30A9 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC30A9 were set to 28334855; 34716203; 37041080 Phenotypes for gene: SLC30A9 were set to Birk-Landau-Perez syndrome, OMIM:617595 Review for gene: SLC30A9 was set to GREEN Added comment: PMID:28334855 - Six patients from a large multigenerational Bedouin kindred had onset of different combinations of intellectual disability, muscle weakness, oculomotor apraxia, and nephropathy in early childhood and they were identified with a homozygous variant in SLC30A9 gene (c.1047_1049delGCA; p.A350del). The age of onset of movement disorder was around 1-2 years of age. PMID:34716203 - A girl of African-American descent was identified with compound heterozygous variants in SLC30A9 gene (c.40delA & c.86_87dupCC) and was reported with a cerebrorenal syndrome. She presented around one year of age with microcephaly and global developmental delay. She also had bilateral sensorineural hearing loss and later developed dystonic movements affecting the whole body (onset was around 5-10 years of age). PMID:37041080 - Eight individuals from four unrelated families were reported with SLC30A9-related disease and they presented with intellectual disability and progressive hyperkinetic movement disorder, associated with oculomotor apraxia and ptosis despite phenotypic variability. The two families of British Pakistani descent harboured homozygous c.1253G>T (p.Gly418Val) variant, Egyptian Palestinian family harboured homozygous c.1049delCAG (pAla350del) variant, while family of European Australian descent had compound heterozygous variants (c.1083dup/ p.Val362Cysfs*5, and c.1413A>G/ p.Ser471=). The age of onset of movement disorder in these patients ranged from around 1-2 years to 16 years of age. This gene has been associated with relevant phenotypes in OMIM (MIM #617595), but not yet in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Classified gene: SLC30A9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Gene: slc30a9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Classified gene: SLC30A9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Gene: slc30a9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update.; to: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update.; to: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Classified gene: SLC30A9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Gene: slc30a9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Classified gene: SLC30A9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are six unrelated families with Intellectual disability/ global developmental delay reported with biallelic variants in this gene. Hence, this gene can be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.215 | SLC30A9 | Achchuthan Shanmugasundram Gene: slc30a9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.214 | SLC30A9 | Achchuthan Shanmugasundram Phenotypes for gene: SLC30A9 were changed from Birk-Landau-Perez syndrome, OMIM:617595 to Birk-Landau-Perez syndrome, OMIM:617595 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.214 | SLC30A9 | Achchuthan Shanmugasundram Phenotypes for gene: SLC30A9 were changed from Birk-Landau-Perez syndrome, OMIM:617595 to Birk-Landau-Perez syndrome, OMIM:617595 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.213 | SLC30A9 | Achchuthan Shanmugasundram Phenotypes for gene: SLC30A9 were changed from Birk-Landau-Perez syndrome, OMIM:617595 to Birk-Landau-Perez syndrome, OMIM:617595 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.213 | SLC30A9 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SLC30A9. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.213 | SLC30A9 | Achchuthan Shanmugasundram Phenotypes for gene: SLC30A9 were changed from Birk-Landau-Perez syndrome, OMIM:617595 to Birk-Landau-Perez syndrome, OMIM:617595 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.213 | SLC30A9 | Achchuthan Shanmugasundram Phenotypes for gene: SLC30A9 were changed from ?Birk-Landau-Perez syndrome 617595 to Birk-Landau-Perez syndrome, OMIM:617595 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.212 | SLC30A9 | Achchuthan Shanmugasundram Publications for gene: SLC30A9 were set to 28334855 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.211 | SLC30A9 | Achchuthan Shanmugasundram reviewed gene: SLC30A9: Rating: GREEN; Mode of pathogenicity: None; Publications: 28334855, 34716203, 37041080; Phenotypes: Birk-Landau-Perez syndrome, OMIM:617595; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.17 | MCOLN1 |
Achchuthan Shanmugasundram changed review comment from: Mucolipidosis type IV caused by biallelic variants in MCOLN1 gene ism a lysosomal disease that primarily affects the central nervous system. It manifests with severely impaired psychomotor development, and later onset, gradual neurological decline paralleled by cerebellar degeneration and neuroaxonal injury. In addition, they also manifest tetinal dystrophy, which develops in the first years of life and rapidly progresses in adolescence, leaving patients legally blind by the second decade (PMID:33965501). The following are some of the reported cases: PMID:17239335 - Compound heterozygous variants in MCOLN1 were identified in a patient with mucolipidosis type IV (ML IV), who had low visual acuity and cloudy corneas since 2 years of age, progressive decrease in visual acuity since the age of 9 years. PMID:25156245 - An Italian child with ML IV was identified with homozygous MCOLN1 variants (c.395_397delCTG & c.468_474dupTTGGACC), while his parents were heterozygous for the same variants. Ophthalmological manifestations included esotropia, bilateral corneal clouding and severe myopia. PMID:35205297 - Six patients from two Omani families with ML IV were identified with a novel variant (c.237+5G>A) in MCOLN1 gene, which is not present in control subjects screened with a high-resolution melting (HRM) assay. The patients displayed ophthalmic manifestations including corneal haziness, pigmentary retinopathy and ERG-rod cone dysfunction. This gene has also been associated with relevant phenotypes both in OMIM (MIM #252650) and DD and eye panels of Gene2Phenotype (with 'definitive' rating). The ophthalmological manifestations including corneal clouding, progressive retinal degeneration and optic atrophy has been reported as part of the OMIM phenotype.; to: Mucolipidosis type IV caused by biallelic variants in MCOLN1 gene ism a lysosomal disease that primarily affects the central nervous system. It manifests with severely impaired psychomotor development, and later onset, gradual neurological decline paralleled by cerebellar degeneration and neuroaxonal injury. In addition, they also manifest retinal dystrophy, which develops in the first years of life and rapidly progresses in adolescence, leaving patients legally blind by the second decade (PMID:33965501). The following are some of the reported cases: PMID:17239335 - Compound heterozygous variants in MCOLN1 were identified in a patient with mucolipidosis type IV (ML IV), who had low visual acuity and cloudy corneas since 2 years of age, progressive decrease in visual acuity since the age of 9 years. PMID:25156245 - An Italian child with ML IV was identified with homozygous MCOLN1 variants (c.395_397delCTG & c.468_474dupTTGGACC), while his parents were heterozygous for the same variants. Ophthalmological manifestations included esotropia, bilateral corneal clouding and severe myopia. PMID:35205297 - Six patients from two Omani families with ML IV were identified with a novel variant (c.237+5G>A) in MCOLN1 gene, which is not present in control subjects screened with a high-resolution melting (HRM) assay. The patients displayed ophthalmic manifestations including corneal haziness, pigmentary retinopathy and ERG-rod cone dysfunction. This gene has also been associated with relevant phenotypes both in OMIM (MIM #252650) and DD and eye panels of Gene2Phenotype (with 'definitive' rating). The ophthalmological manifestations including corneal clouding, progressive retinal degeneration and optic atrophy has been reported as part of the OMIM phenotype. |
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| Retinal disorders v4.17 | MCOLN1 | Achchuthan Shanmugasundram Classified gene: MCOLN1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.17 | MCOLN1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Siying Lin, there is sufficient evidence for this gene to be added with a green rating in this panel as patients with MCOLN1-associated mucolipidosis IV present with a limited ocular phenotype including retinal dystrophy. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.17 | MCOLN1 | Achchuthan Shanmugasundram Gene: mcoln1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.16 | MCOLN1 | Achchuthan Shanmugasundram Publications for gene: MCOLN1 were set to 17239335; 1488220; 18326692 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.15 | MCOLN1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: MCOLN1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.15 | MCOLN1 | Achchuthan Shanmugasundram reviewed gene: MCOLN1: Rating: GREEN; Mode of pathogenicity: None; Publications: 17239335, 25156245, 33965501, 35205297; Phenotypes: Mucolipidosis IV, OMIM:252650; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.15 | PYGM | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are four unrelated cases in support of the association of this gene to retinal disorders. Hence, this gene can be rated green in the next major update.; to: Comment on list classification: As reviewed by Siying Lin, there are four unrelated cases in support of the association of this gene to retinal disorders. Hence, this gene can be rated green in the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.15 | PYGM |
Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PYGM. Tag Q3_23_NHS_review tag was added to gene: PYGM. |
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| Retinal disorders v4.15 | PYGM | Achchuthan Shanmugasundram Classified gene: PYGM as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.15 | PYGM | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are four unrelated cases in support of the association of this gene to retinal disorders. Hence, this gene can be rated green in the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.15 | PYGM | Achchuthan Shanmugasundram Gene: pygm has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.14 | PYGM | Achchuthan Shanmugasundram Phenotypes for gene: PYGM were changed from Macular dystrophy, retinopathy to macular dystrophy, retinal, MONDO:0031166 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.13 | PYGM | Achchuthan Shanmugasundram Publications for gene: PYGM were set to PMID 30316539 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.12 | PYGM | Achchuthan Shanmugasundram reviewed gene: PYGM: Rating: GREEN; Mode of pathogenicity: None; Publications: 30316539; Phenotypes: macular dystrophy, retinal, MONDO:0031166; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.21 | TMEM151A | Achchuthan Shanmugasundram Tag Q3_23_NHS_review tag was added to gene: TMEM151A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.21 | TMEM151A | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There is sufficient evidence (more than 40 unrelated cases and supporting functional evidence) available in support of the association of this gene to PKD. Hence, this gene can be rated Green in the next major update.; to: Comment on list classification: There is sufficient evidence (more than 40 unrelated cases and supporting functional evidence) available in support of the association of this gene to PKD with onset in childhood/ adolescence. Hence, this gene can be rated Green in the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.21 | TMEM151A | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: TMEM151A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.21 | TMEM151A | Achchuthan Shanmugasundram Classified gene: TMEM151A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.21 | TMEM151A | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (more than 40 unrelated cases and supporting functional evidence) available in support of the association of this gene to PKD. Hence, this gene can be rated Green in the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.21 | TMEM151A | Achchuthan Shanmugasundram Gene: tmem151a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.20 | TMEM151A | Achchuthan Shanmugasundram Phenotypes for gene: TMEM151A were changed from Episodic kinesigenic dyskinesia 3 to Episodic kinesigenic dyskinesia 3, OMIM:620245 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.19 | TMEM151A | Achchuthan Shanmugasundram Publications for gene: TMEM151A were set to 34518509; 34820915; 35587630; 35707035; 35727387 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.18 | TMEM151A |
Achchuthan Shanmugasundram changed review comment from: PMID:34518509 - Nine individuals from three unrelated Chines families with paroxysmal kinesigenic dyskinesia (PKD) were identified with autosomal dominant variants in TMEM151A gene. In addition, 8 unrelated patients (isolated cases) with sporadic occurrence of PKD were also identified with heterozygous variants, of which three patients inherited variants from an unaffected parent, suggesting incomplete penetrance. The age of onset of symptoms ranged between 9 and 15 years. In addition, supporting mouse model and in vitro functional assays suggested loss of function as the mechanism of disease. PMID:34820915 - 29 PRRT2-negative Chinese patients from 25 families with PKD identified with 24 heterozygous variants in TMEM151A gene. The mean age of onset of symptoms was 12.93 years, with 13 patients reported with spontaneous remission of the disease around 21 years of age. PMID:35587630 - De novo missense variant in TMEM151A was identified in a French man with PKD and he presented with brief attacks of dystonia after 16 years of age. PMID:35707035 - Screening of patients with PRRT2-negative PKD and other movement disorders identified two novel variants in TMEM151A gene in two patients with PKD. PMID:35727387 - Heterozygous missense variant was identified in four affected members of a 3-generation Chinese family with PKD and the variant segregated with the disorder in the family. This gene has been associated with relevant phenotype in OMIM (MIM #620245), but not in Gene2Phenotype.; to: PMID:34518509 - Nine individuals from three unrelated Chines families with paroxysmal kinesigenic dyskinesia (PKD) were identified with autosomal dominant variants in TMEM151A gene. In addition, 8 unrelated patients (isolated cases) with sporadic occurrence of PKD were also identified with heterozygous variants, of which three patients inherited variants from an unaffected parent, suggesting incomplete penetrance. The age of onset of symptoms ranged between 9 and 15 years. In addition, supporting mouse model and in vitro functional assays suggested loss of function as the mechanism of disease. PMID:34820915 - 29 PRRT2-negative Chinese patients from 25 families with PKD identified with 24 heterozygous variants in TMEM151A gene. The mean age of onset of symptoms was 12.93 years, with 13 patients reported with spontaneous remission of the disease around 21 years of age. PMID:35587630 - De novo missense variant in TMEM151A was identified in a French man with PKD and he presented with brief attacks of dystonia after 16 years of age. PMID:35707035 - Screening of patients with PRRT2-negative PKD and other movement disorders identified two novel variants in TMEM151A gene in two patients with PKD. PMID:35727387 - Heterozygous missense variant was identified in four affected members of a 3-generation Chinese family with PKD and the variant segregated with the disorder in the family. PMID:36724570 - Three patients presenting with PKD were identified with different TMEM151A variants. This gene has been associated with relevant phenotype in OMIM (MIM #620245), but not in Gene2Phenotype. |
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| Childhood onset dystonia, chorea or related movement disorder v3.18 | TMEM151A | Achchuthan Shanmugasundram edited their review of gene: TMEM151A: Changed publications to: 34518509, 34820915, 35587630, 35707035, 35727387, 36724570 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.18 | TMEM151A | Achchuthan Shanmugasundram Publications for gene: TMEM151A were set to (PMID: 34518509; 35707035; 36724570; 34820915) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.17 | TMEM151A | Achchuthan Shanmugasundram reviewed gene: TMEM151A: Rating: GREEN; Mode of pathogenicity: None; Publications: 34518509, 34820915, 35587630, 35707035, 35727387; Phenotypes: Episodic kinesigenic dyskinesia 3, OMIM:620245; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | PPOX |
Achchuthan Shanmugasundram changed review comment from: As reviewed by Zornitza Stark and suggested in PMID:25778941, Variegate porphyria (VP) should be included in this panel. Autosomal dominat variegate porphyria (VP): VP is usually caused by autosomal dominant variants in PPOX gene in the majority of the cases. PMID:30476629 - Eight unrelated individuals with seven different variants in heterozygous state were reported with VP. Autosomal dominant variants in this gene have also been associated with VP in OMIM (MIM #176200). Autosomal recessive variegate porphyria (VP): PMID:9540991 - A severely affected female proband with recessive VP was identified with two missense compound heterozygous variants in PPOX gene (p.Gly169Glu & p.Gly358Arg), as detected by heteroduplex analysis, automated sequencing, and allele specific oligonucleotide hybridization. PMID:10870850 - Two unrelated South African cases with variegate porphyria were reported with onset of the disease usually in infancy and with severe skin manifestations. The variant detection included combined SSCP-heteroduplex analysis followed by direct sequencing and both had the common p.Arg59Trp variant, while the other variant was p.Tyr348Cys in one and p.Arg138Pro in the other. PMID:32247286 - A case of VP was reported from a family with only cutaneous manifestations and was identified with two heterozygous missense variants in PPOX gene (p.Gly41Cys and p.Trp42Arg). The same variants were identified in patient's mother who had skin lesions, whereas father had no clinical involvement and did not have any of these variants. The familly study showed that the two variants occur in cis on the same allele. PMID:33159949 - A novel homozygous variant in PPOX gene (c.808G>T) was identified in a patient with autosomal recessive form of VP. Overall, the autosomal recessive form of VP usually occurs early in in fancy and have markedly reduced levels of protoporphyrinogen oxidase than autosomal dominant form. Autosomal recessive VP has not yet been reported in OMIM.; to: As reviewed by Zornitza Stark in 'Mitochondrial disorders' panel and suggested in PMID:25778941, Variegate porphyria (VP) should be included in this panel. Autosomal dominat variegate porphyria (VP): VP is usually caused by autosomal dominant variants in PPOX gene in the majority of the cases. PMID:30476629 - Eight unrelated individuals with seven different variants in heterozygous state were reported with VP. Autosomal dominant variants in this gene have also been associated with VP in OMIM (MIM #176200). Autosomal recessive variegate porphyria (VP): PMID:9540991 - A severely affected female proband with recessive VP was identified with two missense compound heterozygous variants in PPOX gene (p.Gly169Glu & p.Gly358Arg), as detected by heteroduplex analysis, automated sequencing, and allele specific oligonucleotide hybridization. PMID:10870850 - Two unrelated South African cases with variegate porphyria were reported with onset of the disease usually in infancy and with severe skin manifestations. The variant detection included combined SSCP-heteroduplex analysis followed by direct sequencing and both had the common p.Arg59Trp variant, while the other variant was p.Tyr348Cys in one and p.Arg138Pro in the other. PMID:32247286 - A case of VP was reported from a family with only cutaneous manifestations and was identified with two heterozygous missense variants in PPOX gene (p.Gly41Cys and p.Trp42Arg). The same variants were identified in patient's mother who had skin lesions, whereas father had no clinical involvement and did not have any of these variants. The familly study showed that the two variants occur in cis on the same allele. PMID:33159949 - A novel homozygous variant in PPOX gene (c.808G>T) was identified in a patient with autosomal recessive form of VP. Overall, the autosomal recessive form of VP usually occurs early in in fancy and have markedly reduced levels of protoporphyrinogen oxidase than autosomal dominant form. Autosomal recessive VP has not yet been reported in OMIM. |
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| Possible mitochondrial disorder - nuclear genes v3.33 | PPOX | Achchuthan Shanmugasundram Classified gene: PPOX as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | PPOX | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than three unrelated cases each with both monoallelic and biallelic variants in PPOX gene. Hence, this gene should be promoted to Green at the next GMS update and the MOI should be updated from 'MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown' to 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal'. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.33 | PPOX | Achchuthan Shanmugasundram Gene: ppox has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.32 | PPOX | Achchuthan Shanmugasundram Publications for gene: PPOX were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.31 | PPOX | Achchuthan Shanmugasundram Mode of inheritance for gene: PPOX was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | PPOX | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PPOX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | PPOX | Achchuthan Shanmugasundram reviewed gene: PPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 9540991, 10870850, 25778941, 30476629, 32247286, 33159949; Phenotypes: Porphyria variegata, OMIM:176200; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.37 | PPOX | Achchuthan Shanmugasundram Publications for gene: PPOX were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.36 | PPOX | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: Comment on mode of inheritance: There are at least three cases of variegate porphyria reported with biallelic variants in PPOX gene and sensory neuropathy. Hence, the MOI should be updated from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal" in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.36 | PPOX | Achchuthan Shanmugasundram Mode of inheritance for gene: PPOX was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.35 | PPOX | Achchuthan Shanmugasundram Tag Q3_23_MOI tag was added to gene: PPOX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.35 | PPOX | Achchuthan Shanmugasundram reviewed gene: PPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 8290408, 10870850, 11286631; Phenotypes: Porphyria variegata, OMIM:176200, Sensory neuropathy, HP:0000763; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.470 | PPOX | Achchuthan Shanmugasundram Mode of inheritance for gene: PPOX was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.469 | PPOX | Achchuthan Shanmugasundram Tag Q3_23_MOI was removed from gene: PPOX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.469 | PPOX | Achchuthan Shanmugasundram changed review comment from: Comment on mode of inheritance: There are at least three cases of variegate porphyria reported with biallelic variants in PPOX gene and sensory neuropathy. Hence, the MOI can be updated from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal" in the next GMS review.; to: Comment on mode of inheritance: There are at least three cases of variegate porphyria reported with biallelic variants in PPOX gene and sensory neuropathy. Hence, the MOI should be updated from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.469 | PPOX | Achchuthan Shanmugasundram Tag Q3_23_MOI tag was added to gene: PPOX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.469 | PPOX | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: There are at least three cases of variegate porphyria reported with biallelic variants in PPOX gene and sensory neuropathy. Hence, the MOI can be updated from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal" in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.469 | PPOX | Achchuthan Shanmugasundram Mode of inheritance for gene: PPOX was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.468 | PPOX | Achchuthan Shanmugasundram Publications for gene: PPOX were set to 8290408; 10870850; 11286631 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.467 | PPOX | Achchuthan Shanmugasundram Publications for gene: PPOX were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.466 | PPOX | Achchuthan Shanmugasundram edited their review of gene: PPOX: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy v1.466 | PPOX | Achchuthan Shanmugasundram reviewed gene: PPOX: Rating: ; Mode of pathogenicity: None; Publications: 8290408, 10870850, 11286631; Phenotypes: Porphyria variegata, OMIM:176200, Sensory neuropathy, HP:0000763; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.62 | PPOX | Achchuthan Shanmugasundram Publications for gene: PPOX were set to 9540991; 9811936; 10870850; 12859407; 25778941; 30476629; 32247286; 33159949 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.62 | PPOX | Achchuthan Shanmugasundram Publications for gene: PPOX were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.61 | PPOX | Achchuthan Shanmugasundram Mode of inheritance for gene: PPOX was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Classified gene: PPOX as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than three unrelated cases each with both monoallelic and biallelic variants in PPOX gene. Hence, this gene should be promoted to Green at the next GMS update and the MOI should be updated from 'MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown' to 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal'. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Gene: ppox has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Classified gene: PPOX as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than three unrelated cases each with both monoallelic and biallelic variants in PPOX gene. Hence, this gene should be promoted to Green at the next GMS update and the MOI should be updated from 'MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown' to 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal'. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.60 | PPOX | Achchuthan Shanmugasundram Gene: ppox has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.59 | PPOX |
Achchuthan Shanmugasundram Tag Q3_23_MOI was removed from gene: PPOX. Tag Q3_23_promote_green tag was added to gene: PPOX. |
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| Mitochondrial disorders v4.59 | PPOX | Achchuthan Shanmugasundram Tag Q3_23_MOI tag was added to gene: PPOX. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.59 | PPOX | Achchuthan Shanmugasundram edited their review of gene: PPOX: Changed publications to: 9540991, 10870850, 25778941, 30476629, 32247286, 33159949 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.59 | PPOX |
Achchuthan Shanmugasundram changed review comment from: Autosomal dominat variegate porphyria (VP): VP is usually caused by autosomal dominant variants in PPOX gene in the majority of the cases. PMID:30476629 - Eight unrelated individuals with seven different variants in heterozygous state were reported with VP. Autosomal dominant variants in this gene have also been associated with VP in OMIM (MIM #176200). Autosomal recessive variegate porphyria (VP): PMID:9540991 - A severely affected female proband with recessive VP was identified with two missense compound heterozygous variants in PPOX gene (p.Gly169Glu & p.Gly358Arg), as detected by heteroduplex analysis, automated sequencing, and allele specific oligonucleotide hybridization. PMID:10870850 - Two unrelated South African cases with variegate porphyria were reported with onset of the disease usually in infancy and with severe skin manifestations. The variant detection included combined SSCP-heteroduplex analysis followed by direct sequencing and both had the common p.Arg59Trp variant, while the other variant was p.Tyr348Cys in one and p.Arg138Pro in the other. PMID:32247286 - A case of VP was reported from a family with only cutaneous manifestations and was identified with two heterozygous missense variants in PPOX gene (p.Gly41Cys and p.Trp42Arg). The same variants were identified in patient's mother who had skin lesions, whereas father had no clinical involvement and did not have any of these variants. The familly study showed that the two variants occur in cis on the same allele. PMID:33159949 - A novel homozygous variant in PPOX gene (c.808G>T) was identified in a patient with autosomal recessive form of VP. Overall, the autosomal recessive form of VP usually occurs early in in fancy and have markedly reduced levels of protoporphyrinogen oxidase than autosomal dominant form. Autosomal recessive VP has not yet been reported in OMIM. ; to: As reviewed by Zornitza Stark and suggested in PMID:25778941, Variegate porphyria (VP) should be included in this panel. Autosomal dominat variegate porphyria (VP): VP is usually caused by autosomal dominant variants in PPOX gene in the majority of the cases. PMID:30476629 - Eight unrelated individuals with seven different variants in heterozygous state were reported with VP. Autosomal dominant variants in this gene have also been associated with VP in OMIM (MIM #176200). Autosomal recessive variegate porphyria (VP): PMID:9540991 - A severely affected female proband with recessive VP was identified with two missense compound heterozygous variants in PPOX gene (p.Gly169Glu & p.Gly358Arg), as detected by heteroduplex analysis, automated sequencing, and allele specific oligonucleotide hybridization. PMID:10870850 - Two unrelated South African cases with variegate porphyria were reported with onset of the disease usually in infancy and with severe skin manifestations. The variant detection included combined SSCP-heteroduplex analysis followed by direct sequencing and both had the common p.Arg59Trp variant, while the other variant was p.Tyr348Cys in one and p.Arg138Pro in the other. PMID:32247286 - A case of VP was reported from a family with only cutaneous manifestations and was identified with two heterozygous missense variants in PPOX gene (p.Gly41Cys and p.Trp42Arg). The same variants were identified in patient's mother who had skin lesions, whereas father had no clinical involvement and did not have any of these variants. The familly study showed that the two variants occur in cis on the same allele. PMID:33159949 - A novel homozygous variant in PPOX gene (c.808G>T) was identified in a patient with autosomal recessive form of VP. Overall, the autosomal recessive form of VP usually occurs early in in fancy and have markedly reduced levels of protoporphyrinogen oxidase than autosomal dominant form. Autosomal recessive VP has not yet been reported in OMIM. |
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| Mitochondrial disorders v4.59 | PPOX |
Achchuthan Shanmugasundram changed review comment from: PMID:30476629 - Eight unrelated individuals with seven different variants in heterozygous state were reported with Variegate porphyria (VP). PMID:32247286 - A case of VP was reported from a family with only cutaneous manifestations and was identified with two heterozygous missense variants in PPOX gene (p.Gly41Cys and p.Trp42Arg). The same variants were identified in patient's mother who had skin lesions, whereas father had no clinical involvement and did not have any of these variants. The familly study showed that the two variants occur in cis on the same allele. Autosomal dominant variants in this gene have been associated with Variegate porphyria in OMIM (MIM #176200).; to: Autosomal dominat variegate porphyria (VP): VP is usually caused by autosomal dominant variants in PPOX gene in the majority of the cases. PMID:30476629 - Eight unrelated individuals with seven different variants in heterozygous state were reported with VP. Autosomal dominant variants in this gene have also been associated with VP in OMIM (MIM #176200). Autosomal recessive variegate porphyria (VP): PMID:9540991 - A severely affected female proband with recessive VP was identified with two missense compound heterozygous variants in PPOX gene (p.Gly169Glu & p.Gly358Arg), as detected by heteroduplex analysis, automated sequencing, and allele specific oligonucleotide hybridization. PMID:10870850 - Two unrelated South African cases with variegate porphyria were reported with onset of the disease usually in infancy and with severe skin manifestations. The variant detection included combined SSCP-heteroduplex analysis followed by direct sequencing and both had the common p.Arg59Trp variant, while the other variant was p.Tyr348Cys in one and p.Arg138Pro in the other. PMID:32247286 - A case of VP was reported from a family with only cutaneous manifestations and was identified with two heterozygous missense variants in PPOX gene (p.Gly41Cys and p.Trp42Arg). The same variants were identified in patient's mother who had skin lesions, whereas father had no clinical involvement and did not have any of these variants. The familly study showed that the two variants occur in cis on the same allele. PMID:33159949 - A novel homozygous variant in PPOX gene (c.808G>T) was identified in a patient with autosomal recessive form of VP. Overall, the autosomal recessive form of VP usually occurs early in in fancy and have markedly reduced levels of protoporphyrinogen oxidase than autosomal dominant form. Autosomal recessive VP has not yet been reported in OMIM. |
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| Mitochondrial disorders v4.59 | PPOX | Achchuthan Shanmugasundram edited their review of gene: PPOX: Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.59 | PPOX | Achchuthan Shanmugasundram reviewed gene: PPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: 30476629, 32247286; Phenotypes: Porphyria variegata, OMIM:176200; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.10 | PTPRQ |
Achchuthan Shanmugasundram changed review comment from: PMID:29309402 - A heterozygous nonsense variant (c.6881G>A; p.Trp2294Ter) was identified in a four-generation German family with nonsyndromic mild to severe hearing loss of the mid- to high frequencies and onset from early childhood to second decade in seven members. PMID:31655630 - The same variant (c.6881G>A; p.Trp2294Ter) was identified in a five-generation Polish family with autosomal dominant non-syndromic hearing loss (ADNSHL). Using genome-wide linkage analysis, the authors also found that the studied Polish family and the original German family derive from a common ancestor. PMID:33229591 - PTPRQ variants p.Gly383Glu and p.Arg841Trp were identified in multiplex family age-related hearing loss (mARHL) cases, while p.Ser1022Arg, c.4286-1G>T and p.Leu879Argfs*20 were identified with simplex/sporadic age-related hearing loss (sARHL) cases. However, p.Ser321Cys was identified in control cases with normal hearing.; to: PMID:29309402 - A heterozygous nonsense variant (c.6881G>A; p.Trp2294Ter) was identified in a four-generation German family with nonsyndromic mild to severe hearing loss of the mid- to high frequencies and onset from early childhood to second decade in seven members. PMID:31655630 - The same variant (c.6881G>A; p.Trp2294Ter) was identified in a five-generation Polish family with autosomal dominant non-syndromic hearing loss (ADNSHL). Using genome-wide linkage analysis, the authors also found that the studied Polish family and the original German family derive from a common ancestor. PMID:33229591 - PTPRQ variants p.Gly383Glu and p.Arg841Trp were identified in multiplex family age-related hearing loss (mARHL) cases, while p.Ser1022Arg, c.4286-1G>T and p.Leu879Argfs*20 were identified with simplex/sporadic age-related hearing loss (sARHL) cases. However, p.Ser321Cys was identified in control cases with normal hearing. This gene has been associated with hearing loss caused by both autosomal dominant (MIM #617663) and autosomal recessive (MIM #613391) inheritance in OMIM. |
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| Monogenic hearing loss v4.10 | PTPRQ | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: As there are sufficient cases/ variants reported with monoallelic inheritance and hearing loss, the MOI should be changed from "BIALLELIC, autosomal or pseudoautosomal" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal" in the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.10 | PTPRQ | Achchuthan Shanmugasundram Mode of inheritance for gene: PTPRQ was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.9 | PTPRQ | Achchuthan Shanmugasundram Tag Q3_23_MOI tag was added to gene: PTPRQ. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monogenic hearing loss v4.9 | PTPRQ | Achchuthan Shanmugasundram reviewed gene: PTPRQ: Rating: GREEN; Mode of pathogenicity: None; Publications: 29309402, 31655630, 33229591; Phenotypes: Deafness, autosomal dominant 73, OMIM:617663, Deafness, autosomal recessive 84A, OMIM:613391; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | PMM2 | Eleanor Williams Tag Q3_23_expert_review tag was added to gene: PMM2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | PMM2 | Eleanor Williams Tag Q3_23_demote_red tag was added to gene: PMM2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | PMM2 | Eleanor Williams commented on gene: PMM2: After reviewing the literature no patients were found with a skeletal phenotype so demotion to red on this panel is recommended. This has been confirmed with a Genomics England clinician. It is represented on the other ciliopathy panels, so shouldn't be missed for relevant phenotypes. It was initially added as a ciliopathy mimic. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.10 | EN1 |
Eleanor Williams changed review comment from: The Genomics England clinical team confirm that the rating of this gene should currently be amber based on 1 case and a mouse model.; to: The Genomics England clinical team confirm that the rating of this gene should currently be amber based on 1 case and a mouse model. It has been additionally added to the 'Fetal anomalies' and 'Ataxia and cerebellar anomalies - narrow panel' panels based on the phenotype. If more cases with intellectual disability/seizures are reported then it could be additionally added to those panels at that time. |
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| Ataxia and cerebellar anomalies - narrow panel v4.21 | EN1 | Eleanor Williams Tag watchlist tag was added to gene: EN1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.21 | EN1 | Eleanor Williams commented on gene: EN1: This gene was copied from the Skeletal dysplasia panel to the Ataxia and cerebellar anomalies - narrow panel panel. The Genomics England clinical team have agreed that Fetal anomalies is an appropriate panel for this gene and the rating should currently be amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.10 | EN1 | Eleanor Williams Tag watchlist tag was added to gene: EN1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.92 | EN1 | Eleanor Williams Tag watchlist tag was added to gene: EN1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.92 | EN1 | Eleanor Williams commented on gene: EN1: This gene was copied from the Skeletal dysplasia panel to the Fetal anomalies panel. The Genomics England clinical team have agreed that Fetal anomalies is an appropriate panel for this gene and the rating should currently be amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.92 | EN1 | Eleanor Williams Entity copied from Skeletal dysplasia v4.10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.92 | EN1 |
Eleanor Williams gene: EN1 was added gene: EN1 was added to Fetal anomalies. Sources: Expert Review Amber,Literature Mode of inheritance for gene: EN1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EN1 were set to 33568816 Phenotypes for gene: EN1 were set to ENDOVE syndrome, limb-only type, MIM# 619217; ENDOVE syndrome, limb-brain type, MIM# 619218 |
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| Ataxia and cerebellar anomalies - narrow panel v4.21 | EN1 | Eleanor Williams Entity copied from Skeletal dysplasia v4.10 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.21 | EN1 |
Eleanor Williams gene: EN1 was added gene: EN1 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review Amber,Literature Mode of inheritance for gene: EN1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EN1 were set to 33568816 Phenotypes for gene: EN1 were set to ENDOVE syndrome, limb-only type, MIM# 619217; ENDOVE syndrome, limb-brain type, MIM# 619218 |
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| Skeletal dysplasia v4.10 | EN1 | Eleanor Williams commented on gene: EN1: The Genomics England clinical team confirm that the rating of this gene should currently be amber based on 1 case and a mouse model. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.9 | FGFR2 | Arina Puzriakova Phenotypes for gene: FGFR2 were changed from Epdermal naevi to Keratinocytic epidermal naevi (KENs); Naevoid acanthosis nigricans; RAVEN (round and velvety epidermal naevus) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Vascular skin disorders v1.51 | EPHB4 | Arina Puzriakova Phenotypes for gene: EPHB4 were changed from CAPILLARY MALFORMATION-ARTERIOVENOUS MALFORMATION 2, OMIM:618196 to Capillary malformation-arteriovenous malformation 2, OMIM:618196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary haemorrhagic telangiectasia v3.2 | EPHB4 | Arina Puzriakova Phenotypes for gene: EPHB4 were changed from Capillary malformation-arteriovenous malformation 2, 618196; Capillary malformation, epistaxis, telangiectasia, cerebral AVM to Capillary malformation-arteriovenous malformation 2, OMIM:618196; Capillary malformation, epistaxis, telangiectasia, cerebral AVM | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary lymphoedema v3.3 | EPHB4 | Arina Puzriakova Phenotypes for gene: EPHB4 were changed from Lymphatic malformation 7 617300 to Lymphatic malformation 7, OMIM:617300 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.91 | EPHB4 | Arina Puzriakova Phenotypes for gene: EPHB4 were changed from hydrops fetalis gene to Lymphatic malformation 7, OMIM:617300; hydrops fetalis | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal hydrops v1.61 | EPHB4 | Arina Puzriakova Mode of inheritance for gene: EPHB4 was changed from MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal hydrops v1.60 | EPHB4 | Arina Puzriakova Phenotypes for gene: EPHB4 were changed from Lymphatic malformation 7, MIM#617300 to Lymphatic malformation 7, OMIM:617300 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal hydrops v1.59 | EPHB4 | Arina Puzriakova Classified gene: EPHB4 as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal hydrops v1.59 | EPHB4 | Arina Puzriakova Added comment: Comment on list classification: Sufficient evidence to support hydrops fetalis association as part of MIM:617300, with 3 variants listed in OMIM from 3 families, each with multiple affected individuals (PMIDs: 27400125 and 29905864). Already Green on Fetal anomalies GMS panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal hydrops v1.59 | EPHB4 | Arina Puzriakova Gene: ephb4 has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.8 | EPHB4 | Arina Puzriakova Tag watchlist tag was added to gene: EPHB4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.8 | EPHB4 | Arina Puzriakova Classified gene: EPHB4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.8 | EPHB4 | Arina Puzriakova Added comment: Comment on list classification: Rating Amber for now as only a single case with mosaicism has been reported to date. The patients phenotype was comparable to germline cases but another independent report or functional studies of the variant would help corroborate this association before classifying as diagnostic-grade. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.8 | EPHB4 | Arina Puzriakova Gene: ephb4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.7 | EPHB4 | Arina Puzriakova Publications for gene: EPHB4 were set to PMID: 30760892 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.6 | EPHB4 | Arina Puzriakova Phenotypes for gene: EPHB4 were changed from Capillary malformation-arteriovenous malformation 2 (MIM 618196); Lymphatic malformation 7 (MIM 617300) to Capillary malformation-arteriovenous malformation 2, OMIM:618196 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.5 | EPHB4 | Arina Puzriakova commented on gene: EPHB4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Beckwith-Wiedemann syndrome v0.2 | CDKN1C | Achchuthan Shanmugasundram Mode of inheritance for gene: CDKN1C was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Beckwith-Wiedemann syndrome v0.1 | CDKN1C | Achchuthan Shanmugasundram edited their review of gene: CDKN1C: Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.10 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.10 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than three unrelated cases with infantile nystagmus and hence this gene can be promoted to green in this panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.10 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.9 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from developmental delay; ataxia; complex oculomotor abnormality (nystagmus) to congenital nystagmus, MONDO:0005712 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.8 | DAGLA | Achchuthan Shanmugasundram Publications for gene: DAGLA were set to PMID: 35737950 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.7 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Other to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.6 | DAGLA | Achchuthan Shanmugasundram reviewed gene: DAGLA: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: 35737950; Phenotypes: congenital nystagmus, MONDO:0005712; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.330 | DAGLA |
Achchuthan Shanmugasundram changed review comment from: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. All nine children had ataxia and the age of these children ranged between 4 and 15 years of age. In addition, the functional data suggests potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect (PMID:35737950). This gene has not yet been associated with any relevant phenotypes either in OMIM or in Gene2Phenotype.; to: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. All nine children had ataxia and the age of these children ranged between 4 and 15 years of age. In addition, the functional data suggests potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect (PMID:35737950). This gene has not yet been associated with any relevant phenotypes either in OMIM or in Gene2Phenotype. |
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| Epidermolysis bullosa and congenital skin fragility v2.4 | ATP2A2 | Arina Puzriakova Phenotypes for gene: ATP2A2 were changed from Darier disease, OMIM:124200 to Darier-White disease, OMIM:124200 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.59 | ANO10 | Sarah Leigh Phenotypes for gene: ANO10 were changed from Spinocerebellar ataxia, autosomal recessive 10, 613728 to Spinocerebellar ataxia, autosomal recessive 10, OMIM:613728; autosomal recessive spinocerebellar ataxia 10, MONDO:0013392 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.58 | ANO10 | Sarah Leigh Publications for gene: ANO10 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.57 | ANO10 | Sarah Leigh Tag Q3_23_expert_review tag was added to gene: ANO10. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.57 | BTD | Sarah Leigh Tag Q3_23_expert_review tag was added to gene: BTD. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type IH or S v0.2 | Achchuthan Shanmugasundram Panel name changed from Mucopolysaccharidosis type IH/S to Mucopolysaccharidosis type IH or S | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucolipidosis II and III Alpha or Beta v0.2 | Achchuthan Shanmugasundram Panel name changed from Mucolipidosis II and III Alpha/Beta to Mucolipidosis II and III Alpha or Beta | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.57 | ANO10 | Sarah Leigh reviewed gene: ANO10: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.57 | BTD | Sarah Leigh reviewed gene: BTD: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.330 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.330 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are eight unrelated cases associating monoallelic variants in DAGLA with ataxia. Hence, this gene can be rated Green. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.330 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.329 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from developmental delay; ataxia; complex oculomotor abnormality to Ataxia, HP:0001251 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.328 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Other to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.327 | DAGLA | Achchuthan Shanmugasundram Publications for gene: DAGLA were set to PMID: 35737950 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.326 | DAGLA | Achchuthan Shanmugasundram reviewed gene: DAGLA: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: 35737950; Phenotypes: Ataxia, HP:0001251; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.57 | BTD | Sarah Leigh Phenotypes for gene: BTD were changed from Biotinidase deficiency to Biotinidase deficiency, OMIM:253260; biotinidase deficiency, MONDO:0009665 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.20 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.20 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are eight unrelated cases associating monoallelic variants in DAGLA with ataxia. Hence, this gene should be promoted to Green rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.20 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.211 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.211 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.211 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.19 | DAGLA | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DAGLA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.211 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.211 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.210 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.19 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.210 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.210 | DAGLA | Achchuthan Shanmugasundram Mode of pathogenicity for gene: DAGLA was changed from Other to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram edited their review of gene: DAGLA: Changed mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.18 | DAGLA | Achchuthan Shanmugasundram edited their review of gene: DAGLA: Changed mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.18 | DAGLA |
Achchuthan Shanmugasundram gene: DAGLA was added gene: DAGLA was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature Mode of inheritance for gene: DAGLA was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DAGLA were set to 35737950 Phenotypes for gene: DAGLA were set to Ataxia, HP:0001251 Review for gene: DAGLA was set to GREEN Added comment: There are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. All nine children had ataxia and the age of these children ranged between 4 and 15 years of age. In addition, the functional data suggests potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect (PMID:35737950). This gene has not yet been associated with any relevant phenotypes either in OMIM or in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.209 | DAGLA |
Achchuthan Shanmugasundram changed review comment from: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. Of these nine children, five had intellectual disability and one had low average IQ. In addition, the functional data suggests potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect (PMID:35737950).; to: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. Of these nine children, five had intellectual disability and one had low average IQ. In addition, the functional data suggests potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect (PMID:35737950). This gene has not yet been associated with any relevant phenotypes either in OMIM or in Gene2Phenotype. |
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| Mosaic skin disorders - deep sequencing v2.5 | ATP2A2 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: ATP2A2. Tag Q3_23_NHS_review tag was added to gene: ATP2A2. |
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| Mosaic skin disorders - deep sequencing v2.5 | ATP2A2 | Arina Puzriakova Classified gene: ATP2A2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.5 | ATP2A2 | Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update. At least 6 unrelated cases of mosaic Darier disease reported in literature. ATP2A2 is associated with a relevant phenotype in OMIM that also mentions somatic mosaic disease. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.5 | ATP2A2 | Arina Puzriakova Gene: atp2a2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.4 | ATP2A2 | Arina Puzriakova Phenotypes for gene: ATP2A2 were changed from to Segmental Darier disease OMIM:124200; Darier-White disease OMIM:124200; Acrokeratosis verruciformis, OMIM:101900 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.3 | ATP2A2 | Arina Puzriakova Publications for gene: ATP2A2 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.6 | ARAF |
Arina Puzriakova Tag treatable was removed from gene: ARAF. Tag Q3_23_NHS_review tag was added to gene: ARAF. |
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| Mosaic skin disorders - deep sequencing v2.2 | ARAF | Arina Puzriakova Tag treatable tag was added to gene: ARAF. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.6 | ARAF | Arina Puzriakova Tag treatable tag was added to gene: ARAF. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.6 | ARAF |
Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Tom Cullup (GOSH). ARAF is not currently associated with any phenotype in OMIM or G2P. Although only two patients have been reported with the same missense variant, functional studies including an animal model provide strong support of pathogenicity (outlined below). Evidence of this variant specific gene-disease relationship is sufficiently compelling but the phenotype is more within scope of the R110 Segmental overgrowth disorders – Deep sequencing panel. Therefore rating as amber on this panel and green on R110. - PMID: 31263281 (2019): To date, only two unrelated patients have been reported with the same missense GoF variant in ARAF (c.640T>C:p.S214P) who both had a complex lymphatic anomaly (no haplotype analysis was done). Cells transduced with ARAF-S214P showed elevated ERK1/2 activity, enhanced lymphangiogenic capacity, and disassembly of actin skeleton and VE-cadherin junctions. A zebrafish model recapitulated the lymphatic phenotype. The cellular, zebrafish and patient clinical phenotypes were all rescued with with a MEK inhibitor.; to: Comment on list classification: New gene added by Tom Cullup (GOSH). ARAF is not currently associated with any phenotype in OMIM or G2P. Although only two patients have been reported with the same missense variant, functional studies including an animal model provide strong support of pathogenicity (outlined below). Evidence of this variant specific gene-disease relationship is sufficiently compelling to rate this gene as green at the next GMS panel update. - PMID: 31263281 (2019): To date, only two unrelated patients have been reported with the same missense GoF variant in ARAF (c.640T>C:p.S214P) who both had a complex lymphatic anomaly (no haplotype analysis was done). Cells transduced with ARAF-S214P showed elevated ERK1/2 activity, enhanced lymphangiogenic capacity, and disassembly of actin skeleton and VE-cadherin junctions. A zebrafish model recapitulated the lymphatic phenotype. The cellular, zebrafish and patient clinical phenotypes were all rescued with with a MEK inhibitor. |
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| Segmental overgrowth disorders - Deep sequencing v3.6 | ARAF | Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: ARAF. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.6 | ARAF | Arina Puzriakova Entity copied from Mosaic skin disorders - deep sequencing v2.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental overgrowth disorders - Deep sequencing v3.6 | ARAF |
Arina Puzriakova gene: ARAF was added gene: ARAF was added to Segmental overgrowth disorders - Deep sequencing. Sources: Expert Review Amber,Expert list Mode of inheritance for gene: ARAF was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: ARAF were set to 31263281 Phenotypes for gene: ARAF were set to central conducting lymphatic anomaly Penetrance for gene: ARAF were set to unknown Mode of pathogenicity for gene: ARAF was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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| Mosaic skin disorders - deep sequencing v2.2 | ARAF | Arina Puzriakova Classified gene: ARAF as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mosaic skin disorders - deep sequencing v2.2 | ARAF |
Arina Puzriakova Added comment: Comment on list classification: New gene added by Tom Cullup (GOSH). ARAF is not currently associated with any phenotype in OMIM or G2P. Although only two patients have been reported with the same missense variant, functional studies including an animal model provide strong support of pathogenicity (outlined below). Evidence of this variant specific gene-disease relationship is sufficiently compelling but the phenotype is more within scope of the R110 Segmental overgrowth disorders – Deep sequencing panel. Therefore rating as amber on this panel and green on R110. - PMID: 31263281 (2019): To date, only two unrelated patients have been reported with the same missense GoF variant in ARAF (c.640T>C:p.S214P) who both had a complex lymphatic anomaly (no haplotype analysis was done). Cells transduced with ARAF-S214P showed elevated ERK1/2 activity, enhanced lymphangiogenic capacity, and disassembly of actin skeleton and VE-cadherin junctions. A zebrafish model recapitulated the lymphatic phenotype. The cellular, zebrafish and patient clinical phenotypes were all rescued with with a MEK inhibitor. |
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| Mosaic skin disorders - deep sequencing v2.2 | ARAF | Arina Puzriakova Gene: araf has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DAGLA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.209 | DAGLA | Achchuthan Shanmugasundram Phenotypes for gene: DAGLA were changed from developmental delay; ataxia; complex oculomotor abnormality to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.208 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Classified gene: DAGLA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are more than 3 unrelated cases associating monoallelic variants in this gene to intellectual disability. Hence, this gene can be promoted to Green rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.207 | DAGLA | Achchuthan Shanmugasundram Gene: dagla has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.206 | DAGLA | Achchuthan Shanmugasundram Publications for gene: DAGLA were set to 35737950 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.206 | DAGLA | Achchuthan Shanmugasundram Publications for gene: DAGLA were set to PMID: 35737950 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.205 | DAGLA | Achchuthan Shanmugasundram changed review comment from: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. Of these nine children, five had intellectual disability and one had low average IQ (PMID:35737950).; to: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. Of these nine children, five had intellectual disability and one had low average IQ. In addition, the functional data suggests potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect (PMID:35737950). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.205 | DAGLA | Achchuthan Shanmugasundram changed review comment from: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. Of these nine children, five had intellectual disability and one had low average IQ (PMID:35737950).; to: As reviewed by Irina Ziravecka, there are nine children from eight unrelated families reported with heterozygous de novo variants in DAGLA gene and presenting with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. Of these nine children, five had intellectual disability and one had low average IQ (PMID:35737950). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.205 | DAGLA | Achchuthan Shanmugasundram reviewed gene: DAGLA: Rating: GREEN; Mode of pathogenicity: None; Publications: 35737950; Phenotypes: intellectual disability, MONDO:0001071; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.12 | PYGM |
Siying Lin gene: PYGM was added gene: PYGM was added to Retinal disorders. Sources: Literature Mode of inheritance for gene: PYGM was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PYGM were set to PMID 30316539 Phenotypes for gene: PYGM were set to Macular dystrophy, retinopathy Mode of pathogenicity for gene: PYGM was set to Other Review for gene: PYGM was set to GREEN Added comment: Mahroo et al (PMID 30316539) report on 4 individuals with McArdle disease and biallelic variants in PYGM and similar retinopathy affecting the macula. Screening results for mutations in a number of macular dystrophy genes were negative, supporting the association of this retinopathy with McArdle disease Sources: Literature |
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| Hereditary ataxia with onset in adulthood v4.15 | TDP1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: TDP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.15 | TDP1 | Achchuthan Shanmugasundram edited their review of gene: TDP1: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.15 | TDP1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: This gene can now be promoted to AMBER as there are three unrelated cases. The "founder-effect" tag has been added as they are all of Middle Eastern descent and harboured the same homozygous variant. However, the additional patient reported by Ian Berry (Leeds Genetics Laboratory) had the same variant in compound heterozygous state with another novel variant. Hence, this gene can be considered for promotion to GREEN rating at the next major review.; to: Comment on list classification: This gene can now be promoted to AMBER as there are three unrelated cases. The "founder-effect" tag has been added as they are all of Middle Eastern descent and harboured the same homozygous variant. However, the additional patient reported by Ian Berry (Leeds Genetics Laboratory) had the same variant in compound heterozygous state with another novel variant. As there is an additional variant reported, this gene can be considered for promotion to GREEN rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.15 | TDP1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: This gene can now be promoted to AMBER as there are three unrelated cases. The "founder-effect" tag has been added as they are all of Middle Eastern descent and harboured the same homozygous variant. Hence, it cannot be promoted to green rating.; to: Comment on list classification: This gene can now be promoted to AMBER as there are three unrelated cases. The "founder-effect" tag has been added as they are all of Middle Eastern descent and harboured the same homozygous variant. However, the additional patient reported by Ian Berry (Leeds Genetics Laboratory) had the same variant in compound heterozygous state with another novel variant. Hence, this gene can be considered for promotion to GREEN rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paroxysmal central nervous system disorders v3.1 | RHOBTB2 | Dmitrijs Rots reviewed gene: RHOBTB2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.80 | AMOTL1 | Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: AMOTL1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.80 | AMOTL1 | Arina Puzriakova Publications for gene: AMOTL1 were set to 33026150; 30375152 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.79 | AMOTL1 | Arina Puzriakova Classified gene: AMOTL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.79 | AMOTL1 |
Arina Puzriakova Added comment: Comment on list classification: There is now sufficient evidence to rate this gene as Green at the next GMS panel update. At least 16 individuals from 12 families have been identified with heterozygous variants in a AMOTL1 hotspot (PMIDs: 30375152; 33026150; 36751037). The most common clinical features were orofacial clefting (15/16; 94%), large and dysplastic ears (10/16; 62.5%), congenital heart disease (8/16; 50%), tall stature (7/16; 44%), hearing loss (5/16; 31%), liver disease (5/16; 31%), and neurodevelopmental disease (5/16; 31%). |
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| Clefting v4.79 | AMOTL1 | Arina Puzriakova Gene: amotl1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.170 | MASP1 | Achchuthan Shanmugasundram reviewed gene: MASP1: Rating: AMBER; Mode of pathogenicity: None; Publications: 33765348, 36980886; Phenotypes: 3MC syndrome 1, OMIM:257920; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.90 | ACAN | Arina Puzriakova commented on gene: ACAN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.170 | KANSL1 | Achchuthan Shanmugasundram reviewed gene: KANSL1: Rating: RED; Mode of pathogenicity: None; Publications: 26424144, 29093661, 36980886; Phenotypes: craniosynostosis, MONDO:0015469; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood solid tumours v4.5 | FBXW7 | Arina Puzriakova Classified gene: FBXW7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood solid tumours v4.5 | FBXW7 |
Arina Puzriakova Added comment: Comment on list classification: Rating Amber as at present I do not think there is enough evidence to classify this as a diagnostic-grade cancer gene. There are previous reports of dn/inh germline variants in individuals (likely 7) with tumor predisposition, two had structural alternations that affected other genomic regions and the others were identified from a targeted Wilms cohort. FBXW7 heterozygous variants have also been associated with a neurodevelopmental disorder (OMIM:620012; G2P - moderate) but these individuals not shown malignancy. FBXW7 is not linked to a cancer phenotype in OMIM or G2P. Nonetheless this is a tumour suppressor gene that is worth monitoring for new evidence linking to cancer susceptibility (added watchlist tag). |
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| Childhood solid tumours v4.5 | FBXW7 | Arina Puzriakova Gene: fbxw7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood solid tumours v4.4 | FBXW7 | Arina Puzriakova Phenotypes for gene: FBXW7 were changed from Developmental delay, hypotonia, and impaired language to Wilms tumor, MONDO:0006058; Rhabdoid tumor, MONDO:0002728 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood solid tumours v4.3 | FBXW7 | Arina Puzriakova Publications for gene: FBXW7 were set to 30885698 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood solid tumours v4.2 | FBXW7 | Arina Puzriakova Tag watchlist tag was added to gene: FBXW7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood solid tumours v4.2 | FBXW7 | Arina Puzriakova reviewed gene: FBXW7: Rating: ; Mode of pathogenicity: None; Publications: 19963109, 20332316, 26482194, 30885698; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.5 | CDH1 | Arina Puzriakova Publications for gene: CDH1 were set to 36436516 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.4 | CDH1 | Arina Puzriakova Phenotypes for gene: CDH1 were changed from Lobular breast cancer to Diffuse gastric and lobular breast cancer syndrome with or without cleft lip and/or palate, OMIM:137215 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.3 | CDH1 |
Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: CDH1. Tag Q3_23_expert_review tag was added to gene: CDH1. |
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| Breast cancer pertinent cancer susceptibility v2.3 | CDH1 | Arina Puzriakova Classified gene: CDH1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.3 | CDH1 |
Arina Puzriakova Added comment: Comment on list classification: New gene added to this panel by Lauma Freimane. Germline heterozygous variants have been found in diffuse gastric and lobular breast cancer syndrome. Patients may develop lobular breast cancer only or lobular breast cancer with gastric cancer. Lobular carcinoma of the breast has been reported in up to 60% of female carriers. Overall there is sufficient evidence to classify this as a breast cancer susceptibility gene. However, it should be noted that this gene is already covered by a targeted panel, R215 CDH1-related cancer syndrome. Will leave the decision with the GMS expert group as to whether this phenotype should also be covered by this panel. |
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| Breast cancer pertinent cancer susceptibility v2.3 | CDH1 | Arina Puzriakova Gene: cdh1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.170 | SCARF2 | Achchuthan Shanmugasundram reviewed gene: SCARF2: Rating: RED; Mode of pathogenicity: None; Publications: 29168297, 29620724, 36980886; Phenotypes: Van den Ende-Gupta syndrome, OMIM:600920, craniosynostosis, MONDO:0015469; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.170 | ZCCHC11 |
Achchuthan Shanmugasundram gene: ZCCHC11 was added gene: ZCCHC11 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: ZCCHC11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ZCCHC11 were set to 28808027; 36980886 Phenotypes for gene: ZCCHC11 were set to craniosynostosis, MONDO:0015469 Review for gene: ZCCHC11 was set to RED Added comment: An individual was described with metopic synostosis and a novel de novo frameshift variant in ZCCHC11 (p.Glu1275fs) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.169 | ZBTB20 |
Achchuthan Shanmugasundram gene: ZBTB20 was added gene: ZBTB20 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: ZBTB20 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ZBTB20 were set to 34429528; 36980886 Phenotypes for gene: ZBTB20 were set to Primrose syndrome, OMIM:259050; craniosynostosis, MONDO:0015469 Review for gene: ZBTB20 was set to RED Added comment: A de novo missense variant (c.1948A>C; p.Asn650His) was identified in an individual from the 100k genomes project with craniosynostosis, congenital heart disease, intellectual disability, and spinal anomalies (PMID:34429528). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.168 | TWIST2 | Achchuthan Shanmugasundram Publications for gene: TWIST2 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.167 | TWIST2 | Achchuthan Shanmugasundram Mode of inheritance for gene: TWIST2 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.166 | TWIST2 | Achchuthan Shanmugasundram reviewed gene: TWIST2: Rating: RED; Mode of pathogenicity: None; Publications: 31292255, 36980886; Phenotypes: craniosynostosis, MONDO:0015469; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.166 | TMEM251 |
Achchuthan Shanmugasundram gene: TMEM251 was added gene: TMEM251 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: TMEM251 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TMEM251 were set to 33252156; 36980886 Phenotypes for gene: TMEM251 were set to Dysostosis multiplex, Ain-Naz type, OMIM:619345; craniosynostosis, MONDO:0015469 Review for gene: TMEM251 was set to RED Added comment: Whole-exome sequencing identified two homozygous variants c.133C>T/ p.Arg45Trp (absent from gnomAD) and c.215dupA/ p.Tyr72Ter (2 alleles in gnomAD, annotated as pathogenic in ClinVar), in two families. Immunofluorescence and confocal studies show that the p.Arg45Trp mutant TMEM251 protein was targeted less efficiently to the Golgi complex compared to wildtype protein (PMID:33252156). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.165 | SRCAP |
Achchuthan Shanmugasundram gene: SRCAP was added gene: SRCAP was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SRCAP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SRCAP were set to 33288889; 36980886 Review for gene: SRCAP was set to RED Added comment: One individual was described with a stop-gain variant in SRCAP (c.7303C>T; p.Arg2435Ter) in the Norwegian cohort (PMID:33288889). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.164 | SPRY4 |
Achchuthan Shanmugasundram gene: SPRY4 was added gene: SPRY4 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SPRY4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SPRY4 were set to 28808027; 36980886 Phenotypes for gene: SPRY4 were set to craniosynostosis, MONDO:0015469 Review for gene: SPRY4 was set to RED Added comment: An individual was described with a heterozygous de novo variant in SPRY4 (p.Glu160Ter) (PMID:28808027). This gene has a low pLI (0) suggesting tolerance to loss-of-function. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.163 | SP7 |
Achchuthan Shanmugasundram gene: SP7 was added gene: SP7 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SP7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SP7 were set to 35121733; 36980886 Phenotypes for gene: SP7 were set to craniosynostosis, MONDO:0015469 Review for gene: SP7 was set to RED Added comment: A de novo missense variant (c.926 C>G; p.Ser309Trp) in SP7 was identified in a patient with craniosynostosis, cranial hyperostosis, and long bone fragility. Mice with the corresponding variant also show a complex skeletal phenotype distinct from that of Sp7-null mice (PMID:35121733). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.162 | SMURF1 |
Achchuthan Shanmugasundram changed review comment from: An individual was described with metopic synostosis and a de novo variant in SMURF1 (p.Arg468Trp) (PMID:28808027) Sources: Literature; to: An individual was described with metopic synostosis and a de novo variant in SMURF1 (p.Arg468Trp) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.162 | SMURF1 |
Achchuthan Shanmugasundram gene: SMURF1 was added gene: SMURF1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SMURF1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SMURF1 were set to 28808027; 36980886 Phenotypes for gene: SMURF1 were set to craniosynostosis, MONDO:0015469 Review for gene: SMURF1 was set to RED Added comment: An individual was described with metopic synostosis and a de novo variant in SMURF1 (p.Arg468Trp) (PMID:28808027) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.161 | SMC1A |
Achchuthan Shanmugasundram gene: SMC1A was added gene: SMC1A was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SMC1A was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: SMC1A were set to 29037998; 36980886 Phenotypes for gene: SMC1A were set to Cornelia de Lange syndrome 2, OMIM:300590; craniosynostosis, MONDO:0015469 Review for gene: SMC1A was set to RED Added comment: An X-linked dominant variant (c.3581A>G; p.Tyr1194Cys) was identified in an individual with Cornelia de Lange syndrome (characterised by dysmorphic facial features, growth, and developmental delay and syndromic craniosynostosis). Their mother was mosaic for the variant (PMID:29037998). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.160 | SMARCD2 |
Achchuthan Shanmugasundram gene: SMARCD2 was added gene: SMARCD2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SMARCD2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SMARCD2 were set to 28808027; 36980886 Phenotypes for gene: SMARCD2 were set to craniosynostosis, MONDO:0015469 Review for gene: SMARCD2 was set to RED Added comment: An individual was described with metopic synostosis and a de novo variant in SMARCD2 (p.Arg73Ter) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.159 | SMAD2 |
Achchuthan Shanmugasundram gene: SMAD2 was added gene: SMAD2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SMAD2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SMAD2 were set to 34429528; 36980886 Phenotypes for gene: SMAD2 were set to Loeys-Dietz syndrome 6, OMIM:619656 Review for gene: SMAD2 was set to RED Added comment: A de novo variant in SMAD2 (c.1223T>C; p.Leu408Pro) was identified in an individual within the craniosynostosis cohort of the 100k genomes project. The variant was absent from gnomAD and was predicted to affect a residue within a functional domain (PMID:34429528). Sources: Literature |
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| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | EZR |
Boaz Palterer gene: EZR was added gene: EZR was added to Primary immunodeficiency or monogenic inflammatory bowel disease. Sources: Literature Mode of inheritance for gene: EZR was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EZR were set to 37301410 Phenotypes for gene: EZR were set to hypogammaglobulinemia; immunodeficiency Penetrance for gene: EZR were set to unknown Review for gene: EZR was set to RED Added comment: One kindred with 1 affected subject (homozygous EZR p.A129T), disease segregates with the variant. Extensive functional analysis. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.158 | SIX2 |
Achchuthan Shanmugasundram gene: SIX2 was added gene: SIX2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SIX2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SIX2 were set to 26581443; 36980886 Phenotypes for gene: SIX2 were set to six2-related frontonasal dysplasia, MONDO:0044628; craniosynostosis, MONDO:0015469 Review for gene: SIX2 was set to RED Added comment: A family with a dominantly inherited craniofacial phenotype (frontal bossing with high hairline, ptosis, hypertelorism, broad nasal tip, large anterior fontanelle, cranial base anomalies, and sagittal synostosis (only confirmed in one individual)) were identified on chromosomal microarray to harbour a heterozygous 108.3 kilobase deletion of chromosome 2p21 (disrupting SIX2 and the surround non-coding DNA) (PMID:26581443). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.157 | SH3BP4 |
Achchuthan Shanmugasundram gene: SH3BP4 was added gene: SH3BP4 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SH3BP4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SH3BP4 were set to 35080095; 36980886 Phenotypes for gene: SH3BP4 were set to craniosynostosis, MONDO:0015469 Review for gene: SH3BP4 was set to RED Added comment: A patient was described with a recessive variant in SH3BP4 (c.128C>A; p.Pro43His) in the Norwegian craniosynostosis cohort. The variant has a CADD score of 33 and a gnomAD allele frequency of 9.6 x 10-5 (no homozygotes are reported in gnomAD). The patient presented with a Chiari I malformation, exophthalmos, eating difficulties as an infant, microcephaly, recurrent infections, dysmorphic features, Kabuki-like syndrome, and pan-synostosis. This patient also harbours two variants in KMT2D: c.11599C>A; p.Gln3867Lys (CADD = 22) and c.7182C>A; p.Ser2394Arg (CADD = 20); gnomAD frequency 1.2 x 10-5 and absent, respectively (PMID:35080095). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.156 | SCN8A |
Achchuthan Shanmugasundram changed review comment from: A heterozygous duplication involving SCN8A was identified in an individual with hearing impairment, hypermobility, intellectual disability, ventricular septal defect and craniosynostosis (c.3924dup; p.Arg1309Thrfs*3) (PMID:34429528) Sources: Literature; to: A heterozygous duplication involving SCN8A was identified in an individual with hearing impairment, hypermobility, intellectual disability, ventricular septal defect and craniosynostosis (c.3924dup; p.Arg1309Thrfs*3) (PMID:34429528). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.156 | SCN8A |
Achchuthan Shanmugasundram gene: SCN8A was added gene: SCN8A was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: SCN8A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SCN8A were set to 34429528; 36980886 Phenotypes for gene: SCN8A were set to craniosynostosis, MONDO:0015469 Review for gene: SCN8A was set to RED Added comment: A heterozygous duplication involving SCN8A was identified in an individual with hearing impairment, hypermobility, intellectual disability, ventricular septal defect and craniosynostosis (c.3924dup; p.Arg1309Thrfs*3) (PMID:34429528) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.155 | RASAL2 |
Achchuthan Shanmugasundram gene: RASAL2 was added gene: RASAL2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: RASAL2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: RASAL2 were set to 28808027; 36980886 Phenotypes for gene: RASAL2 were set to craniosynostosis, MONDO:0015469 Review for gene: RASAL2 was set to RED Added comment: An individual was described with sagittal synostosis and a de novo variant in RASAL2 (p.Arg571Pro) (PMID:28808027) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.154 | PUF60 |
Achchuthan Shanmugasundram gene: PUF60 was added gene: PUF60 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: PUF60 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PUF60 were set to 36367278; 36980886 Phenotypes for gene: PUF60 were set to craniosynostosis, MONDO:0015469 Review for gene: PUF60 was set to RED Added comment: A patient presenting with Verheij syndrome, characterised by craniofacial dysmorphism, multiple congenital anomalies and variable neurodevelopmental delay, was identified with a heterozygous variant in the splicing factor PUF60 (c.436C>T; p.Arg146Cys). They displayed fusion of the coronal and sagittal suture (PMID:36367278). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.153 | PTH2R |
Achchuthan Shanmugasundram gene: PTH2R was added gene: PTH2R was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: PTH2R was set to Other Publications for gene: PTH2R were set to 26044810; 36980886 Phenotypes for gene: PTH2R were set to craniosynostosis, MONDO:0015469 Review for gene: PTH2R was set to RED Added comment: A boy presenting with sagittal and metopic synostosis was found to harbour a complex paracentric inversion involving 2q14.3 and 2q3. An intronic break of the PTH2R gene was detected by whole genome sequencing and fluorescence in situ hybridisation (PMID:26044810). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.152 | PSMD12 |
Achchuthan Shanmugasundram gene: PSMD12 was added gene: PSMD12 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: PSMD12 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: PSMD12 were set to 34429528; 36980886 Phenotypes for gene: PSMD12 were set to craniosynostosis, MONDO:0015469 Review for gene: PSMD12 was set to RED Added comment: A heterozygous variant was identified in the UK 100k genomes project (parents were not available for testing): c.1284G>A; p.Trp428* (PMID:34429528) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.151 | PSMC5 |
Achchuthan Shanmugasundram gene: PSMC5 was added gene: PSMC5 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: PSMC5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PSMC5 were set to 28808027; 36980886 Phenotypes for gene: PSMC5 were set to craniosynostosis, MONDO:0015469 Review for gene: PSMC5 was set to RED Added comment: An individual was described with metopic synostosis and a de novo variant in PSMC5 (p.Arg317Trp) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.150 | PSMC2 |
Achchuthan Shanmugasundram gene: PSMC2 was added gene: PSMC2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: PSMC2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: PSMC2 were set to 28808027; 36980886 Phenotypes for gene: PSMC2 were set to craniosynostosis, MONDO:0015469 Review for gene: PSMC2 was set to RED Added comment: An individual was described with metopic synostosis and a de novo variant in PSMC2 (p.Arg297Gly) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.149 | POLR2A |
Achchuthan Shanmugasundram gene: POLR2A was added gene: POLR2A was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: POLR2A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: POLR2A were set to 35080095; 36980886 Phenotypes for gene: POLR2A were set to Neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities, OMIM:618603; craniosynostosis, MONDO:0015469 Review for gene: POLR2A was set to RED Added comment: A de novo insertion was identified in the Norwegian sequencing study: c.4329_4330delinsAA; p.Ala1444Thr. The variant is absent from gnomAD (v.2.1.1) but is not predicted to affect a functional domain. The patient displayed metopic synostosis, impaired motor skills, hypospadias, hypermobile joints and hyperactive behaviour (PMID:35080095). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.148 | PITX2 |
Achchuthan Shanmugasundram gene: PITX2 was added gene: PITX2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: PITX2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: PITX2 were set to 36980886 Review for gene: PITX2 was set to RED Added comment: Tooze et al has reviewed in PMID:36980886 from unpublished data that two cases of de novo missense variants are known with craniosynostosis, but not reported. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.147 | OSTM1 | Achchuthan Shanmugasundram Phenotypes for gene: OSTM1 were changed from AR osteopetrosis 5 to Osteopetrosis, autosomal recessive 5, OMIM:259720; craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.146 | OSTM1 | Achchuthan Shanmugasundram Publications for gene: OSTM1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.145 | OSTM1 | Achchuthan Shanmugasundram Mode of inheritance for gene: OSTM1 was changed from to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.144 | OSTM1 | Achchuthan Shanmugasundram edited their review of gene: OSTM1: Changed phenotypes to: Osteopetrosis, autosomal recessive 5, OMIM:259720, craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.144 | OSTM1 | Achchuthan Shanmugasundram changed review comment from: An individual was reported with osteopetrosis, craniosynostosis, and Chiari malformation type 1 and two novel homozygous variants in OSTEM1. The first was a missense variant c.265T>A (p.Val122Asp), which was considered neutral. The second variant was a synonymous change (c.108C>T) but was predicted to create a new donor splice site and disrupt mRNA processing (PMID:23772242).; to: An individual was reported with osteopetrosis, craniosynostosis, and Chiari malformation type 1 and two novel homozygous variants in OSTEM1. The first was a missense variant c.265T>A (p.Val122Asp), which was considered neutral. The second variant was a synonymous change (c.108C>T) but was predicted to create a new donor splice site and disrupt mRNA processing (PMID:23772242). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.144 | OSTM1 | Achchuthan Shanmugasundram reviewed gene: OSTM1: Rating: RED; Mode of pathogenicity: None; Publications: 23772242, 36980886; Phenotypes: craniosynostosis, MONDO:0015469; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.144 | NTRK2 |
Achchuthan Shanmugasundram gene: NTRK2 was added gene: NTRK2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: NTRK2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: NTRK2 were set to 27884935; 36980886 Phenotypes for gene: NTRK2 were set to Obesity, hyperphagia, and developmental delay, OMIM:613886; craniosynostosis, MONDO:0015469 Review for gene: NTRK2 was set to RED Added comment: A heterozygous stop-gain variant was identified in an individual with unicoronal synostosis, language delay, hyperphagic obesity, and aggression (c.1330G>T; p.Gly444*). It was suspected that the variant arose de novo but the father’s sample was not available for testing (PMID:27884935). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.143 | NAA25 |
Achchuthan Shanmugasundram gene: NAA25 was added gene: NAA25 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: NAA25 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: NAA25 were set to 30152016; 36980886 Phenotypes for gene: NAA25 were set to craniosynostosis, MONDO:0015469 Review for gene: NAA25 was set to RED Added comment: One individual was described with sagittal synostosis to harbour a de novo frameshifting variant in NAA25 (p.Phe359fs*) (PMID:30152016). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.142 | MMP21 |
Achchuthan Shanmugasundram gene: MMP21 was added gene: MMP21 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: MMP21 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MMP21 were set to 34429528; 36980886 Phenotypes for gene: MMP21 were set to craniosynostosis, MONDO:0015469 Review for gene: MMP21 was set to RED Added comment: Compound heterozygous variants (c.671_684del/ p.Val224Glyfs*29 and c.775C>G/ p.His259Asp) were identified in an individual within the 100kGP with heterotaxy and craniosynostosis (PMID:34429528) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.141 | MED13L |
Achchuthan Shanmugasundram gene: MED13L was added gene: MED13L was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: MED13L was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: MED13L were set to 28371282; 36980886 Phenotypes for gene: MED13L were set to Impaired intellectual development and distinctive facial features with or without cardiac defects, OMIM:616789; craniosynostosis, MONDO:0015469 Review for gene: MED13L was set to RED Added comment: Two siblings exhibited an intragenic deletion of exons 3-14 resulting in MED13L haploinsufficiency syndrome (intellectual disability, developmental delay, heart defects and dysmorphic features). The deletion was inherited from their mother who showed low frequency mosaicism. The older sibling also presented with craniosynostosis (PMID:28371282). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.140 | MACF1 |
Achchuthan Shanmugasundram gene: MACF1 was added gene: MACF1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: MACF1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: MACF1 were set to 28808027; 36980886 Phenotypes for gene: MACF1 were set to craniosynostosis, MONDO:0015469 Review for gene: MACF1 was set to RED Added comment: An individual was described with sagittal synostosis and a novel splicing variant in MACF1 (IVS89+1G>A) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.139 | KPTN | Achchuthan Shanmugasundram Classified gene: KPTN as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.139 | KPTN | Achchuthan Shanmugasundram Gene: kptn has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.138 | KPTN |
Achchuthan Shanmugasundram gene: KPTN was added gene: KPTN was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: KPTN was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: KPTN were set to 24239382; 36980886 Phenotypes for gene: KPTN were set to Intellectual developmental disorder, autosomal recessive 41, OMIM:615637; craniosynostosis, MONDO:0015469 Review for gene: KPTN was set to AMBER Added comment: Four families were described with variants in KPTN and suspected craniosynostosis. Sagittal synostosis was confirmed in one individual from a family with three affected individuals. All families harboured a variant encoding p.Ser259*; this was homozygous in four individuals and in trans with another heterozygous variant (p.Met241_Gln246dup) in five individuals (PMID:24239382). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.137 | KMT5B |
Achchuthan Shanmugasundram gene: KMT5B was added gene: KMT5B was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: KMT5B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: KMT5B were set to 34429528; 36980886 Phenotypes for gene: KMT5B were set to craniosynostosis, MONDO:0015469 Review for gene: KMT5B was set to RED Added comment: A de novo loss of function variant was identified within the 100kGP craniosynostosis cohort: c.557T>A; p.Leu186* (PMID:34429528). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.136 | IFRD1 |
Achchuthan Shanmugasundram gene: IFRD1 was added gene: IFRD1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: IFRD1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: IFRD1 were set to 35997807; 36980886 Phenotypes for gene: IFRD1 were set to craniosynostosis, MONDO:0015469 Review for gene: IFRD1 was set to RED Added comment: A de novo variant was identified in a cohort of patients with lambdoid synostosis (p.Gly6fs*) (PMID:35997807). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.135 | HIST1H1E |
Achchuthan Shanmugasundram gene: HIST1H1E was added gene: HIST1H1E was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature new-gene-name tags were added to gene: HIST1H1E. Mode of inheritance for gene: HIST1H1E was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: HIST1H1E were set to 36118902; 36980886 Phenotypes for gene: HIST1H1E were set to craniosynostosis, MONDO:0015469 Review for gene: HIST1H1E was set to RED Added comment: A patient with syndromic unilambdoid synostosis was found to harbour a frameshifting variant in HIST1H1E (c.433_434insC; p.Thr146Hisfs*50). The variant is reported as pathogenic for Rahman syndrome in ClinVar and absent from gnomAD (PMID:36118902). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.134 | HDAC4 |
Achchuthan Shanmugasundram gene: HDAC4 was added gene: HDAC4 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature cnv tags were added to gene: HDAC4. Mode of inheritance for gene: HDAC4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: HDAC4 were set to 33288889; 36980886 Phenotypes for gene: HDAC4 were set to craniosynostosis, MONDO:0015469 Review for gene: HDAC4 was set to RED Added comment: A patient was described with two copy number variants: g.233110452_ 243028452 and del g.210300_ 8664358dup. The second variant was maternally inherited (PMID:33288889) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.133 | H3F3B |
Achchuthan Shanmugasundram gene: H3F3B was added gene: H3F3B was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: H3F3B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: H3F3B were set to 33268356; 36980886 Phenotypes for gene: H3F3B were set to craniosynostosis, MONDO:0015469 Review for gene: H3F3B was set to RED Added comment: In a cohort of 33 patients with H3F3A variants and 13 patients with H3F3B variants, 5/13 (~40%) individuals with H3F3B variants were reported with “craniosynostosis or abnormal head shape”. Of these, it is not clear if these were radiologically confirmed and what proportion of this subset of patients had synostosis compared to dysmorphic features (PMID:33268356). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.132 | H3F3A |
Achchuthan Shanmugasundram gene: H3F3A was added gene: H3F3A was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: H3F3A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: H3F3A were set to 33268356; 36980886 Phenotypes for gene: H3F3A were set to craniosynostosis, MONDO:0015469 Review for gene: H3F3A was set to RED Added comment: In a cohort of 33 patients with H3F3A variants and 13 patients with H3F3B variants, 9/33 (~30%) individuals with H3F3A variants were reported with “craniosynostosis or abnormal head shape”. Of these, it is not clear if these were radiologically confirmed and what proportion of this subset of patients had synostosis compared to dysmorphic features (PMID:33268356). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.131 | GLIS3 |
Achchuthan Shanmugasundram gene: GLIS3 was added gene: GLIS3 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: GLIS3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GLIS3 were set to 26259131; 36980886 Phenotypes for gene: GLIS3 were set to craniosynostosis, MONDO:0015469 Review for gene: GLIS3 was set to RED Added comment: One patient was described with a variant in GLIS3 and sagittal craniosynostosis requiring surgical intervention. The patient harboured a homozygous deletion of exons 9 – 11; consanguinity was not confirmed but suspected (PMID:26259131). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.130 | GPC4 |
Achchuthan Shanmugasundram gene: GPC4 was added gene: GPC4 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: GPC4 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: GPC4 were set to 31292255; 36980886 Phenotypes for gene: GPC4 were set to craniosynostosis, MONDO:0015469 Review for gene: GPC4 was set to RED Added comment: A variant in GPC4 was identified in an individual with syndromic craniosynostosis. The variant encoding p.Val152fs arose de novo in the mother (PMID:31292255) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.129 | GLI2 |
Achchuthan Shanmugasundram gene: GLI2 was added gene: GLI2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: GLI2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: GLI2 were set to 31292255; 36980886 Phenotypes for gene: GLI2 were set to craniosynostosis, MONDO:0015469 Review for gene: GLI2 was set to RED Added comment: A de novo GLI2 variant (p.Ala551Thr) was identified in an individual with syndromic craniosynostosis (PMID:31292255). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.128 | FUZ |
Achchuthan Shanmugasundram gene: FUZ was added gene: FUZ was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: FUZ was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FUZ were set to 34719684; 36980886 Phenotypes for gene: FUZ were set to craniosynostosis, MONDO:0015469 Review for gene: FUZ was set to RED Added comment: A pair of monozygotic twins were described with craniosynostosis and a novel variant in FUZ (c.851G>C; p.Arg284Pro) (PMID:34719684). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.127 | FTO |
Achchuthan Shanmugasundram gene: FTO was added gene: FTO was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: FTO was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FTO were set to 26697951; 36980886 Phenotypes for gene: FTO were set to craniosynostosis, MONDO:0015469 Review for gene: FTO was set to RED Added comment: A homozygous variant in FTO (c.956G>A; p.Arg322Gln) was described in one individual with multiple malformation syndrome, which included craniosynostosis. Craniosynostosis is not a consistent feature of variants in FTO (PMID:26697951). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.126 | FOXO1 |
Achchuthan Shanmugasundram gene: FOXO1 was added gene: FOXO1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: FOXO1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: FOXO1 were set to 35997807; 36980886 Phenotypes for gene: FOXO1 were set to craniosynostosis, MONDO:0015469 Review for gene: FOXO1 was set to RED Added comment: PMID:35997807 reported a cohort of patients with lambdoid synostosis, where a de novo variant (p.Arg180Trp) was identified in FOXO1. Hence, this gene should be added with a red rating. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.125 | FOXP2 |
Achchuthan Shanmugasundram gene: FOXP2 was added gene: FOXP2 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: FOXP2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: FOXP2 were set to 35080095; 36980886 Phenotypes for gene: FOXP2 were set to craniosynostosis, MONDO:0015469 Review for gene: FOXP2 was set to RED Added comment: A familial variant in FOXP2 (c.484del; p.Gln162fs) was identified in individuals with developmental delay, hypermetropia, orofacial dyspraxia and sagittal craniosynostosis. The variant is absent from gnomAD (PMID:35080095) Sources: Literature |
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| Paediatric disorders - additional genes v3.3 | FOXL2 | Arina Puzriakova commented on gene: FOXL2: Helen Brittain (Genomics England Clinical Team) supports inclusion of BPES and blepharophimosis genes on this panel as these are features that would be considered under the dysmorphism indication. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.7 | ISCA-37467-Gain | Arina Puzriakova changed review comment from: Comment on list classification: Adding to this panel under the suggestion of Helen Brittain (Genomics England Clinical Team) as this region is associated with limb malformation phenotypes. Enough evidence to rate this gene as Green at the next GMS panel update.; to: Comment on list classification: Adding to this panel under the suggestion of Helen Brittain (Genomics England Clinical Team) as this region is associated with limb malformation phenotypes. Enough evidence to rate as Green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.7 | ISCA-37467-Gain | Arina Puzriakova Tag Q3_23_promote_green tag was added to Region: ISCA-37467-Gain. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.7 | ISCA-37467-Gain | Arina Puzriakova Classified Region: ISCA-37467-Gain as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.7 | ISCA-37467-Gain | Arina Puzriakova Added comment: Comment on list classification: Adding to this panel under the suggestion of Helen Brittain (Genomics England Clinical Team) as this region is associated with limb malformation phenotypes. Enough evidence to rate this gene as Green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.7 | ISCA-37467-Gain | Arina Puzriakova Region: isca-37467-gain has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.6 | ISCA-37467-Gain | Arina Puzriakova Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.6 | ISCA-37467-Gain | Arina Puzriakova Entity copied from Clefting v4.78 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.6 | ISCA-37467-Gain |
Arina Puzriakova Region: ISCA-37467-Gain was added Region: ISCA-37467-Gain was added to Limb disorders. Sources: ClinGen,Expert Review Green Mode of inheritance for Region: ISCA-37467-Gain was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for Region: ISCA-37467-Gain were set to 19291772; 18417549; 18178630 Phenotypes for Region: ISCA-37467-Gain were set to human triphalangeal thumb and polysyndactyly (TPT-PS) phenotype; 174500; Triphalangeal thumbpolysyndactyly syndrome; syndactyly type IV with tibial hypoplasia |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.124 | FOXP1 |
Achchuthan Shanmugasundram gene: FOXP1 was added gene: FOXP1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: FOXP1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: FOXP1 were set to 29330474; 36980886 Phenotypes for gene: FOXP1 were set to craniosynostosis, MONDO:0015469 Review for gene: FOXP1 was set to RED Added comment: Whole exome sequencing identified a de novo splicing variant in FOXP1 (c.1428+1 G>A; p.Ala450GLyfs*13) in a patient with syndromic intellectual disability and trigonocephaly (PMID:29330474). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.123 | EXTL3 |
Achchuthan Shanmugasundram changed review comment from: A recessive variant in EXTL3 (c.2392G>A; p.Val798Met) was identified in a patient with metopic craniosynostosis, intellectual disability, short stature, microcephaly, hip dysplasia, kyphosis, delayed skeletal age and immunodeficiency. The variant is absent from gnomAD and affects the glycosyl transferase family 64 domain (PMID:35080095). Craniosynostosis has been recorded as part of the phenotype in OMIM (MIM #617425) Sources: Literature; to: A recessive variant in EXTL3 (c.2392G>A; p.Val798Met) was identified in a patient with metopic craniosynostosis, intellectual disability, short stature, microcephaly, hip dysplasia, kyphosis, delayed skeletal age and immunodeficiency. The variant is absent from gnomAD and affects the glycosyl transferase family 64 domain (PMID:35080095). Craniosynostosis has been recorded as part of the phenotype in OMIM (MIM #617425). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.123 | EXTL3 |
Achchuthan Shanmugasundram changed review comment from: A recessive variant in EXTL3 (c.2392G>A; p.Val798Met) was identified in a patient with metopic craniosynostosis, intellectual disability, short stature, microcephaly, hip dysplasia, kyphosis, delayed skeletal age and immunodeficiency. The variant is absent from gnomAD and affects the glycosyl transferase family 64 domain (PMID:35080095). Sources: Literature; to: A recessive variant in EXTL3 (c.2392G>A; p.Val798Met) was identified in a patient with metopic craniosynostosis, intellectual disability, short stature, microcephaly, hip dysplasia, kyphosis, delayed skeletal age and immunodeficiency. The variant is absent from gnomAD and affects the glycosyl transferase family 64 domain (PMID:35080095). Craniosynostosis has been recorded as part of the phenotype in OMIM (MIM #617425) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.123 | EXTL3 | Achchuthan Shanmugasundram edited their review of gene: EXTL3: Changed phenotypes to: Immunoskeletal dysplasia with neurodevelopmental abnormalities, OMIM:617425 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.123 | EXTL3 | Achchuthan Shanmugasundram Phenotypes for gene: EXTL3 were changed from craniosynostosis, MONDO:0015469 to Immunoskeletal dysplasia with neurodevelopmental abnormalities, OMIM:617425 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.122 | EXTL3 |
Achchuthan Shanmugasundram gene: EXTL3 was added gene: EXTL3 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: EXTL3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EXTL3 were set to 35080095; 36980886 Phenotypes for gene: EXTL3 were set to craniosynostosis, MONDO:0015469 Review for gene: EXTL3 was set to RED Added comment: A recessive variant in EXTL3 (c.2392G>A; p.Val798Met) was identified in a patient with metopic craniosynostosis, intellectual disability, short stature, microcephaly, hip dysplasia, kyphosis, delayed skeletal age and immunodeficiency. The variant is absent from gnomAD and affects the glycosyl transferase family 64 domain (PMID:35080095). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.121 | EIF5A |
Achchuthan Shanmugasundram gene: EIF5A was added gene: EIF5A was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: EIF5A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: EIF5A were set to 36118902; 36980886 Phenotypes for gene: EIF5A were set to craniosynostosis, MONDO:0015469 Review for gene: EIF5A was set to RED Added comment: An intronic variant was identified in EIF5A (c.271-1G>C) within the Chinese cohort in a patient with metopic synostosis (PMID:36118902). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.120 | EHMT1 |
Achchuthan Shanmugasundram gene: EHMT1 was added gene: EHMT1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: EHMT1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: EHMT1 were set to 33288889; 36980886 Phenotypes for gene: EHMT1 were set to craniosynostosis, MONDO:0015469 Review for gene: EHMT1 was set to RED Added comment: A de novo splicing variant was identified in EHMT1 (c.2018+1G>C) within the Norwegian cohort with syndromic craniosynostosis (PMID:33288889). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.119 | DVL3 |
Achchuthan Shanmugasundram gene: DVL3 was added gene: DVL3 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: DVL3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: DVL3 were set to 28808027; 36980886 Phenotypes for gene: DVL3 were set to craniosynostosis, MONDO:0015469 Review for gene: DVL3 was set to RED Added comment: An individual was described with sagittal synostosis and a de novo variant in DVL3 (p.Gly327fs*) (PMID:28808027). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.118 | DDX3X |
Achchuthan Shanmugasundram changed review comment from: A novel de novo missense variant was identified in the DDX3X gene (c.625C>G) by whole exome sequencing in a child with craniofacial dysmorphisms: brachycephaly and a flattened triangular-asymmetrical face characterized by micrognathia, mild hypertelorism, wide and prominent nose, short philtrum, thin lips and macroglossia (PMID:33789733). Exome-sequencing identified three distinct de novo heterozygous variants in DDX3X: c.1511G>A; p.(Gly504Glu) (Patient 1), c.1436_1439delinsTCTC; p.(Asp479Arg480delinsValSer) (Patient 2), and c.641_643delTCA; p.(Ile214del) (Patient 3). The patients showed severe intellectual disability/developmental disorders, microcephaly, and dysmorphic features. Plagiocephaly was observed in Patient 1 and Patient 2 was diagnosed with sensorineural hearing loss and trigonocephaly. However, craniosynostosis was only radiologically confirmed in Patient 2 (PMID:30936465). A de novo variant in DDX3X was identified in an additional patient with trigonocephaly, delay in speech acquisition and motor developmental delay: c.1616-2A>G; p.(?) (PMID:32530565). Sources: Literature; to: A novel de novo missense variant was identified in the DDX3X gene (c.625C>G) by whole exome sequencing in a child with craniofacial dysmorphisms: brachycephaly and a flattened triangular-asymmetrical face characterized by micrognathia, mild hypertelorism, wide and prominent nose, short philtrum, thin lips and macroglossia (PMID:33789733). Exome-sequencing identified three distinct de novo heterozygous variants in DDX3X: c.1511G>A; p.(Gly504Glu) (Patient 1), c.1436_1439delinsTCTC; p.(Asp479Arg480delinsValSer) (Patient 2), and c.641_643delTCA; p.(Ile214del) (Patient 3). The patients showed severe intellectual disability/developmental disorders, microcephaly, and dysmorphic features. Plagiocephaly was observed in Patient 1 and Patient 2 was diagnosed with sensorineural hearing loss and trigonocephaly. However, craniosynostosis was only radiologically confirmed in Patient 2 (PMID:30936465). A de novo variant in DDX3X was identified in an additional patient with trigonocephaly, delay in speech acquisition and motor developmental delay: c.1616-2A>G (PMID:32530565). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.118 | DDX3X | Achchuthan Shanmugasundram Classified gene: DDX3X as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.118 | DDX3X | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are five unrelated cases reported with DDX3X variants and likely craniosynostosis, only two are radiologically confirmed cases of craniosynostosis. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.118 | DDX3X | Achchuthan Shanmugasundram Gene: ddx3x has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.117 | DDX3X | Achchuthan Shanmugasundram Phenotypes for gene: DDX3X were changed from craniosynostosis, MONDO:0015469 to Intellectual developmental disorder, X-linked syndromic, Snijders Blok type, OMIM:300958; craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.116 | DDX3X | Achchuthan Shanmugasundram edited their review of gene: DDX3X: Changed phenotypes to: Intellectual developmental disorder, X-linked syndromic, Snijders Blok type, OMIM:300958, craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.116 | DDX3X |
Achchuthan Shanmugasundram gene: DDX3X was added gene: DDX3X was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: DDX3X was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: DDX3X were set to 30936465; 32530565; 33789733; 36980886 Phenotypes for gene: DDX3X were set to craniosynostosis, MONDO:0015469 Review for gene: DDX3X was set to AMBER Added comment: A novel de novo missense variant was identified in the DDX3X gene (c.625C>G) by whole exome sequencing in a child with craniofacial dysmorphisms: brachycephaly and a flattened triangular-asymmetrical face characterized by micrognathia, mild hypertelorism, wide and prominent nose, short philtrum, thin lips and macroglossia (PMID:33789733). Exome-sequencing identified three distinct de novo heterozygous variants in DDX3X: c.1511G>A; p.(Gly504Glu) (Patient 1), c.1436_1439delinsTCTC; p.(Asp479Arg480delinsValSer) (Patient 2), and c.641_643delTCA; p.(Ile214del) (Patient 3). The patients showed severe intellectual disability/developmental disorders, microcephaly, and dysmorphic features. Plagiocephaly was observed in Patient 1 and Patient 2 was diagnosed with sensorineural hearing loss and trigonocephaly. However, craniosynostosis was only radiologically confirmed in Patient 2 (PMID:30936465). A de novo variant in DDX3X was identified in an additional patient with trigonocephaly, delay in speech acquisition and motor developmental delay: c.1616-2A>G; p.(?) (PMID:32530565). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.115 | CTNNA1 |
Achchuthan Shanmugasundram gene: CTNNA1 was added gene: CTNNA1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: CTNNA1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CTNNA1 were set to 31292255; 36980886 Phenotypes for gene: CTNNA1 were set to craniosynostosis, MONDO:0015469 Review for gene: CTNNA1 was set to RED Added comment: A de novo insertion (p.Val374_375ins) was identified in an individual from a screen of patients with syndromic craniosynostosis. This patient had sagittal craniosynostosis (PMID:31292255). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.114 | COL11A1 |
Achchuthan Shanmugasundram gene: COL11A1 was added gene: COL11A1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: COL11A1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: COL11A1 were set to 34429528; 36980886 Phenotypes for gene: COL11A1 were set to craniosynostosis, MONDO:0015469 Review for gene: COL11A1 was set to RED Added comment: A de novo loss of function variant (c.2852+5G>A) was identified in an individual with craniosynostosis and a hearing impairment from the UK 100k genomes project (PMID:34429528) Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.113 | CHD3 |
Achchuthan Shanmugasundram gene: CHD3 was added gene: CHD3 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: CHD3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CHD3 were set to 30397230; 36980886 Phenotypes for gene: CHD3 were set to craniosynostosis, MONDO:0015469 Review for gene: CHD3 was set to RED Added comment: One of 35 individuals identified with Snijders Blok Campeau syndrome (neurodevelopmental disorder, macrocephaly and impaired speech and language) and with monoallelic variants in CHD3 gene (c.3482A>G; p.His1161Arg) presented with sagittal synostosis (PMID:30397230). In addition, one of 28 patients with sequence variants (c.52_53inv; p.Ser18Glu) in the DECIPHER database (https://www.deciphergenomics.org/) was reported with craniosynostosis as one of the phenotypes./ Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.112 | CDK8 |
Achchuthan Shanmugasundram gene: CDK8 was added gene: CDK8 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: CDK8 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CDK8 were set to 30905399; 36980886 Phenotypes for gene: CDK8 were set to craniosynostosis, MONDO:0015469 Review for gene: CDK8 was set to RED Added comment: Metopic synostosis was described in one individual out of 12 reported with variants in CDK8 from PMID:30905399. This individual harboured a de novo c.88G>A (p.Gly30Ser) variant. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.111 | CACNA1E | Achchuthan Shanmugasundram Phenotypes for gene: CACNA1E were changed from crannieynostosis, MONDO:0015469s to craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.110 | CACNA1E | Achchuthan Shanmugasundram edited their review of gene: CACNA1E: Changed phenotypes to: craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.110 | CACNA1E |
Achchuthan Shanmugasundram gene: CACNA1E was added gene: CACNA1E was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: CACNA1E was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CACNA1E were set to 32530565; 36980886 Phenotypes for gene: CACNA1E were set to crannieynostosis, MONDO:0015469s Review for gene: CACNA1E was set to RED Added comment: A heterozygous splice variant (c.3674+5A>G) was identified in an individual from a cohort of patients with trigonocephaly (PMID:32530565). Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.109 | BRWD3 |
Achchuthan Shanmugasundram changed review comment from: A de novo stop-gain variant (p.Gln1338*) was identified in an individual with craniosynostosis within the 100k genomes project cohort (PMID:34429528). In addition, one of 20 patients with sequence variants in BRWD3 gene from DECIPHER database (https://www.deciphergenomics.org/) was reported with craniosynostosis as one of the phenotypes. Sources: Literature; to: A de novo stop-gain variant (p.Gln1338*) was identified in an individual with craniosynostosis within the 100k genomes project cohort (PMID:34429528). In addition, one of 20 patients with sequence variants in BRWD3 gene (p.Gly707Val) from DECIPHER database (https://www.deciphergenomics.org/) was reported with craniosynostosis as one of the phenotypes. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.109 | BRWD3 | Achchuthan Shanmugasundram Phenotypes for gene: BRWD3 were changed from to craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.108 | BRWD3 | Achchuthan Shanmugasundram edited their review of gene: BRWD3: Changed phenotypes to: craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.108 | BRWD3 |
Achchuthan Shanmugasundram gene: BRWD3 was added gene: BRWD3 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: BRWD3 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: BRWD3 were set to 34429528; 36980886 Review for gene: BRWD3 was set to RED Added comment: A de novo stop-gain variant (p.Gln1338*) was identified in an individual with craniosynostosis within the 100k genomes project cohort (PMID:34429528). In addition, one of 20 patients with sequence variants in BRWD3 gene from DECIPHER database (https://www.deciphergenomics.org/) was reported with craniosynostosis as one of the phenotypes. Sources: Literature |
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| Nephrocalcinosis or nephrolithiasis v4.1 | SLC26A1 | Detlef Bockenhauer reviewed gene: SLC26A1: Rating: RED; Mode of pathogenicity: None; Publications: 36719378; Phenotypes: hyperoxaluria; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.107 | AXIN1 |
Achchuthan Shanmugasundram gene: AXIN1 was added gene: AXIN1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: AXIN1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: AXIN1 were set to 28808027; 36980886 Phenotypes for gene: AXIN1 were set to craniosynostosis, MONDO:0015469 Review for gene: AXIN1 was set to RED Added comment: PMID:28808027 reported an individual with sagittal synostosis and a de novo heterozygous variant in AXIN1 gene. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.106 | ARAP3 |
Achchuthan Shanmugasundram gene: ARAP3 was added gene: ARAP3 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: ARAP3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ARAP3 were set to 28808027; 36980886 Phenotypes for gene: ARAP3 were set to craniosynostosis, MONDO:0015469 Review for gene: ARAP3 was set to RED Added comment: PMID:28808027 reported an individual identified with a de novo variant in ARAP3 (IVS6+1delGT) and presenting with metopic synostosis. As there is only one case reported so far, this gene should be rated red. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.105 | ANKH | Achchuthan Shanmugasundram Classified gene: ANKH as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.105 | ANKH | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two cases reported in total with craniosynostosis. Hence, this gene can be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.105 | ANKH | Achchuthan Shanmugasundram Gene: ankh has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.104 | ANKH |
Achchuthan Shanmugasundram gene: ANKH was added gene: ANKH was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: ANKH was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ANKH were set to 36118902; 36980886 Phenotypes for gene: ANKH were set to Craniometaphyseal dysplasia, OMIM:123000; craniosynostosis, MONDO:0015469 Review for gene: ANKH was set to AMBER Added comment: PMID:36118902 reported a single patient with variant in ANKH (c.1129_1132delinsC; p.Phe377del) from a Chinese cohort with syndromic bicoronal and sagittal synostosis. This variant is reported as pathogenic for craniometaphyseal dysplasia in ClinVar and is absent from gnomAD v.2.1.1. DECIPHER database (https://www.deciphergenomics.org) reported craniosynostosis as one of the clinical presentations in a single patient with heterozygous sequence variant (c.559C>T; p.Arg187Trp) in ANKH gene. This variant was reported as likely pathogenic. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.103 | ACVRL1 |
Achchuthan Shanmugasundram changed review comment from: PMID:35997807 reported a cohort of patients with lambdoid synostosis, where a de novo variant (p.Val228Ile) in was identified in ACVRL1. Hence, this gene should be added with a red rating. Sources: Literature; to: PMID:35997807 reported a cohort of patients with lambdoid synostosis, where a de novo variant (p.Val228Ile) was identified in ACVRL1. Hence, this gene should be added with a red rating. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.103 | ACVR2A |
Achchuthan Shanmugasundram gene: ACVR2A was added gene: ACVR2A was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: ACVR2A was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ACVR2A were set to 35997807; 36980886 Phenotypes for gene: ACVR2A were set to craniosynostosis, MONDO:0015469 Review for gene: ACVR2A was set to RED Added comment: PMID:35997807 reported a cohort of patients with lambdoid synostosis, where a de novo variant (p.Thr63Ala) was identified in ACVR2A. Hence, this gene should be added with a red rating. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.102 | ACVRL1 | Achchuthan Shanmugasundram Phenotypes for gene: ACVRL1 were changed from to craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.101 | ACVRL1 | Achchuthan Shanmugasundram edited their review of gene: ACVRL1: Changed phenotypes to: craniosynostosis, MONDO:0015469 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.101 | ACVRL1 |
Achchuthan Shanmugasundram gene: ACVRL1 was added gene: ACVRL1 was added to Rare syndromic craniosynostosis or isolated multisuture synostosis. Sources: Literature Mode of inheritance for gene: ACVRL1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ACVRL1 were set to 35997807; 36980886 Review for gene: ACVRL1 was set to RED Added comment: PMID:35997807 reported a cohort of patients with lambdoid synostosis, where a de novo variant (p.Val228Ile) in was identified in ACVRL1. Hence, this gene should be added with a red rating. Sources: Literature |
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| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.100 | ABCC9 | Achchuthan Shanmugasundram changed review comment from: PMID:24352916 reported a Japanese family with Cantu syndrome, of which the boy had bicoronal synostosis, which was absent in the father. This gene should only be rated red as there is only one case reported so far.; to: PMID:24352916 reported a Japanese family with Cantu syndrome, of which the boy had bicoronal synostosis, which was absent in the father. Craniosynostosis has not previously been reported as part of Cantu syndrome. This gene should only be rated red as there is only one case reported so far. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.100 | ABCC9 | Achchuthan Shanmugasundram Publications for gene: ABCC9 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.99 | ABCC9 | Achchuthan Shanmugasundram Mode of inheritance for gene: ABCC9 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rare syndromic craniosynostosis or isolated multisuture synostosis v4.98 | ABCC9 | Achchuthan Shanmugasundram reviewed gene: ABCC9: Rating: RED; Mode of pathogenicity: None; Publications: 24352916, 36980886; Phenotypes: Hypertrichotic osteochondrodysplasia (Cantu syndrome), OMIM: 239850; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paroxysmal central nervous system disorders v3.1 | ALPK1 |
Dmitrijs Rots gene: ALPK1 was added gene: ALPK1 was added to Paroxysmal central nervous system disorders. Sources: Literature Mode of inheritance for gene: ALPK1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ALPK1 were set to PMID: 30967659 Phenotypes for gene: ALPK1 were set to ROSAH syndrome Mode of pathogenicity for gene: ALPK1 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: ALPK1 was set to GREEN Added comment: ALPK1 is associated with ROSAH syndrome, which commonly include episodic migraine or other headaches. Sources: Literature |
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| Severe microcephaly v4.28 | BUB1 | Arina Puzriakova Entity copied from Intellectual disability - microarray and sequencing v5.205 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.28 | BUB1 |
Arina Puzriakova gene: BUB1 was added gene: BUB1 was added to Severe microcephaly. Sources: Expert Review Amber,Literature Q4_22_promote_green tags were added to gene: BUB1. Mode of inheritance for gene: BUB1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: BUB1 were set to 35044816 Phenotypes for gene: BUB1 were set to Microcephaly 30, primary, autosomal recessive, OMIM:620183 Penetrance for gene: BUB1 were set to Complete |
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| Intellectual disability v5.205 | BUB1 | Arina Puzriakova Phenotypes for gene: BUB1 were changed from Congenital microcephaly; Global developmental delay; Intellectual disability; Abnormal heart morphology; Growth delay to Microcephaly 30, primary, autosomal recessive, OMIM:620183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | BUB1 | Arina Puzriakova commented on gene: BUB1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | BUB1 | Arina Puzriakova Tag Q4_22_MOI was removed from gene: BUB1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.11 | TAB2 | Arina Puzriakova Entity copied from Paediatric or syndromic cardiomyopathy v3.15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.11 | TAB2 |
Arina Puzriakova gene: TAB2 was added gene: TAB2 was added to Dilated and arrhythmogenic cardiomyopathy. Sources: Expert Review Amber,NHS GMS,London South GLH Q3_23_promote_green tags were added to gene: TAB2. Mode of inheritance for gene: TAB2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: TAB2 were set to 28464518; 29700987; 32183715; 34456334; 34990405; 34741306; 36000780; 37153890 Phenotypes for gene: TAB2 were set to Congenital heart defects, nonsyndromic, 2, OMIM:614980 |
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| Paediatric disorders - additional genes v3.3 | TAB2 | Arina Puzriakova Entity copied from Paediatric or syndromic cardiomyopathy v3.15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric disorders - additional genes v3.3 | TAB2 |
Arina Puzriakova gene: TAB2 was added gene: TAB2 was added to Paediatric disorders - additional genes. Sources: Expert Review Amber,NHS GMS,London South GLH Q3_23_promote_green tags were added to gene: TAB2. Mode of inheritance for gene: TAB2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: TAB2 were set to 28464518; 29700987; 32183715; 34456334; 34990405; 34741306; 36000780; 37153890 Phenotypes for gene: TAB2 were set to Congenital heart defects, nonsyndromic, 2, OMIM:614980 |
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| Paediatric or syndromic cardiomyopathy v3.15 | TAB2 | Arina Puzriakova Classified gene: TAB2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.15 | TAB2 | Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.15 | TAB2 | Arina Puzriakova Gene: tab2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.14 | TAB2 | Arina Puzriakova Mode of inheritance for gene: TAB2 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.13 | TAB2 | Arina Puzriakova Publications for gene: TAB2 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.12 | TAB2 | Arina Puzriakova Tag Q3_23_promote_green tag was added to gene: TAB2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.12 | TAB2 | Arina Puzriakova edited their review of gene: TAB2: Changed publications to: 28464518, 29700987, 32183715, 34456334, 34990405, 34741306, 36000780, 37153890; Changed phenotypes to: Congenital heart defects, nonsyndromic, 2, OMIM:614980 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.12 | TAB2 | Arina Puzriakova reviewed gene: TAB2: Rating: GREEN; Mode of pathogenicity: None; Publications: Congenital heart defects, nonsyndromic, 2, OMIM:614980; Phenotypes: 28464518, 29700987, 32183715, 34456334, 34990405, 34741306, 36000780, 37153890; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Infantile nystagmus v1.6 | DAGLA |
Irina Ziravecka gene: DAGLA was added gene: DAGLA was added to Infantile nystagmus. Sources: Literature Mode of inheritance for gene: DAGLA was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DAGLA were set to PMID: 35737950 Phenotypes for gene: DAGLA were set to developmental delay; ataxia; complex oculomotor abnormality (nystagmus) Mode of pathogenicity for gene: DAGLA was set to Other Review for gene: DAGLA was set to GREEN Added comment: PMID: 35737950 - nine children from eight families with heterozygous, de novo truncating variants in the last exon of DAGLA with a neuro-ocular phenotype. Sources: Literature |
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| Hereditary ataxia v1.326 | DAGLA |
Irina Ziravecka gene: DAGLA was added gene: DAGLA was added to Hereditary ataxia. Sources: Literature Mode of inheritance for gene: DAGLA was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DAGLA were set to PMID: 35737950 Phenotypes for gene: DAGLA were set to developmental delay; ataxia; complex oculomotor abnormality Mode of pathogenicity for gene: DAGLA was set to Other Review for gene: DAGLA was set to GREEN Added comment: PMID: 35737950 - nine children from eight families with heterozygous, de novo truncating variants in the last exon of DAGLA with a neuro-ocular phenotype. Sources: Literature |
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| Intellectual disability v5.204 | DAGLA |
Irina Ziravecka gene: DAGLA was added gene: DAGLA was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: DAGLA was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DAGLA were set to PMID: 35737950 Phenotypes for gene: DAGLA were set to developmental delay; ataxia; complex oculomotor abnormality Mode of pathogenicity for gene: DAGLA was set to Other Review for gene: DAGLA was set to GREEN Added comment: PMID: 35737950 - nine children from eight families with heterozygous, de novo truncating variants in the last exon of DAGLA with a neuro-ocular phenotype. Sources: Literature |
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| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | MECOM |
Boaz Palterer gene: MECOM was added gene: MECOM was added to Primary immunodeficiency or monogenic inflammatory bowel disease. Sources: Literature Mode of inheritance for gene: MECOM was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: MECOM were set to 37407873 Phenotypes for gene: MECOM were set to Radioulnar synostosis with amegakaryocytic thrombocytopenia 2, OMIM:616738; Hypocellular bone marrow; congenital thrombocytopenia; B-cell lymphopenia; hypogammaglobulinemia; radioulnar synostosis; digit abnormalities; clubfoot; cardiac defects; facial dysmorphism Penetrance for gene: MECOM were set to unknown Review for gene: MECOM was set to GREEN Added comment: Bone marrow failure syndrome included in the 2022 IUIS IEI classification. A subset of patients presents B cell deficiency and hypogammaglobulinemia. The phenotype is relevant for the panel. Sources: Literature |
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| Childhood onset dystonia, chorea or related movement disorder v3.17 | TMEM151A | Lucy Jackson edited their review of gene: TMEM151A: Changed publications to: 34518509, 35707035, 36724570, 34820915 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.17 | TMEM151A |
Lucy Jackson gene: TMEM151A was added gene: TMEM151A was added to Childhood onset dystonia, chorea or related movement disorder. Sources: NHS GMS Mode of inheritance for gene: TMEM151A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TMEM151A were set to (PMID: 34518509; 35707035; 36724570; 34820915) Phenotypes for gene: TMEM151A were set to Episodic kinesigenic dyskinesia 3 Review for gene: TMEM151A was set to GREEN Added comment: LOF variants have been shown to cause autosomal dominant Episodic kinesigenic dyskinesia 3 Sources: NHS GMS |
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| Adult onset neurodegenerative disorder v4.28 | PPP2R2B_CAG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | PPP2R2B_CAG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: PPP2R2B_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | NOP56_GGCCTG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | NOP56_GGCCTG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: NOP56_GGCCTG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | FXN_GAA | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | FXN_GAA | Sarah Leigh Tag Q3_23_promote_green was removed from STR: FXN_GAA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CSTB_CCCCGCCCCGCG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CSTB_CCCCGCCCCGCG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: CSTB_CCCCGCCCCGCG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CACNA1A_CAG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CACNA1A_CAG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: CACNA1A_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN7_CAG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN7_CAG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: ATXN7_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN3_CAG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN3_CAG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: ATXN3_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN2_CAG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN2_CAG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: ATXN2_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN10_ATTCT | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN1_CAG | Sarah Leigh Deleted their review | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN1_CAG | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN1_CAG | Sarah Leigh Tag Q3_23_promote_green was removed from STR: ATXN1_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN10_ATTCT | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN10_ATTCT | Sarah Leigh Tag Q3_23_promote_green was removed from STR: ATXN10_ATTCT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.56 | SLC22A5 | Sarah Leigh changed review comment from: Numerous SLC22A5 variants are associated with a relevant phenotype in OMIM (OMIM:212140) and SLC22A5 has a definitive association in Gen2Phen for Systemic Carnitine Deficiency. A supportive mouse model has also been reported (PMID: 17884651).; to: Numerous SLC22A5 variants have been associated with OMIM:212140, and SLC22A5 has a definitive association in Gen2Phen for Systemic Carnitine Deficiency. A supportive mouse model has also been reported (PMID: 17884651). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.56 | SLC22A5 | Sarah Leigh edited their review of gene: SLC22A5: Added comment: Numerous SLC22A5 variants are associated with a relevant phenotype in OMIM (OMIM:212140) and SLC22A5 has a definitive association in Gen2Phen for Systemic Carnitine Deficiency. A supportive mouse model has also been reported (PMID: 17884651).; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.56 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 9916797; 17884651; 25778941 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.55 | SLC22A5 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: SLC22A5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.55 | SLC22A5 | Sarah Leigh Classified gene: SLC22A5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.55 | SLC22A5 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.55 | SLC22A5 | Sarah Leigh Gene: slc22a5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.54 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to 9916797; 25778941; 17884651; 25778941 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.53 | SLC22A5 | Sarah Leigh Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary, 212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.52 | SLC22A5 | Sarah Leigh Publications for gene: SLC22A5 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| RASopathies v1.78 | MAP4K4 |
Irina Ziravecka gene: MAP4K4 was added gene: MAP4K4 was added to RASopathies. Sources: Literature Mode of inheritance for gene: MAP4K4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: MAP4K4 were set to PMID: 37126546 Phenotypes for gene: MAP4K4 were set to neurodevelopmental differences; multiple congenital anomalies Mode of pathogenicity for gene: MAP4K4 was set to Other Review for gene: MAP4K4 was set to GREEN Added comment: PMID: 37126546 - "a cohort of 26 affected individuals from 21 unrelated families with neurodevelopmental differences, cardiac issues, and CFAs who share a phenotype overlap with RASopathies and harbor a series of rare variants in MAP4K4. Functional studies in zebrafish showed that MAP4K4 variants caused hypomorphic, LOF, or DN effects." Sources: Literature |
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| DDG2P v3.6 | MAP4K4 |
Irina Ziravecka gene: MAP4K4 was added gene: MAP4K4 was added to DDG2P. Sources: Literature Mode of inheritance for gene: MAP4K4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: MAP4K4 were set to PMID: 37126546 Phenotypes for gene: MAP4K4 were set to neurodevelopmental differences; multiple congenital anomalies Mode of pathogenicity for gene: MAP4K4 was set to Other Review for gene: MAP4K4 was set to GREEN Added comment: PMID: 37126546 - "a cohort of 26 affected individuals from 21 unrelated families with neurodevelopmental differences, cardiac issues, and CFAs who share a phenotype overlap with RASopathies and harbor a series of rare variants in MAP4K4. Functional studies in zebrafish showed that MAP4K4 variants caused hypomorphic, LOF, or DN effects." Sources: Literature |
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| DDG2P v3.6 | AMOTL1 |
Irina Ziravecka edited their review of gene: AMOTL1: Added comment: PMID: 36751037 - this cohort suggests that heterozygous missense variants in AMOTL1, most commonly affecting amino acid residues 157–161, define a new orofacial clefting syndrome, and indicates an important functional role for this undefined region. 5 out of 16 patients in this cohort have developmental delay.; Changed phenotypes to: orofacial clefting, cardiac anomalies, tall stature, distinct dysmorphisms (abnormal head shape, craniosynostosis, hypertelorism, and large ears), myopia, hearing loss, micrognathia, immune dysfunction, scoliosis, chronic constipation, liver dysfunction, global developmental delay |
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| DDG2P v3.6 | AMOTL1 | Irina Ziravecka Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.6 | AMOTL1 |
Irina Ziravecka changed review comment from: PMID: 36751037 - this cohort suggests that heterozygous missense variants in AMOTL1, most commonly affecting amino acid residues 157–161, define a new orofacial clefting syndrome, and indicates an important functional role for this undefined region. Sources: Other; to: PMID: 36751037 - this cohort suggests that heterozygous missense variants in AMOTL1, most commonly affecting amino acid residues 157–161, define a new orofacial clefting syndrome, and indicates an important functional role for this undefined region. 5 out of 16 patients in this cohort have developmental delay. |
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| DDG2P v3.6 | AMOTL1 |
Irina Ziravecka gene: AMOTL1 was added gene: AMOTL1 was added to DDG2P. Sources: Other Mode of inheritance for gene: AMOTL1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: AMOTL1 were set to PMID: 36751037 Phenotypes for gene: AMOTL1 were set to orofacial clefting; cardiac anomalies; tall stature Mode of pathogenicity for gene: AMOTL1 was set to Other Review for gene: AMOTL1 was set to GREEN Added comment: PMID: 36751037 - this cohort suggests that heterozygous missense variants in AMOTL1, most commonly affecting amino acid residues 157–161, define a new orofacial clefting syndrome, and indicates an important functional role for this undefined region. Sources: Other |
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| Clefting v4.78 | AMOTL1 | Irina Ziravecka reviewed gene: AMOTL1: Rating: GREEN; Mode of pathogenicity: Other; Publications: PMID: 36751037; Phenotypes: orofacial clefting, cardiac anomalies, tall stature; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.10 | SETD5 |
Tracy Lester gene: SETD5 was added gene: SETD5 was added to Skeletal dysplasia. Sources: NHS GMS Mode of inheritance for gene: SETD5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SETD5 were set to 28881385 Phenotypes for gene: SETD5 were set to Skeletal dysplasia; intellectual disability; developmental delay; facial dysmorphism Penetrance for gene: SETD5 were set to Incomplete Review for gene: SETD5 was set to GREEN Added comment: This gene is associated with an autosomal dominant neurodevelopmental disorder characterised by developmental delay, intellectual disability, and variable dysmorphic and skeletal abnormalities. Expressivity is variable and non-penetrance has been reported. As the skeletal features might appear before the ID/DD I think this gene should be added to the SD panel. We recently found a pathogenic fs in this gene in a child with short stature, short long bones and facial dysmorphism but without mention of DD/ID; however case was only 10m old at referral. Sources: NHS GMS |
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| Hereditary ataxia with onset in adulthood v4.15 | PRPS1 | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: All female cases from the three families were reported with X-linked dominant variants in PRPS1 gene. Hence, the MOI should be changed to "X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.15 | PRPS1 | Achchuthan Shanmugasundram Mode of inheritance for gene: PRPS1 was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.14 | PRPS1 | Achchuthan Shanmugasundram Phenotypes for gene: PRPS1 were changed from Ataxia; deafness; eye disease to cerebellar ataxia, MONDO:0000437 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.13 | PRPS1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: Three families reported with adult-onset ataxia. Although ataxia has been reported in the proband and her mother with X-linked dominant variant in a family in PMID:28967191, it was not reported in the older sister from the family with the same variant. Due to the reduced penetrance in this family, this gene should only be rated amber.; to: Comment on list classification: As reviewed by Zornitza Stark, three families were reported with adult-onset ataxia. Although ataxia has been reported in the proband and her mother with X-linked dominant variant in a family in PMID:28967191, it was not reported in the older sister from the family with the same variant. Due to the reduced penetrance in this family, this gene should only be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.13 | PRPS1 | Achchuthan Shanmugasundram Classified gene: PRPS1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.13 | PRPS1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Three families reported with adult-onset ataxia. Although ataxia has been reported in the proband and her mother with X-linked dominant variant in a family in PMID:28967191, it was not reported in the older sister from the family with the same variant. Due to the reduced penetrance in this family, this gene should only be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.13 | PRPS1 | Achchuthan Shanmugasundram Gene: prps1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.12 | PRPS1 | Achchuthan Shanmugasundram reviewed gene: PRPS1: Rating: AMBER; Mode of pathogenicity: None; Publications: 25491489, 28967191, 33898739; Phenotypes: cerebellar ataxia, MONDO:0000437; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | PTPA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | PTPA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | PTPA | Achchuthan Shanmugasundram Classified gene: PTPA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | PTPA | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Konstantinos Varvagiannis, there are two unrelated cases with intellectual disability and hence this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.204 | PTPA | Achchuthan Shanmugasundram Gene: ptpa has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Classified gene: PTPA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Konstantinos Varvagiannis, there are two unrelated cases with intellectual disability and hence this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Gene: ptpa has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Classified gene: PTPA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Konstantinos Varvagiannis, there are two unrelated cases with intellectual disability and hence this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Gene: ptpa has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Classified gene: PTPA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Konstantinos Varvagiannis, there are two unrelated cases with intellectual disability and hence this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.203 | PTPA | Achchuthan Shanmugasundram Gene: ptpa has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.202 | PTPA | Achchuthan Shanmugasundram Phenotypes for gene: PTPA were changed from Intellectual disability, MONDO:0001071 to Intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.202 | PTPA | Achchuthan Shanmugasundram Phenotypes for gene: PTPA were changed from Intellectual disability, MONDO:0001071 to Intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.201 | PTPA | Achchuthan Shanmugasundram Phenotypes for gene: PTPA were changed from Intellectual disability, MONDO:0001071 to Intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.201 | PTPA | Achchuthan Shanmugasundram Phenotypes for gene: PTPA were changed from Intellectual disability, MONDO:0001071 to Intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.201 | PTPA | Achchuthan Shanmugasundram Phenotypes for gene: PTPA were changed from Intellectual disability; Parkinsonism to Intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | PTPA | Achchuthan Shanmugasundram reviewed gene: PTPA: Rating: AMBER; Mode of pathogenicity: None; Publications: 36073231; Phenotypes: Intellectual disability, MONDO:0001071; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber.; to: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay supported by functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.200 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Classified gene: FOXR1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is one case with global developmental delay and supporting functional evidence including mouse model. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.199 | FOXR1 | Achchuthan Shanmugasundram Gene: foxr1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.198 | FOXR1 | Achchuthan Shanmugasundram Phenotypes for gene: FOXR1 were changed from Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 to Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.198 | FOXR1 | Achchuthan Shanmugasundram Phenotypes for gene: FOXR1 were changed from Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 to Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.198 | FOXR1 | Achchuthan Shanmugasundram Phenotypes for gene: FOXR1 were changed from Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 to Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.198 | FOXR1 | Achchuthan Shanmugasundram Phenotypes for gene: FOXR1 were changed from Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 to Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.197 | FOXR1 | Achchuthan Shanmugasundram Phenotypes for gene: FOXR1 were changed from Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 to Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.197 | FOXR1 | Achchuthan Shanmugasundram Phenotypes for gene: FOXR1 were changed from Postnatal microcephaly, progressive brain atrophy and global developmental delay to Global developmental delay, HP:0001263; microcephaly, MONDO:0001149; Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.196 | FOXR1 | Achchuthan Shanmugasundram edited their review of gene: FOXR1: Changed phenotypes to: Global developmental delay, HP:0001263, microcephaly, MONDO:0001149, Brain atrophy, HP:0012444 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.196 | FOXR1 | Achchuthan Shanmugasundram reviewed gene: FOXR1: Rating: AMBER; Mode of pathogenicity: None; Publications: 34723967; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Renal tubulopathies v4.1 | RMND1 |
John Sayer gene: RMND1 was added gene: RMND1 was added to Renal tubulopathies. Sources: Expert list Mode of inheritance for gene: RMND1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: RMND1 were set to 32911714; 31889854; 31568715 Phenotypes for gene: RMND1 were set to tubulopathy; renal tubular acidosis; interstitial nephritis; end-stage renal disease; tubular atrophy Penetrance for gene: RMND1 were set to Complete Mode of pathogenicity for gene: RMND1 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: RMND1 was set to GREEN Added comment: Sources: Expert list |
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| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.1 | HBB | Achchuthan Shanmugasundram changed review comment from: HBB has been added to the panel for R288 GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB with a green rating as agreed with the NHS Genomic Medicine Service.; to: HBB has been added to the panel for R361 Haemoglobinopathy trait or carrier testing with a green rating as agreed with the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.1 | HBA1 | Achchuthan Shanmugasundram changed review comment from: HBA1 has been added to the panel for R288 GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB with a green rating as agreed with the NHS Genomic Medicine Service.; to: HBA1 has been added to the panel for R361 Haemoglobinopathy trait or carrier testing with a green rating as agreed with the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.196 | KDM6B | Sarah Leigh Phenotypes for gene: KDM6B were changed from Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities, 618505 to Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities, OMIM:618505; neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities, MONDO:0032790 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.67 | KDM6B | Sarah Leigh edited their review of gene: KDM6B: Added comment: KDM6B variants have been associated with relevant phenotype in OMIM and as strong Gen2Phen gene for KDM6B-related developmental disorder (monoallelic). PMID: 37196654 reports that in their cohort, 9/69 (13%) of individuals had seizures.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.67 | KDM6B | Sarah Leigh Classified gene: KDM6B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.67 | KDM6B | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.67 | KDM6B | Sarah Leigh Gene: kdm6b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.66 | KDM6B | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: KDM6B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.66 | KDM6B | Sarah Leigh Phenotypes for gene: KDM6B were changed from Global developmental delay; Intellectual disability; Hypotonia; Joint hypermobility; seizures; Overgrowth to Neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities, OMIM:618505; neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities, MONDO:0032790 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.65 | KDM6B | Sarah Leigh Publications for gene: KDM6B were set to PMID: 37196654 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.195 | KDM6B | Sarah Leigh Publications for gene: KDM6B were set to 21937992; 31124279 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.64 | DALRD3 | Arina Puzriakova Classified gene: DALRD3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.64 | DALRD3 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. Rating Amber as this is a good candidate gene but only a single family has been reported to date with variants. Additional evidence needed prior to adding the gene as diagnostic-grade. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.64 | DALRD3 | Arina Puzriakova Gene: dalrd3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.63 | DALRD3 | Arina Puzriakova Classified gene: DALRD3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.63 | DALRD3 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. Rating Amber as this is a good candidate gene but only a single family has been reported to date with variants. Additional evidence needed prior to adding the gene as diagnostic-grade. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.63 | DALRD3 | Arina Puzriakova Gene: dalrd3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.194 | DALRD3 | Arina Puzriakova Classified gene: DALRD3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.194 | DALRD3 | Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. Rating Amber as this is a good candidate gene but only a single family has been reported to date with variants. Additional evidence needed prior to adding the gene as diagnostic-grade. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.194 | DALRD3 | Arina Puzriakova Gene: dalrd3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial breast cancer v1.20 | ATRIP | Arina Puzriakova Mode of inheritance for gene: ATRIP was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial breast cancer v1.19 | ATRIP | Arina Puzriakova Classified gene: ATRIP as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial breast cancer v1.19 | ATRIP | Arina Puzriakova Added comment: Comment on list classification: New gene added to this panel by Lauma Freimane. More evidence is required prior to adding this gene to the panel. The metanalysis paper identified by reviewer is still at the preprint stage. The findings are detailed below but this needs to be revisited once the article has been published. This is a good candidate gene for breast cancer susceptibility but for now can only classify as Amber (with watchlist tag), awaiting peer-review and additional publication of supporting evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial breast cancer v1.19 | ATRIP | Arina Puzriakova Gene: atrip has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial breast cancer v1.18 | ATRIP | Arina Puzriakova commented on gene: ATRIP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.2 | ATRIP |
Arina Puzriakova changed review comment from: Enrichment for ATRIP variants was found in meta-analysis of breast cancer cohorts and UK Biobank. ATRIP carriers had a higher proportion of high-grade, low-stage ductal breast cancer but none of the associations with tumor characteristics were statistically significant. Another study (PMID: 36977412) also identified three Polish women with familial breast cancer and variants in this gene including a c.69_75dup (p.Thr26Alafs∗23) frameshift insertion (not discussed further in paper) and a founder c.1152_1155del (p.Gly385Ter) frameshift deletion in two women. The founder variant was also found in validation cohorts with 42/16,085 unselected Polish breast cancer-affected individuals and 11/9,285 control subjects (OR = 2.14, 95% CI = 1.13-4.28, p = 0.02) harbouring the variant. UK Biobank data showed ATRIP loss-of-function variants among 13/15,643 breast cancer-affected individuals versus 40/157,943 control subjects (OR = 3.28, 95% CI = 1.76-6.14, p < 0.001). Immunohistochemistry and functional studies showed the ATRIP c.1152_1155del variant allele is weakly expressed compared to the wild-type allele, and truncated ATRIP fails to perform its normal function to prevent replicative stress. ----- ATRIP is currently not associated with any phenotype in OMIM or G2P. It codes for a DNA damage response protein which forms a complex with ATR. ATR-ATRIP is involved in the process that activates checkpoint signalling when single-stranded DNA is detected following the processing of DNA double-stranded breaks or stalled replication forks.; to: Enrichment for ATRIP variants was found in meta-analysis of breast cancer cohorts and UK Biobank. ATRIP carriers had a higher proportion of high-grade, low-stage ductal breast cancer but none of the associations with tumor characteristics were statistically significant (https://doi.org/10.1101/2022.06.17.22276537). Another study (PMID: 36977412) also identified three Polish women with familial breast cancer and variants in this gene including a c.69_75dup (p.Thr26Alafs∗23) frameshift insertion (not discussed further in paper) and a founder c.1152_1155del (p.Gly385Ter) frameshift deletion in two women. The founder variant was also found in validation cohorts with 42/16,085 unselected Polish breast cancer-affected individuals and 11/9,285 control subjects (OR = 2.14, 95% CI = 1.13-4.28, p = 0.02) harbouring the variant. UK Biobank data showed ATRIP loss-of-function variants among 13/15,643 breast cancer-affected individuals versus 40/157,943 control subjects (OR = 3.28, 95% CI = 1.76-6.14, p < 0.001). Immunohistochemistry and functional studies showed the ATRIP c.1152_1155del variant allele is weakly expressed compared to the wild-type allele, and truncated ATRIP fails to perform its normal function to prevent replicative stress. ----- ATRIP is currently not associated with any phenotype in OMIM or G2P. It codes for a DNA damage response protein which forms a complex with ATR. ATR-ATRIP is involved in the process that activates checkpoint signalling when single-stranded DNA is detected following the processing of DNA double-stranded breaks or stalled replication forks. |
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| Breast cancer pertinent cancer susceptibility v2.2 | ATRIP | Arina Puzriakova Classified gene: ATRIP as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.2 | ATRIP | Arina Puzriakova Added comment: Comment on list classification: New gene added to this panel by Lauma Freimane. More evidence is required prior to adding this gene to the panel. The metanalysis paper identified by reviewer is still at the preprint stage. The findings are detailed below but this needs to be revisited once the article has been published. This is a good candidate gene for breast cancer susceptibility but for now can only classify as Amber (with watchlist tag), awaiting peer-review and additional publication of supporting evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.2 | ATRIP | Arina Puzriakova Gene: atrip has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.1 | ATRIP | Arina Puzriakova Tag watchlist tag was added to gene: ATRIP. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.1 | ATRIP | Arina Puzriakova commented on gene: ATRIP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.193 | SMCHD1 | Arina Puzriakova Mode of inheritance for gene: SMCHD1 was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Facioscapulohumeral muscular dystrophy - extended testing v0.1 | SMCHD1 | Arina Puzriakova Tag digenic tag was added to gene: SMCHD1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited polyposis and early onset colorectal cancer - germline testing v2.6 | GREM1 | Arina Puzriakova Mode of pathogenicity for gene: GREM1 was changed from to Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult solid tumours for rare disease v1.36 | PDGFRA | Sumir Pandit reviewed gene: PDGFRA: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 29486293; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited polyposis and early onset colorectal cancer - germline testing v2.5 | GREM1 |
Arina Puzriakova Added comment: Comment on phenotypes: Previous phenotypes: Hereditary Mixed Polyposis Syndrome;Oligosyndactyly of the hands, Cenani-Linz-like (Dimitrov (2010) J Med Genet 47,569);Polyposis Syndrome, Hereditary Mixed, 1;Mixed polyposis syndrome (Jaeger (2012) Nat Genet 44,699);{Colorectal cancer, increased risk, association with}(Peters (2012) Hum Genet 131,217) |
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| Inherited polyposis and early onset colorectal cancer - germline testing v2.5 | GREM1 | Arina Puzriakova Phenotypes for gene: GREM1 were changed from Hereditary Mixed Polyposis Syndrome; Oligosyndactyly of the hands, Cenani-Linz-like (Dimitrov (2010) J Med Genet 47,569); Polyposis Syndrome, Hereditary Mixed, 1; Mixed polyposis syndrome (Jaeger (2012) Nat Genet 44,699); {Colorectal cancer, increased risk, association with}(Peters (2012) Hum Genet 131,217) to Hereditary mixed polyposis syndrome, MONDO:0011023 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Paediatric or syndromic cardiomyopathy v3.12 | ELAC2 |
Matthew Edwards gene: ELAC2 was added gene: ELAC2 was added to Paediatric or syndromic cardiomyopathy. Sources: Expert Review Mode of inheritance for gene: ELAC2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ELAC2 were set to PMID: 23849775 Penetrance for gene: ELAC2 were set to unknown Review for gene: ELAC2 was set to GREEN Added comment: Oxidative phosphorylation deficiency-17 manifests as severe infantile-onset hypertrophic cardiomyopathy (green gene on several metabolic panels, but presenting feature is HCM in first year of life) Also recent diagnostic case through our GLH Sources: Expert Review |
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| Retinal disorders v4.12 | MCOLN1 |
Siying Lin gene: MCOLN1 was added gene: MCOLN1 was added to Retinal disorders. Sources: Literature Mode of inheritance for gene: MCOLN1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MCOLN1 were set to 17239335; 1488220; 18326692 Mode of pathogenicity for gene: MCOLN1 was set to Other Review for gene: MCOLN1 was set to GREEN Added comment: Retinal degeneration is a known feature of MCOLN1-associated mucolipidosis IV, and there are reports of patients presenting with a limited ocular phenotype including retinal dystrophy Sources: Literature |
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| Hereditary ataxia v1.326 | DMXL2 | Arina Puzriakova Mode of inheritance for gene: DMXL2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.17 | DMXL2 | Arina Puzriakova Mode of inheritance for gene: DMXL2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.16 | DMXL2 | Arina Puzriakova Classified gene: DMXL2 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.16 | DMXL2 | Arina Puzriakova Added comment: Comment on list classification: Downgraded from Amber to Red. Ataxia (onset in adolescence) has only been reported in one consanguineous family to date (PMID: 25248098) and this finding has not since been replicated. Therefore demoting the gene rating, inline with review by Dmitrijs Rots. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.16 | DMXL2 | Arina Puzriakova Gene: dmxl2 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.325 | DMXL2 | Arina Puzriakova Publications for gene: DMXL2 were set to 27657680; 22875945; 25248098 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.15 | DMXL2 | Arina Puzriakova Publications for gene: DMXL2 were set to 25248098; 22875945; 27657680 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.324 | DMXL2 | Arina Puzriakova Phenotypes for gene: DMXL2 were changed from ?Polyendocrine-polyneuropathy syndrome , OMIM:616113 to ?Polyendocrine-polyneuropathy syndrome, OMIM:616113 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.14 | DMXL2 | Arina Puzriakova Phenotypes for gene: DMXL2 were changed from Sensorineural Hearing Loss; ORPHA90636; OMIM:612186 to ?Polyendocrine-polyneuropathy syndrome, OMIM:616113 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.323 | DMXL2 | Arina Puzriakova Phenotypes for gene: DMXL2 were changed from Sensorineural Hearing Loss; ORPHA90636; OMIM:612186 to ?Polyendocrine-polyneuropathy syndrome , OMIM:616113 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.322 | DMXL2 | Arina Puzriakova Classified gene: DMXL2 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.322 | DMXL2 | Arina Puzriakova Added comment: Comment on list classification: Downgraded from Amber to Red. Ataxia (onset in adolescence) has only been reported in one consanguineous family to date (PMID: 25248098) and this finding has not since been replicated. Therefore demoting the gene rating, inline with review by Dmitrijs Rots. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia v1.322 | DMXL2 | Arina Puzriakova Gene: dmxl2 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.62 | CPA6 |
John Taylor changed review comment from: The pathology of this gene is predicated on two publications: Salzmann et al. (2012) PubMed: 21922598 and Sapio et al. (2012) PubMed: 23105115. Both of these publications were issued prior to large population-based allele assessments and the evidence for pathogenicity is reliant on circumstantial evidence. None of the variants that form the foundation of this disease link would have sufficient evidence in support pathogenicity using current classification criteria. This gene should be recategorized as having a Red rating. Evidence against pathogenicity for the reported variants: Salzmann et al. (2012) proposed haploinsufficiency rather than gain of function; however, there is no obvious constraint score across the length of the gene. Previously reported pathogenic variants are, in some cases (see below), present in gnomAD at allele frequencies contrary to the incidence of the associated condition. CPA6 p.(Ala270Val) rs114402678 has been reported has a homozygous variant in gnomADv3.1.2 in the non-neuro sub category (only samples that were not collected as part of a neurologic or psychiatric case/control study, or samples collected as part of a neurologic or psychiatric case/control study but designated as controls). The allele frequency and the observed number of homozygotes is not significantly different from the number of expected homozygote alleles based on the Hardy-Weinberg equilibrium. CPA6(NM_020361.5):c.799G>A p.(Gly267Arg) rs61738009 was reported as a heterozygous pathogenic variant; however, this variant has been reported in >860 heterozygous individuals in gnomADv2.1.1 and v3.1.2.; to: The pathology of this gene is predicated on two publications: Salzmann et al. (2012) PubMed: 21922598 and Sapio et al. (2012) PubMed: 23105115. Both of these publications were issued prior to large population-based allele assessments and the evidence for pathogenicity is reliant on circumstantial evidence. None of the variants that form the foundation of this disease link would have sufficient evidence in support pathogenicity using current classification criteria. This gene should be recategorized as having a Red rating. Evidence against pathogenicity for the reported variants: Salzmann et al. (2012) proposed haploinsufficiency rather than gain of function; however, there is no obvious constraint score across the length of the gene. Previously reported pathogenic variants are, in some cases (see below), present in gnomAD at allele frequencies contrary to the incidence of the associated condition. CPA6 p.(Ala270Val) rs114402678 has been reported has a homozygous variant in gnomADv3.1.2 in the non-neuro sub category (only samples that were not collected as part of a neurologic or psychiatric case/control study, or samples collected as part of a neurologic or psychiatric case/control study but designated as controls). The allele frequency and the observed number of homozygotes is not significantly different from the number of expected homozygote alleles based on the Hardy-Weinberg equilibrium. CPA6(NM_020361.5):c.799G>A p.(Gly267Arg) rs61738009 was reported as a heterozygous pathogenic variant; however, this variant has been reported in >860 heterozygous individuals in gnomADv2.1.1 and v3.1.2. |
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| Early onset or syndromic epilepsy v4.62 | CPA6 | John Taylor reviewed gene: CPA6: Rating: RED; Mode of pathogenicity: Other; Publications: PMID:21922598, 23105115; Phenotypes: ; Mode of inheritance: Other | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Wiskott-Aldrich syndrome v0.1 | WAS | Achchuthan Shanmugasundram reviewed gene: WAS: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Wilson disease v0.1 | ATP7B | Achchuthan Shanmugasundram reviewed gene: ATP7B: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| von Willebrand disease v0.1 | VWF | Achchuthan Shanmugasundram reviewed gene: VWF: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Von Hippel Lindau syndrome v0.1 | VHL | Achchuthan Shanmugasundram reviewed gene: VHL: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Variegate porphyria v0.1 | PPOX | Achchuthan Shanmugasundram reviewed gene: PPOX: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Van der Woude syndrome v0.1 | IRF6 | Achchuthan Shanmugasundram reviewed gene: IRF6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Tuberous sclerosis v0.1 | TSC2 | Achchuthan Shanmugasundram reviewed gene: TSC2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Tuberous sclerosis v0.1 | TSC1 | Achchuthan Shanmugasundram reviewed gene: TSC1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Thiamine metabolism dysfunction syndrome 2 v0.1 | SLC19A3 | Achchuthan Shanmugasundram reviewed gene: SLC19A3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Thanatophoric dysplasia v0.1 | FGFR3 | Achchuthan Shanmugasundram reviewed gene: FGFR3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sickle cell, thalassaemia and other haemoglobinopathies v0.1 | HBB | Achchuthan Shanmugasundram reviewed gene: HBB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sickle cell, thalassaemia and other haemoglobinopathies v0.1 | HBA1 | Achchuthan Shanmugasundram reviewed gene: HBA1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Tay-Sachs disease v0.1 | HEXA | Achchuthan Shanmugasundram reviewed gene: HEXA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Syndromic and non syndromic craniosynostosis involving midline sutures v0.1 | SMAD6 | Achchuthan Shanmugasundram changed review comment from: SMAD6 has been added to the panel for R416 Syndromic and non syndromic craniosynostosis involving midline sutures only with a green rating as agreed with the NHS Genomic Medicine Service.; to: SMAD6 has been added to the panel for R416 Syndromic and non syndromic craniosynostosis involving midline sutures with a green rating as agreed with the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Syndromic and non syndromic craniosynostosis involving midline sutures v0.1 | SMAD6 | Achchuthan Shanmugasundram reviewed gene: SMAD6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Subcutaneous panniculitis T-cell lymphoma (SPTCL) v0.1 | HAVCR2 | Achchuthan Shanmugasundram reviewed gene: HAVCR2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Spinal muscular atrophy type 1 rare mutation testing v0.1 | SMN1 | Achchuthan Shanmugasundram reviewed gene: SMN1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Smith-Lemli-Opitz syndrome v0.1 | DHCR7 | Achchuthan Shanmugasundram reviewed gene: DHCR7: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sitosterolaemia v0.1 | ABCG8 | Achchuthan Shanmugasundram reviewed gene: ABCG8: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sitosterolaemia v0.1 | ABCG5 | Achchuthan Shanmugasundram reviewed gene: ABCG5: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Short stature - SHOX deficiency v0.1 | SHOX | Achchuthan Shanmugasundram reviewed gene: SHOX: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe combined immunodeficiency with PNP deficiency v0.1 | PNP | Achchuthan Shanmugasundram reviewed gene: PNP: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe combined immunodeficiency with adenosine deaminase deficiency v0.1 | ADA | Achchuthan Shanmugasundram reviewed gene: ADA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Segmental or atypical neurofibromatosis type 1 testing v0.1 | NF1 | Achchuthan Shanmugasundram reviewed gene: NF1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| SCID with features of gamma chain deficiency v0.1 | IL2RG | Achchuthan Shanmugasundram reviewed gene: IL2RG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sandhoff disease v0.1 | HEXB | Achchuthan Shanmugasundram reviewed gene: HEXB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinoblastoma v0.1 | RB1 | Achchuthan Shanmugasundram reviewed gene: RB1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Pulmonary alveolar microlithiasis v0.1 | SLC34A2 | Achchuthan Shanmugasundram reviewed gene: SLC34A2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| PTEN Hamartoma Tumour Syndrome v0.1 | PTEN | Achchuthan Shanmugasundram reviewed gene: PTEN: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Pseudoxanthoma elasticum v0.1 | ENPP1 | Achchuthan Shanmugasundram reviewed gene: ENPP1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Pseudoxanthoma elasticum v0.1 | ABCC6 | Achchuthan Shanmugasundram reviewed gene: ABCC6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary hyperaldosteronism - KCNJ5 v0.1 | KCNJ5 | Achchuthan Shanmugasundram reviewed gene: KCNJ5: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| POLG-related disorder v0.1 | POLG | Achchuthan Shanmugasundram reviewed gene: POLG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Phenylketonuria v0.1 | PAH | Achchuthan Shanmugasundram reviewed gene: PAH: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Peutz Jeghers Syndrome v0.1 | STK11 | Achchuthan Shanmugasundram reviewed gene: STK11: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nijmegen breakage syndrome v0.1 | NBN | Achchuthan Shanmugasundram reviewed gene: NBN: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Niemann-Pick disease type A or B v0.1 | SMPD1 | Achchuthan Shanmugasundram reviewed gene: SMPD1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Niemann Pick disease type C v0.1 | NPC2 | Achchuthan Shanmugasundram reviewed gene: NPC2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Niemann Pick disease type C v0.1 | NPC1 | Achchuthan Shanmugasundram reviewed gene: NPC1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome v0.1 | SUFU | Achchuthan Shanmugasundram reviewed gene: SUFU: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome v0.1 | PTCH1 | Achchuthan Shanmugasundram reviewed gene: PTCH1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neutropaenia consistent with ELANE mutations v0.1 | ELANE | Achchuthan Shanmugasundram reviewed gene: ELANE: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neuronal ceroid lipofuscinosis type 2 v0.1 | TPP1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neuronal ceroid lipofuscinosis type 2 v0.1 | TPP1 | Achchuthan Shanmugasundram changed review comment from: TPP1 has been added to the panel for R271 Neuronal ceroid lipofuscinosis type 2 with a green rating as agreed with the NHS Genomic Medicine Service.; to: TPP1 has been added to the panel for R271 Neuronal ceroid lipofuscinosis type 2 with a green rating as agreed with the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neuronal ceroid lipofuscinosis type 2 v0.1 | TPP1 | Achchuthan Shanmugasundram commented on gene: TPP1: TPP1 has been added to the panel for R271 Neuronal ceroid lipofuscinosis type 2 with a green rating as agreed with the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neuronal ceroid lipofuscinosis type 2 v0.1 | TPP1 | Achchuthan Shanmugasundram reviewed gene: TPP1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neurofibromatosis type 1 (GMS) v0.1 | SPRED1 | Achchuthan Shanmugasundram reviewed gene: SPRED1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neurofibromatosis type 1 (GMS) v0.1 | NF1 | Achchuthan Shanmugasundram reviewed gene: NF1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neonatal diabetes - small panel v0.1 | KCNJ11 | Achchuthan Shanmugasundram reviewed gene: KCNJ11: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neonatal diabetes - small panel v0.1 | ABCC8 | Achchuthan Shanmugasundram reviewed gene: ABCC8: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| NARP syndrome or maternally inherited Leigh syndrome v0.1 | MT-ND6 | Achchuthan Shanmugasundram reviewed gene: MT-ND6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MITOCHONDRIAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| NARP syndrome or maternally inherited Leigh syndrome v0.1 | MT-ATP6 | Achchuthan Shanmugasundram reviewed gene: MT-ATP6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MITOCHONDRIAL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Multiple exostoses v0.1 | EXT2 | Achchuthan Shanmugasundram reviewed gene: EXT2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Multiple exostoses v0.1 | EXT1 | Achchuthan Shanmugasundram reviewed gene: EXT1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Multiple endocrine neoplasia type 2 v0.1 | RET | Achchuthan Shanmugasundram reviewed gene: RET: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type VI v0.1 | ARSB | Achchuthan Shanmugasundram reviewed gene: ARSB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type IVA v0.1 | GALNS | Achchuthan Shanmugasundram reviewed gene: GALNS: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type IIIB v0.1 | NAGLU | Achchuthan Shanmugasundram reviewed gene: NAGLU: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type IIIA v0.2 | SGSH | Achchuthan Shanmugasundram reviewed gene: SGSH: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type II v0.1 | IDS | Achchuthan Shanmugasundram reviewed gene: IDS: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucopolysaccharidosis type IH or S v0.1 | IDUA | Achchuthan Shanmugasundram reviewed gene: IDUA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mucolipidosis II and III Alpha or Beta v0.1 | GNPTAB | Achchuthan Shanmugasundram reviewed gene: GNPTAB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Monitoring for G(M)CSF escape mutations v0.1 | CSF3R | Achchuthan Shanmugasundram reviewed gene: CSF3R: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial neurogastrointestinal encephalopathy v0.1 | TYMP | Achchuthan Shanmugasundram reviewed gene: TYMP: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial Complex V deficiency, TMEM70 type v0.1 | TMEM70 | Achchuthan Shanmugasundram reviewed gene: TMEM70: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lysosomal acid lipase deficiency v0.1 | LIPA | Achchuthan Shanmugasundram reviewed gene: LIPA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Lymphoproliferative syndrome with absent SAP expression v0.1 | SH2D1A | Achchuthan Shanmugasundram reviewed gene: SH2D1A: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Krabbe disease - Saposin A deficiency v0.1 | PSAP | Achchuthan Shanmugasundram reviewed gene: PSAP: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Krabbe disease - GALC deficiency v0.1 | GALC | Achchuthan Shanmugasundram reviewed gene: GALC: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| IPEX - Immunodysregulation Polyendocrinopathy and Enteropathy, X-Linked v0.1 | FOXP3 | Achchuthan Shanmugasundram reviewed gene: FOXP3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) v0.1 | PAX5 | Achchuthan Shanmugasundram reviewed gene: PAX5: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) v0.1 | ETV6 | Achchuthan Shanmugasundram reviewed gene: ETV6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited parathyroid cancer v0.1 | CDC73 | Achchuthan Shanmugasundram reviewed gene: CDC73: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Incontinentia pigmenti v0.1 | IKBKG | Achchuthan Shanmugasundram reviewed gene: IKBKG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hirschsprung disease v0.1 | RET | Achchuthan Shanmugasundram reviewed gene: RET: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary angioedema types I and II v0.1 | SERPING1 | Achchuthan Shanmugasundram reviewed gene: SERPING1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Haemophagocytic syndrome with absent XIAP expression v0.1 | XIAP | Achchuthan Shanmugasundram reviewed gene: XIAP: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Haemophagocytic syndrome with absent perforin expression v0.1 | PRF1 | Achchuthan Shanmugasundram reviewed gene: PRF1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.1 | HBB | Achchuthan Shanmugasundram reviewed gene: HBB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.1 | HBA1 | Achchuthan Shanmugasundram reviewed gene: HBA1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB v0.1 | GLB1 | Achchuthan Shanmugasundram reviewed gene: GLB1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Glycogen storage disease V v0.1 | PYGM | Achchuthan Shanmugasundram reviewed gene: PYGM: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Glucokinase-related fasting hyperglycaemia v0.1 | GCK | Achchuthan Shanmugasundram reviewed gene: GCK: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Generalised arterial calcification in infancy v0.1 | ENPP1 | Achchuthan Shanmugasundram reviewed gene: ENPP1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Generalised arterial calcification in infancy v0.1 | ABCC6 | Achchuthan Shanmugasundram reviewed gene: ABCC6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Gaucher disease v0.1 | GBA | Achchuthan Shanmugasundram reviewed gene: GBA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fumarate hydratase-related tumour syndromes v0.1 | FH | Achchuthan Shanmugasundram reviewed gene: FH: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial tumours of the nervous system v0.1 | SUFU | Achchuthan Shanmugasundram reviewed gene: SUFU: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial tumours of the nervous system v0.1 | SMARCE1 | Achchuthan Shanmugasundram reviewed gene: SMARCE1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial tumours of the nervous system v0.1 | SMARCB1 | Achchuthan Shanmugasundram reviewed gene: SMARCB1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial tumours of the nervous system v0.1 | NF2 | Achchuthan Shanmugasundram reviewed gene: NF2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial tumours of the nervous system v0.1 | LZTFL1 | Achchuthan Shanmugasundram reviewed gene: LZTFL1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial tumours of the nervous system v0.1 | DGCR8 | Achchuthan Shanmugasundram reviewed gene: DGCR8: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial dysalbuminaemic hyperthyroxinaemia v0.1 | ALB | Achchuthan Shanmugasundram reviewed gene: ALB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor XIII deficiency v0.1 | F13B | Achchuthan Shanmugasundram reviewed gene: F13B: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor XIII deficiency v0.1 | F13A1 | Achchuthan Shanmugasundram reviewed gene: F13A1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor XI deficiency v0.1 | F11 | Achchuthan Shanmugasundram reviewed gene: F11: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor X deficiency v0.1 | F10 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor X deficiency v0.1 | F10 | Achchuthan Shanmugasundram commented on gene: F10: F10 has been added to the panel for R119 Factor X deficiency with a green rating as agreed with the NHS Genomic Medicine Service. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor X deficiency v0.1 | F10 | Achchuthan Shanmugasundram reviewed gene: F10: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor VIII deficiency v0.1 | F8 | Achchuthan Shanmugasundram reviewed gene: F8: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor VII deficiency v0.1 | F7 | Achchuthan Shanmugasundram reviewed gene: F7: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor V deficiency v0.1 | F5 | Achchuthan Shanmugasundram reviewed gene: F5: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor IX deficiency v0.1 | F9 | Achchuthan Shanmugasundram reviewed gene: F9: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor II deficiency v0.1 | F2 | Achchuthan Shanmugasundram reviewed gene: F2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Facioscapulohumeral muscular dystrophy - extended testing v0.1 | SMCHD1 | Achchuthan Shanmugasundram reviewed gene: SMCHD1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fabry disease v0.1 | GLA | Achchuthan Shanmugasundram reviewed gene: GLA: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Elastin-related phenotypes v0.1 | ELN | Achchuthan Shanmugasundram reviewed gene: ELN: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Duchenne or Becker muscular dystrophy v0.1 | DMD | Achchuthan Shanmugasundram reviewed gene: DMD: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DICER1-related cancer predisposition v0.1 | DICER1 | Achchuthan Shanmugasundram reviewed gene: DICER1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystinosis v0.1 | CTNS | Achchuthan Shanmugasundram reviewed gene: CTNS: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic fibrosis diagnostic test v0.1 | CFTR | Achchuthan Shanmugasundram edited their review of gene: CFTR: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic fibrosis diagnostic test v0.1 | CFTR | Achchuthan Shanmugasundram reviewed gene: CFTR: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital adrenal hyperplasia diagnostic test v0.1 | CYP21A2 | Achchuthan Shanmugasundram reviewed gene: CYP21A2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Combined vitamin K-dependent clotting factor deficiency v0.1 | VKORC1 | Achchuthan Shanmugasundram reviewed gene: VKORC1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Combined vitamin K-dependent clotting factor deficiency v0.1 | GGCX | Achchuthan Shanmugasundram reviewed gene: GGCX: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cleidocranial Dysplasia v0.1 | RUNX2 | Achchuthan Shanmugasundram reviewed gene: RUNX2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Central congenital hypoventilation v0.1 | PHOX2B | Achchuthan Shanmugasundram reviewed gene: PHOX2B: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Carney complex v0.1 | PRKAR1A | Achchuthan Shanmugasundram reviewed gene: PRKAR1A: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Calcium-sensing receptor phenotypes v0.1 | CASR | Achchuthan Shanmugasundram reviewed gene: CASR: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| CADASIL v0.1 | NOTCH3 | Achchuthan Shanmugasundram reviewed gene: NOTCH3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Blepharophimosis ptosis and epicanthus inversus v0.1 | FOXL2 | Achchuthan Shanmugasundram reviewed gene: FOXL2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Beckwith-Wiedemann syndrome v0.1 | CDKN1C | Achchuthan Shanmugasundram reviewed gene: CDKN1C: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Barth syndrome v0.1 | TAZ | Achchuthan Shanmugasundram reviewed gene: TAZ: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| BAP1 associated tumour predisposition syndrome v0.2 | BAP1 | Achchuthan Shanmugasundram reviewed gene: BAP1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Autoimmune Polyendocrine Syndrome v0.2 | AIRE | Achchuthan Shanmugasundram edited their review of gene: AIRE: Changed rating: GREEN; Changed mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Autoimmune Polyendocrine Syndrome v0.2 | AIRE | Achchuthan Shanmugasundram commented on gene: AIRE | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| von Willebrand disease v0.1 | VWF |
Achchuthan Shanmugasundram gene: VWF was added gene: VWF was added to von Willebrand disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: VWF was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal |
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| Wiskott-Aldrich syndrome v0.1 | WAS |
Achchuthan Shanmugasundram gene: WAS was added gene: WAS was added to Wiskott-Aldrich syndrome. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: WAS was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Wilson disease v0.1 | ATP7B |
Achchuthan Shanmugasundram gene: ATP7B was added gene: ATP7B was added to Wilson disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ATP7B was set to BIALLELIC, autosomal or pseudoautosomal |
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| Von Hippel Lindau syndrome v0.1 | VHL |
Achchuthan Shanmugasundram gene: VHL was added gene: VHL was added to Von Hippel Lindau syndrome. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: VHL was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Variegate porphyria v0.1 | PPOX |
Achchuthan Shanmugasundram gene: PPOX was added gene: PPOX was added to Variegate porphyria. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: PPOX was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Van der Woude syndrome v0.1 | IRF6 |
Achchuthan Shanmugasundram gene: IRF6 was added gene: IRF6 was added to Van der Woude syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: IRF6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Tuberous sclerosis v0.1 | TSC2 |
Achchuthan Shanmugasundram gene: TSC2 was added gene: TSC2 was added to Tuberous sclerosis. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: TSC2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Tuberous sclerosis v0.1 | TSC1 |
Achchuthan Shanmugasundram gene: TSC1 was added gene: TSC1 was added to Tuberous sclerosis. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: TSC1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Thiamine metabolism dysfunction syndrome 2 v0.1 | SLC19A3 |
Achchuthan Shanmugasundram gene: SLC19A3 was added gene: SLC19A3 was added to Thiamine metabolism dysfunction syndrome 2. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: SLC19A3 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Thanatophoric dysplasia v0.1 | FGFR3 |
Achchuthan Shanmugasundram gene: FGFR3 was added gene: FGFR3 was added to Thanatophoric dysplasia. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: FGFR3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Sickle cell, thalassaemia and other haemoglobinopathies v0.1 | HBB |
Achchuthan Shanmugasundram gene: HBB was added gene: HBB was added to Thalassaemia and other haemoglobinopathies. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: HBB was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Sickle cell, thalassaemia and other haemoglobinopathies v0.1 | HBA1 |
Achchuthan Shanmugasundram gene: HBA1 was added gene: HBA1 was added to Thalassaemia and other haemoglobinopathies. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: HBA1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal |
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| Tay-Sachs disease v0.1 | HEXA |
Achchuthan Shanmugasundram gene: HEXA was added gene: HEXA was added to Tay-Sachs disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: HEXA was set to BIALLELIC, autosomal or pseudoautosomal |
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| Syndromic and non syndromic craniosynostosis involving midline sutures v0.1 | SMAD6 |
Achchuthan Shanmugasundram gene: SMAD6 was added gene: SMAD6 was added to Syndromic and non syndromic craniosynostosis involving midline sutures. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: SMAD6 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Subcutaneous panniculitis T-cell lymphoma (SPTCL) v0.1 | HAVCR2 |
Achchuthan Shanmugasundram gene: HAVCR2 was added gene: HAVCR2 was added to Subcutaneous panniculitis T-cell lymphoma (SPTCL). Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: HAVCR2 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Spinal muscular atrophy type 1 rare mutation testing v0.1 | SMN1 |
Achchuthan Shanmugasundram gene: SMN1 was added gene: SMN1 was added to Spinal muscular atrophy type 1 rare mutation testing. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SMN1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Smith-Lemli-Opitz syndrome v0.1 | DHCR7 |
Achchuthan Shanmugasundram gene: DHCR7 was added gene: DHCR7 was added to Smith-Lemli-Opitz syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: DHCR7 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Sitosterolaemia v0.1 | ABCG8 |
Achchuthan Shanmugasundram gene: ABCG8 was added gene: ABCG8 was added to Sitosterolaemia. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ABCG8 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Sitosterolaemia v0.1 | ABCG5 |
Achchuthan Shanmugasundram gene: ABCG5 was added gene: ABCG5 was added to Sitosterolaemia. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ABCG5 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Short stature - SHOX deficiency v0.1 | SHOX |
Achchuthan Shanmugasundram gene: SHOX was added gene: SHOX was added to Short stature - SHOX deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: SHOX was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal |
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| Severe combined immunodeficiency with PNP deficiency v0.1 | PNP |
Achchuthan Shanmugasundram gene: PNP was added gene: PNP was added to Severe combined immunodeficiency with PNP deficiency. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: PNP was set to BIALLELIC, autosomal or pseudoautosomal |
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| Severe combined immunodeficiency with adenosine deaminase deficiency v0.1 | ADA |
Achchuthan Shanmugasundram gene: ADA was added gene: ADA was added to Severe combined immunodeficiency with adenosine deaminase deficiency. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ADA was set to BIALLELIC, autosomal or pseudoautosomal |
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| Segmental or atypical neurofibromatosis type 1 testing v0.1 | NF1 |
Achchuthan Shanmugasundram gene: NF1 was added gene: NF1 was added to Segmental or atypical neurofibromatosis type 1 testing. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: NF1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| SCID with features of gamma chain deficiency v0.1 | IL2RG |
Achchuthan Shanmugasundram gene: IL2RG was added gene: IL2RG was added to SCID with features of gamma chain deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: IL2RG was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Sandhoff disease v0.1 | HEXB |
Achchuthan Shanmugasundram gene: HEXB was added gene: HEXB was added to Sandhoff disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: HEXB was set to BIALLELIC, autosomal or pseudoautosomal |
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| Retinoblastoma v0.1 | RB1 |
Achchuthan Shanmugasundram gene: RB1 was added gene: RB1 was added to Retinoblastoma. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: RB1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Phenylketonuria v0.1 | PAH |
Achchuthan Shanmugasundram gene: PAH was added gene: PAH was added to Phenylketonuria. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: PAH was set to BIALLELIC, autosomal or pseudoautosomal |
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| Pulmonary alveolar microlithiasis v0.1 | SLC34A2 |
Achchuthan Shanmugasundram gene: SLC34A2 was added gene: SLC34A2 was added to Pulmonary alveolar microlithiasis. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: SLC34A2 was set to BIALLELIC, autosomal or pseudoautosomal |
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| PTEN Hamartoma Tumour Syndrome v0.1 | PTEN |
Achchuthan Shanmugasundram gene: PTEN was added gene: PTEN was added to PTEN Hamartoma Tumor Syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: PTEN was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Pseudoxanthoma elasticum v0.1 | ENPP1 |
Achchuthan Shanmugasundram gene: ENPP1 was added gene: ENPP1 was added to Pseudoxanthoma elasticum. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: ENPP1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Pseudoxanthoma elasticum v0.1 | ABCC6 |
Achchuthan Shanmugasundram gene: ABCC6 was added gene: ABCC6 was added to Pseudoxanthoma elasticum. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: ABCC6 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Primary hyperaldosteronism - KCNJ5 v0.1 | KCNJ5 |
Achchuthan Shanmugasundram gene: KCNJ5 was added gene: KCNJ5 was added to Primary hyperaldosteronism - KCNJ5. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: KCNJ5 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| POLG-related disorder v0.1 | POLG |
Achchuthan Shanmugasundram gene: POLG was added gene: POLG was added to POLG-related disorder. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: POLG was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Peutz Jeghers Syndrome v0.1 | STK11 |
Achchuthan Shanmugasundram gene: STK11 was added gene: STK11 was added to Peutz Jeghers Syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: STK11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome v0.1 | SUFU |
Achchuthan Shanmugasundram gene: SUFU was added gene: SUFU was added to Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SUFU was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome v0.1 | PTCH1 |
Achchuthan Shanmugasundram gene: PTCH1 was added gene: PTCH1 was added to Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: PTCH1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Nijmegen breakage syndrome v0.1 | NBN |
Achchuthan Shanmugasundram gene: NBN was added gene: NBN was added to Nijmegen breakage syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: NBN was set to BIALLELIC, autosomal or pseudoautosomal |
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| Niemann-Pick disease type A or B v0.1 | SMPD1 |
Achchuthan Shanmugasundram gene: SMPD1 was added gene: SMPD1 was added to Niemann-Pick disease type A or B. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: SMPD1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Niemann Pick disease type C v0.1 | NPC2 |
Achchuthan Shanmugasundram gene: NPC2 was added gene: NPC2 was added to Niemann Pick disease type C. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: NPC2 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Niemann Pick disease type C v0.1 | NPC1 |
Achchuthan Shanmugasundram gene: NPC1 was added gene: NPC1 was added to Niemann Pick disease type C. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: NPC1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Neutropaenia consistent with ELANE mutations v0.1 | ELANE |
Achchuthan Shanmugasundram gene: ELANE was added gene: ELANE was added to Neutropaenia consistent with ELANE mutations. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: ELANE was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Neuronal ceroid lipofuscinosis type 2 v0.1 | TPP1 |
Achchuthan Shanmugasundram gene: TPP1 was added gene: TPP1 was added to Neuronal ceroid lipofuscinosis type 2. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: TPP1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Neurofibromatosis type 1 (GMS) v0.1 | SPRED1 |
Achchuthan Shanmugasundram gene: SPRED1 was added gene: SPRED1 was added to Neurofibromatosis type 1 (GMS). Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SPRED1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Neurofibromatosis type 1 (GMS) v0.1 | NF1 |
Achchuthan Shanmugasundram gene: NF1 was added gene: NF1 was added to Neurofibromatosis type 1 (GMS). Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: NF1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Neonatal diabetes - small panel v0.1 | KCNJ11 |
Achchuthan Shanmugasundram gene: KCNJ11 was added gene: KCNJ11 was added to Neonatal diabetes - small panel. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: KCNJ11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Neonatal diabetes - small panel v0.1 | ABCC8 |
Achchuthan Shanmugasundram gene: ABCC8 was added gene: ABCC8 was added to Neonatal diabetes - small panel. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ABCC8 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| NARP syndrome or maternally inherited Leigh syndrome v0.1 | MT-ND6 |
Achchuthan Shanmugasundram gene: MT-ND6 was added gene: MT-ND6 was added to NARP syndrome or maternally inherited Leigh syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene gene: MT-ND6 was set to MITOCHONDRIAL |
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| NARP syndrome or maternally inherited Leigh syndrome v0.1 | MT-ATP6 |
Achchuthan Shanmugasundram gene: MT-ATP6 was added gene: MT-ATP6 was added to NARP syndrome or maternally inherited Leigh syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene gene: MT-ATP6 was set to MITOCHONDRIAL |
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| Multiple exostoses v0.1 | EXT2 |
Achchuthan Shanmugasundram gene: EXT2 was added gene: EXT2 was added to Multiple exostoses. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: EXT2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Multiple exostoses v0.1 | EXT1 |
Achchuthan Shanmugasundram gene: EXT1 was added gene: EXT1 was added to Multiple exostoses. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: EXT1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Multiple endocrine neoplasia type 2 v0.1 | RET |
Achchuthan Shanmugasundram gene: RET was added gene: RET was added to Multiple endocrine neoplasia type 2. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: RET was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Mucopolysaccharidosis type II v0.1 | IDS |
Achchuthan Shanmugasundram gene: IDS was added gene: IDS was added to Mucopolysaccharidosis type II. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: IDS was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Mucopolysaccharidosis type VI v0.1 | ARSB |
Achchuthan Shanmugasundram gene: ARSB was added gene: ARSB was added to Mucopolysaccharidosis type VI. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: ARSB was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mucopolysaccharidosis type IVA v0.1 | GALNS |
Achchuthan Shanmugasundram gene: GALNS was added gene: GALNS was added to Mucopolysaccharidosis type IVA. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: GALNS was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mucopolysaccharidosis type IIIB v0.1 | NAGLU |
Achchuthan Shanmugasundram gene: NAGLU was added gene: NAGLU was added to Mucopolysaccharidosis type IIIB. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: NAGLU was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mucopolysaccharidosis type IIIA v0.1 | SGSH |
Achchuthan Shanmugasundram gene: SGSH was added gene: SGSH was added to Mucopolysaccharidosis type IIIA. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SGSH was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mucopolysaccharidosis type IH or S v0.1 | IDUA |
Achchuthan Shanmugasundram gene: IDUA was added gene: IDUA was added to Mucopolysaccharidosis type IH/S. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: IDUA was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mucolipidosis II and III Alpha or Beta v0.1 | GNPTAB |
Achchuthan Shanmugasundram gene: GNPTAB was added gene: GNPTAB was added to Mucolipidosis II and III Alpha/Beta. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: GNPTAB was set to BIALLELIC, autosomal or pseudoautosomal |
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| Monitoring for G(M)CSF escape mutations v0.1 | CSF3R |
Achchuthan Shanmugasundram gene: CSF3R was added gene: CSF3R was added to Monitoring for G(M)CSF escape mutations. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CSF3R was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mitochondrial neurogastrointestinal encephalopathy v0.1 | TYMP |
Achchuthan Shanmugasundram gene: TYMP was added gene: TYMP was added to Mitochondrial neurogastrointestinal encephalopathy. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: TYMP was set to BIALLELIC, autosomal or pseudoautosomal |
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| Mitochondrial Complex V deficiency, TMEM70 type v0.1 | TMEM70 |
Achchuthan Shanmugasundram gene: TMEM70 was added gene: TMEM70 was added to Mitochondrial Complex V deficiency, TMEM70 type. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: TMEM70 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Lysosomal acid lipase deficiency v0.1 | LIPA |
Achchuthan Shanmugasundram gene: LIPA was added gene: LIPA was added to Lysosomal acid lipase deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: LIPA was set to BIALLELIC, autosomal or pseudoautosomal |
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| Lymphoproliferative syndrome with absent SAP expression v0.1 | SH2D1A |
Achchuthan Shanmugasundram gene: SH2D1A was added gene: SH2D1A was added to Lymphoproliferative syndrome with absent SAP expression. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SH2D1A was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Krabbe disease - Saposin A deficiency v0.1 | PSAP |
Achchuthan Shanmugasundram gene: PSAP was added gene: PSAP was added to Krabbe disease - Saposin A deficiency. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: PSAP was set to BIALLELIC, autosomal or pseudoautosomal |
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| Krabbe disease - GALC deficiency v0.1 | GALC |
Achchuthan Shanmugasundram gene: GALC was added gene: GALC was added to Krabbe disease - GALC deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: GALC was set to BIALLELIC, autosomal or pseudoautosomal |
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| Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) v0.1 | PAX5 |
Achchuthan Shanmugasundram gene: PAX5 was added gene: PAX5 was added to Inherited susceptibility to acute lymphoblastoid leukaemia (ALL). Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: PAX5 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) v0.1 | ETV6 |
Achchuthan Shanmugasundram gene: ETV6 was added gene: ETV6 was added to Inherited susceptibility to acute lymphoblastoid leukaemia (ALL). Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ETV6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Adult onset neurodegenerative disorder v4.28 | FXN_GAA | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: FXN_GAA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | FXN_GAA | Sarah Leigh edited their review of STR: FXN_GAA: Added comment: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| IPEX - Immunodysregulation Polyendocrinopathy and Enteropathy, X-Linked v0.1 | FOXP3 |
Achchuthan Shanmugasundram gene: FOXP3 was added gene: FOXP3 was added to IPEX - Immunodysregulation Polyendocrinopathy and Enteropathy, X-Linked. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: FOXP3 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Inherited parathyroid cancer v0.1 | CDC73 |
Achchuthan Shanmugasundram gene: CDC73 was added gene: CDC73 was added to Inherited parathyroid cancer. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CDC73 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Inherited breast cancer and ovarian cancer v2.7 | RAD51D | Achchuthan Shanmugasundram Source NHS GMS was added to RAD51D. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited breast cancer and ovarian cancer v2.7 | RAD51C | Achchuthan Shanmugasundram Source NHS GMS was added to RAD51C. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Incontinentia pigmenti v0.1 | IKBKG |
Achchuthan Shanmugasundram gene: IKBKG was added gene: IKBKG was added to Incontinentia pigmenti. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: IKBKG was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) |
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| Hirschsprung disease v0.1 | RET |
Achchuthan Shanmugasundram gene: RET was added gene: RET was added to Hirschsprung disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: RET was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Hereditary angioedema types I and II v0.1 | SERPING1 |
Achchuthan Shanmugasundram gene: SERPING1 was added gene: SERPING1 was added to Hereditary angioedema types I and II. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: SERPING1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Haemophagocytic syndrome with absent XIAP expression v0.1 | XIAP |
Achchuthan Shanmugasundram gene: XIAP was added gene: XIAP was added to Haemophagocytic syndrome with absent XIAP expression. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: XIAP was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) |
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| Haemophagocytic syndrome with absent perforin expression v0.1 | PRF1 |
Achchuthan Shanmugasundram gene: PRF1 was added gene: PRF1 was added to Haemophagocytic syndrome with absent perforin expression. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: PRF1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.1 | HBB |
Achchuthan Shanmugasundram gene: HBB was added gene: HBB was added to Haemoglobinopathy trait or carrier testing. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: HBB was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.1 | HBA1 |
Achchuthan Shanmugasundram gene: HBA1 was added gene: HBA1 was added to Haemoglobinopathy trait or carrier testing. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: HBA1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal |
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| GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB v0.1 | GLB1 |
Achchuthan Shanmugasundram gene: GLB1 was added gene: GLB1 was added to GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: GLB1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Glycogen storage disease V v0.1 | PYGM |
Achchuthan Shanmugasundram gene: PYGM was added gene: PYGM was added to Glycogen storage disease V. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: PYGM was set to BIALLELIC, autosomal or pseudoautosomal |
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| Glucokinase-related fasting hyperglycaemia v0.1 | GCK |
Achchuthan Shanmugasundram gene: GCK was added gene: GCK was added to Glucokinase-related fasting hyperglycaemia. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: GCK was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Generalised arterial calcification in infancy v0.1 | ENPP1 |
Achchuthan Shanmugasundram gene: ENPP1 was added gene: ENPP1 was added to Generalised arterial calcification in infancy. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ENPP1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Generalised arterial calcification in infancy v0.1 | ABCC6 |
Achchuthan Shanmugasundram gene: ABCC6 was added gene: ABCC6 was added to Generalised arterial calcification in infancy. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ABCC6 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Gaucher disease v0.1 | GBA |
Achchuthan Shanmugasundram gene: GBA was added gene: GBA was added to Gaucher disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: GBA was set to BIALLELIC, autosomal or pseudoautosomal |
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| Fumarate hydratase-related tumour syndromes v0.1 | FH |
Achchuthan Shanmugasundram gene: FH was added gene: FH was added to Fumarate hydratase-related tumour syndromes. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: FH was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Familial tumours of the nervous system v0.1 | SUFU |
Achchuthan Shanmugasundram gene: SUFU was added gene: SUFU was added to Familial tumours of the nervous system. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SUFU was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Familial tumours of the nervous system v0.1 | SMARCE1 |
Achchuthan Shanmugasundram gene: SMARCE1 was added gene: SMARCE1 was added to Familial tumours of the nervous system. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SMARCE1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Familial tumours of the nervous system v0.1 | SMARCB1 |
Achchuthan Shanmugasundram gene: SMARCB1 was added gene: SMARCB1 was added to Familial tumours of the nervous system. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SMARCB1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Familial tumours of the nervous system v0.1 | NF2 |
Achchuthan Shanmugasundram gene: NF2 was added gene: NF2 was added to Familial tumours of the nervous system. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: NF2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Familial tumours of the nervous system v0.1 | LZTFL1 |
Achchuthan Shanmugasundram gene: LZTFL1 was added gene: LZTFL1 was added to Familial tumours of the nervous system. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: LZTFL1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Familial tumours of the nervous system v0.1 | DGCR8 |
Achchuthan Shanmugasundram gene: DGCR8 was added gene: DGCR8 was added to Familial tumours of the nervous system. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: DGCR8 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Adult onset hereditary spastic paraplegia v3.10 | ATXN10_ATTCT | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN10_ATTCT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Familial dysalbuminaemic hyperthyroxinaemia v0.1 | ALB |
Achchuthan Shanmugasundram gene: ALB was added gene: ALB was added to Familial dysalbuminaemic hyperthyroxinaemia. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ALB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Adult onset hereditary spastic paraplegia v3.10 | ATXN10_ATTCT | Sarah Leigh reviewed STR: ATXN10_ATTCT: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor XIII deficiency v0.1 | F13B |
Achchuthan Shanmugasundram gene: F13B was added gene: F13B was added to Factor XIII deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: F13B was set to BIALLELIC, autosomal or pseudoautosomal |
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| Factor XIII deficiency v0.1 | F13A1 |
Achchuthan Shanmugasundram gene: F13A1 was added gene: F13A1 was added to Factor XIII deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: F13A1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | PPP2R2B_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: PPP2R2B_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor XI deficiency v0.1 | F11 |
Achchuthan Shanmugasundram gene: F11 was added gene: F11 was added to Factor XI deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: F11 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | CACNA1A_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: CACNA1A_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor X deficiency v0.1 | F10 |
Achchuthan Shanmugasundram gene: F10 was added gene: F10 was added to Factor X deficiency. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: F10 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | ATXN3_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN3_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor VIII deficiency v0.1 | F8 |
Achchuthan Shanmugasundram gene: F8 was added gene: F8 was added to Factor VIII deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: F8 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | ATXN2_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN2_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor VII deficiency v0.1 | F7 |
Achchuthan Shanmugasundram gene: F7 was added gene: F7 was added to Factor VII deficiency. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: F7 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | ATXN1_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN1_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.4 | CSTB_CCCCGCCCCGCG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: CSTB_CCCCGCCCCGCG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.4 | PPP2R2B_CAG | Sarah Leigh reviewed STR: PPP2R2B_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.4 | CACNA1A_CAG | Sarah Leigh reviewed STR: CACNA1A_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor V deficiency v0.1 | F5 |
Achchuthan Shanmugasundram gene: F5 was added gene: F5 was added to Factor V deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: F5 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | ATXN3_CAG | Sarah Leigh reviewed STR: ATXN3_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor IX deficiency v0.1 | F9 |
Achchuthan Shanmugasundram gene: F9 was added gene: F9 was added to Factor IX deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: F9 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | ATXN2_CAG | Sarah Leigh reviewed STR: ATXN2_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Factor II deficiency v0.1 | F2 |
Achchuthan Shanmugasundram gene: F2 was added gene: F2 was added to Factor II deficiency. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: F2 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Adult onset dystonia, chorea or related movement disorder v3.4 | ATXN1_CAG | Sarah Leigh reviewed STR: ATXN1_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.4 | CSTB_CCCCGCCCCGCG | Sarah Leigh edited their review of STR: CSTB_CCCCGCCCCGCG: Added comment: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Facioscapulohumeral muscular dystrophy - extended testing v0.1 | SMCHD1 |
Achchuthan Shanmugasundram gene: SMCHD1 was added gene: SMCHD1 was added to Facioscapulohumeral muscular dystrophy - extended testing. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: SMCHD1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Fabry disease v0.1 | GLA |
Achchuthan Shanmugasundram gene: GLA was added gene: GLA was added to Fabry disease. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: GLA was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) |
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| Elastin-related phenotypes v0.1 | ELN |
Achchuthan Shanmugasundram gene: ELN was added gene: ELN was added to Elastin-related phenotypes. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: ELN was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Duchenne or Becker muscular dystrophy v0.1 | DMD |
Achchuthan Shanmugasundram gene: DMD was added gene: DMD was added to Duchenne or Becker muscular dystrophy. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: DMD was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| DICER1-related cancer predisposition v0.1 | DICER1 |
Achchuthan Shanmugasundram gene: DICER1 was added gene: DICER1 was added to DICER1-related cancer predisposition. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: DICER1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Adult onset neurodegenerative disorder v4.28 | NOP56_GGCCTG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: NOP56_GGCCTG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | PPP2R2B_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: PPP2R2B_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CSTB_CCCCGCCCCGCG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: CSTB_CCCCGCCCCGCG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CACNA1A_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: CACNA1A_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN7_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN7_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN3_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN3_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN2_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN2_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN1_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN1_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN10_ATTCT | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATXN10_ATTCT. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | TBP_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: TBP_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | JPH3_CTG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: JPH3_CTG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | PPP2R2B_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | PPP2R2B_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | JPH3_CTG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CSTB_CCCCGCCCCGCG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CSTB_CCCCGCCCCGCG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CACNA1A_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN7_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN3_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN2_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN1_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN10_ATTCT | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | TBP_CAG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | JPH3_CTG | Sarah Leigh changed review comment from: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; to: It is recommended this STR be promoted to Green following GMS review, as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | NOP56_GGCCTG | Sarah Leigh reviewed STR: NOP56_GGCCTG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | PPP2R2B_CAG | Sarah Leigh reviewed STR: PPP2R2B_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | JPH3_CTG | Sarah Leigh commented on STR: JPH3_CTG: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CSTB_CCCCGCCCCGCG | Sarah Leigh edited their review of STR: CSTB_CCCCGCCCCGCG: Added comment: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | CACNA1A_CAG | Sarah Leigh reviewed STR: CACNA1A_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN7_CAG | Sarah Leigh reviewed STR: ATXN7_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN3_CAG | Sarah Leigh reviewed STR: ATXN3_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN2_CAG | Sarah Leigh reviewed STR: ATXN2_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN1_CAG | Sarah Leigh reviewed STR: ATXN1_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATXN10_ATTCT | Sarah Leigh reviewed STR: ATXN10_ATTCT: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | TBP_CAG | Sarah Leigh reviewed STR: TBP_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | JPH3_CTG | Sarah Leigh edited their review of STR: JPH3_CTG: Added comment: It is recommended this STR be promoted to Green following GMS review as the testing method for this clinicial indication is now WGS.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATN1_CAG | Sarah Leigh Tag Q3_23_promote_green tag was added to STR: ATN1_CAG. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | ATN1_CAG | Sarah Leigh reviewed STR: ATN1_CAG: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystinosis v0.1 | CTNS |
Achchuthan Shanmugasundram gene: CTNS was added gene: CTNS was added to Cystinosis. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CTNS was set to BIALLELIC, autosomal or pseudoautosomal |
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| Cystic fibrosis diagnostic test v0.1 | CFTR |
Achchuthan Shanmugasundram gene: CFTR was added gene: CFTR was added to Cystic fibrosis diagnostic test. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CFTR was set to BIALLELIC, autosomal or pseudoautosomal |
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| Congenital adrenal hyperplasia diagnostic test v0.1 | CYP21A2 |
Achchuthan Shanmugasundram gene: CYP21A2 was added gene: CYP21A2 was added to Congenital adrenal hyperplasia diagnostic test. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CYP21A2 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Combined vitamin K-dependent clotting factor deficiency v0.1 | VKORC1 |
Achchuthan Shanmugasundram gene: VKORC1 was added gene: VKORC1 was added to Combined vitamin K-dependent clotting factor deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: VKORC1 was set to BIALLELIC, autosomal or pseudoautosomal |
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| Combined vitamin K-dependent clotting factor deficiency v0.1 | GGCX |
Achchuthan Shanmugasundram gene: GGCX was added gene: GGCX was added to Combined vitamin K-dependent clotting factor deficiency. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: GGCX was set to BIALLELIC, autosomal or pseudoautosomal |
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| Cleidocranial Dysplasia v0.1 | RUNX2 |
Achchuthan Shanmugasundram gene: RUNX2 was added gene: RUNX2 was added to Cleidocranial Dysplasia. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: RUNX2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Central congenital hypoventilation v0.1 | PHOX2B |
Achchuthan Shanmugasundram gene: PHOX2B was added gene: PHOX2B was added to Central congenital hypoventilation. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: PHOX2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Carney complex v0.1 | PRKAR1A |
Achchuthan Shanmugasundram gene: PRKAR1A was added gene: PRKAR1A was added to Carney complex. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: PRKAR1A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Calcium-sensing receptor phenotypes v0.1 | CASR |
Achchuthan Shanmugasundram gene: CASR was added gene: CASR was added to Calcium-sensing receptor phenotypes. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CASR was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| CADASIL v0.1 | NOTCH3 |
Achchuthan Shanmugasundram gene: NOTCH3 was added gene: NOTCH3 was added to CADASIL. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: NOTCH3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted |
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| Blepharophimosis ptosis and epicanthus inversus v0.1 | FOXL2 |
Achchuthan Shanmugasundram gene: FOXL2 was added gene: FOXL2 was added to Blepharophimosis ptosis and epicanthus inversus. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: FOXL2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal |
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| Beckwith-Wiedemann syndrome v0.1 | CDKN1C |
Achchuthan Shanmugasundram gene: CDKN1C was added gene: CDKN1C was added to Beckwith-Wiedemann syndrome. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: CDKN1C was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Barth syndrome v0.1 | TAZ |
Achchuthan Shanmugasundram gene: TAZ was added gene: TAZ was added to Barth syndrome. Sources: NHS GMS,Expert Review Green Mode of inheritance for gene: TAZ was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females |
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| BAP1 associated tumour predisposition syndrome v0.2 | BAP1 |
Achchuthan Shanmugasundram gene: BAP1 was added gene: BAP1 was added to BAP1 associated tumour predisposition syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: BAP1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown |
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| Autoimmune Polyendocrine Syndrome v0.2 | AIRE |
Achchuthan Shanmugasundram gene: AIRE was added gene: AIRE was added to Autoimmune Polyendocrine Syndrome. Sources: Expert Review Green,NHS GMS Mode of inheritance for gene: AIRE was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal |
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| Agammaglobulinaemia with absent BTK expression v0.7 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute intermittent porphyria v0.8 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Autoimmune lymphoproliferative syndrome with defective apoptosis v0.6 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia telangiectasia - mutation testing v0.7 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| APC associated Polyposis v0.8 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Alveolar capillary dysplasia with misalignment of pulmonary veins v0.6 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Alstrom syndrome v0.6 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Albright hereditary osteodystrophy, pseudohypoparathyroidism, pseudopseudohypoparathyroidism, acrodysostosis and osteoma cutis v0.7 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Wiskott-Aldrich syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Wiskott-Aldrich syndrome Set list of related panels to R20 Set panel types to: GMS Rare Disease |
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| Wilson disease v0.0 |
Achchuthan Shanmugasundram Added Panel Wilson disease Set list of related panels to R172 Set panel types to: GMS Rare Disease |
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| von Willebrand disease v0.0 |
Achchuthan Shanmugasundram Added Panel von Willebrand disease Set list of related panels to R121 Set panel types to: GMS Rare Disease |
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| Von Hippel Lindau syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Von Hippel Lindau syndrome Set list of related panels to R225 Set panel types to: GMS Rare Disease |
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| Variegate porphyria v0.0 |
Achchuthan Shanmugasundram Added Panel Variegate porphyria Set list of related panels to R170 Set panel types to: GMS Rare Disease |
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| Van der Woude syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Van der Woude syndrome Set list of related panels to R284 Set panel types to: GMS Rare Disease |
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| Tuberous sclerosis v0.0 |
Achchuthan Shanmugasundram Added Panel Tuberous sclerosis Set list of related panels to R228 Set panel types to: GMS Rare Disease |
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| Thiamine metabolism dysfunction syndrome 2 v0.0 |
Achchuthan Shanmugasundram Added Panel Thiamine metabolism dysfunction syndrome 2 Set list of related panels to R395 Set panel types to: GMS Rare Disease |
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| Thanatophoric dysplasia v0.0 |
Achchuthan Shanmugasundram Added Panel Thanatophoric dysplasia Set list of related panels to R25 Set panel types to: GMS Rare Disease |
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| Sickle cell, thalassaemia and other haemoglobinopathies v0.0 |
Achchuthan Shanmugasundram Added Panel Thalassaemia and other haemoglobinopathies Set list of related panels to R93 Set panel types to: GMS Rare Disease |
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| Tay-Sachs disease v0.0 |
Achchuthan Shanmugasundram Added Panel Tay-Sachs disease Set list of related panels to R286 Set panel types to: GMS Rare Disease |
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| Syndromic and non syndromic craniosynostosis involving midline sutures v0.0 |
Achchuthan Shanmugasundram Added Panel Syndromic and non syndromic craniosynostosis involving midline sutures Set list of related panels to R416 Set panel types to: GMS Rare Disease |
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| Subcutaneous panniculitis T-cell lymphoma (SPTCL) v0.0 |
Achchuthan Shanmugasundram Added Panel Subcutaneous panniculitis T-cell lymphoma (SPTCL) Set list of related panels to R424 Set panel types to: GMS Rare Disease |
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| Spinal muscular atrophy type 1 rare mutation testing v0.0 |
Achchuthan Shanmugasundram Added Panel Spinal muscular atrophy type 1 rare mutation testing Set list of related panels to R71 Set panel types to: GMS Rare Disease |
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| Smith-Lemli-Opitz syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Smith-Lemli-Opitz syndrome Set list of related panels to R270 Set panel types to: GMS Rare Disease |
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| Sitosterolaemia v0.0 |
Achchuthan Shanmugasundram Added Panel Sitosterolaemia Set list of related panels to R323 Set panel types to: GMS Rare Disease |
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| Short stature - SHOX deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Short stature - SHOX deficiency Set list of related panels to R52 Set panel types to: GMS Rare Disease |
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| Severe combined immunodeficiency with PNP deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Severe combined immunodeficiency with PNP deficiency Set list of related panels to R234 Set panel types to: GMS Rare Disease |
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| Severe combined immunodeficiency with adenosine deaminase deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Severe combined immunodeficiency with adenosine deaminase deficiency Set list of related panels to R16 Set panel types to: GMS Rare Disease |
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| Segmental or atypical neurofibromatosis type 1 testing v0.0 |
Achchuthan Shanmugasundram Added Panel Segmental or atypical neurofibromatosis type 1 testing Set list of related panels to R376 Set panel types to: GMS Rare Disease |
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| SCID with features of gamma chain deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel SCID with features of gamma chain deficiency Set list of related panels to R235 Set panel types to: GMS Rare Disease |
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| Sandhoff disease v0.0 |
Achchuthan Shanmugasundram Added Panel Sandhoff disease Set list of related panels to R285 Set panel types to: GMS Rare Disease |
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| Retinoblastoma v0.0 |
Achchuthan Shanmugasundram Added Panel Retinoblastoma Set list of related panels to R219 Set panel types to: GMS Rare Disease |
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| Pulmonary alveolar microlithiasis v0.0 |
Achchuthan Shanmugasundram Added Panel Pulmonary alveolar microlithiasis Set list of related panels to R426 Set panel types to: GMS Rare Disease |
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| PTEN Hamartoma Tumour Syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel PTEN Hamartoma Tumor Syndrome Set list of related panels to R213 Set panel types to: GMS Rare Disease |
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| Pseudoxanthoma elasticum v0.0 |
Achchuthan Shanmugasundram Added Panel Pseudoxanthoma elasticum Set list of related panels to R420 Set panel types to: GMS Rare Disease |
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| Primary hyperaldosteronism - KCNJ5 v0.0 |
Achchuthan Shanmugasundram Added Panel Primary hyperaldosteronism - KCNJ5 Set list of related panels to R344 Set panel types to: GMS Rare Disease |
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| POLG-related disorder v0.0 |
Achchuthan Shanmugasundram Added Panel POLG-related disorder Set list of related panels to R315 Set panel types to: GMS Rare Disease |
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| Phenylketonuria v0.0 |
Achchuthan Shanmugasundram Added Panel Phenylketonuria Set list of related panels to R283 Set panel types to: GMS Rare Disease |
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| Peutz Jeghers Syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Peutz Jeghers Syndrome Set list of related panels to R212 Set panel types to: GMS Rare Disease |
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| Nijmegen breakage syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Nijmegen breakage syndrome Set list of related panels to R259.2 Set panel types to: GMS Rare Disease |
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| Niemann-Pick disease type A or B v0.0 |
Achchuthan Shanmugasundram Added Panel Niemann-Pick disease type A or B Set list of related panels to R282 Set panel types to: GMS Rare Disease |
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| Niemann Pick disease type C v0.0 |
Achchuthan Shanmugasundram Added Panel Niemann Pick disease type C Set list of related panels to R380 Set panel types to: GMS Rare Disease |
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| Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Nevoid Basal Cell Carcinoma Syndrome or Gorlin syndrome Set list of related panels to R214 Set panel types to: GMS Rare Disease |
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| Neutropaenia consistent with ELANE mutations v0.0 |
Achchuthan Shanmugasundram Added Panel Neutropaenia consistent with ELANE mutations Set list of related panels to R313 Set panel types to: GMS Rare Disease |
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| Neuronal ceroid lipofuscinosis type 2 v0.0 |
Achchuthan Shanmugasundram Added Panel Neuronal ceroid lipofuscinosis type 2 Set list of related panels to R271 Set panel types to: GMS Rare Disease |
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| Neurofibromatosis type 1 (GMS) v0.0 |
Achchuthan Shanmugasundram Added Panel Neurofibromatosis type 1 (GMS) Set list of related panels to R222 Set panel types to: GMS Rare Disease |
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| Neonatal diabetes - small panel v0.0 |
Achchuthan Shanmugasundram Added Panel Neonatal diabetes - small panel Set list of related panels to R143 Set panel types to: GMS Rare Disease |
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| NARP syndrome or maternally inherited Leigh syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel NARP syndrome or maternally inherited Leigh syndrome Set list of related panels to R351 Set panel types to: GMS Rare Disease |
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| Multiple exostoses v0.0 |
Achchuthan Shanmugasundram Added Panel Multiple exostoses Set list of related panels to R390 Set panel types to: GMS Rare Disease |
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| Multiple endocrine neoplasia type 2 v0.0 |
Achchuthan Shanmugasundram Added Panel Multiple endocrine neoplasia type 2 Set list of related panels to R218 Set panel types to: GMS Rare Disease |
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| Mucopolysaccharidosis type VI v0.0 |
Achchuthan Shanmugasundram Added Panel Mucopolysaccharidosis type VI Set list of related panels to R290 Set panel types to: GMS Rare Disease |
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| Mucopolysaccharidosis type IVA v0.0 |
Achchuthan Shanmugasundram Added Panel Mucopolysaccharidosis type IVA Set list of related panels to R287 Set panel types to: GMS Rare Disease |
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| Mucopolysaccharidosis type IIIB v0.0 |
Achchuthan Shanmugasundram Added Panel Mucopolysaccharidosis type IIIB Set list of related panels to R292 Set panel types to: GMS Rare Disease |
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| Mucopolysaccharidosis type IIIA v0.0 |
Achchuthan Shanmugasundram Added Panel Mucopolysaccharidosis type IIIA Set list of related panels to R291 Set panel types to: GMS Rare Disease |
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| Mucopolysaccharidosis type II v0.0 |
Achchuthan Shanmugasundram Added Panel Mucopolysaccharidosis type II Set list of related panels to R278 Set panel types to: GMS Rare Disease |
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| Mucopolysaccharidosis type IH or S v0.0 |
Achchuthan Shanmugasundram Added Panel Mucopolysaccharidosis type IH/S Set list of related panels to R277 Set panel types to: GMS Rare Disease |
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| Mucolipidosis II and III Alpha or Beta v0.0 |
Achchuthan Shanmugasundram Added Panel Mucolipidosis II and III Alpha/Beta Set list of related panels to R289 Set panel types to: GMS Rare Disease |
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| Monitoring for G(M)CSF escape mutations v0.0 |
Achchuthan Shanmugasundram Added Panel Monitoring for G(M)CSF escape mutations Set list of related panels to R338 Set panel types to: GMS Rare Disease |
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| Mitochondrial neurogastrointestinal encephalopathy v0.0 |
Achchuthan Shanmugasundram Added Panel Mitochondrial neurogastrointestinal encephalopathy Set list of related panels to R394 Set panel types to: GMS Rare Disease |
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| Mitochondrial Complex V deficiency, TMEM70 type v0.0 |
Achchuthan Shanmugasundram Added Panel Mitochondrial Complex V deficiency, TMEM70 type Set list of related panels to R396 Set panel types to: GMS Rare Disease |
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| Lysosomal acid lipase deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Lysosomal acid lipase deficiency Set list of related panels to R325 Set panel types to: GMS Rare Disease |
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| Lymphoproliferative syndrome with absent SAP expression v0.0 |
Achchuthan Shanmugasundram Added Panel Lymphoproliferative syndrome with absent SAP expression Set list of related panels to R17 Set panel types to: GMS Rare Disease |
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| Krabbe disease - Saposin A deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Krabbe disease - Saposin A deficiency Set list of related panels to R281 Set panel types to: GMS Rare Disease |
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| Krabbe disease - GALC deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Krabbe disease - GALC deficiency Set list of related panels to R280 Set panel types to: GMS Rare Disease |
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| IPEX - Immunodysregulation Polyendocrinopathy and Enteropathy, X-Linked v0.0 |
Achchuthan Shanmugasundram Added Panel IPEX - Immunodysregulation Polyendocrinopathy and Enteropathy, X-Linked Set list of related panels to R157 Set panel types to: GMS Rare Disease |
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| Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) v0.0 |
Achchuthan Shanmugasundram Added Panel Inherited susceptibility to acute lymphoblastoid leukaemia (ALL) Set list of related panels to R366 Set panel types to: GMS Rare Disease |
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| Inherited parathyroid cancer v0.0 |
Achchuthan Shanmugasundram Added Panel Inherited parathyroid cancer Set list of related panels to R226 Set panel types to: GMS Rare Disease |
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| Incontinentia pigmenti v0.0 |
Achchuthan Shanmugasundram Added Panel Incontinentia pigmenti Set list of related panels to R239 Set panel types to: GMS Rare Disease |
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| Hirschsprung disease v0.0 |
Achchuthan Shanmugasundram Added Panel Hirschsprung disease Set list of related panels to R177 Set panel types to: GMS Rare Disease |
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| Hereditary angioedema types I and II v0.0 |
Achchuthan Shanmugasundram Added Panel Hereditary angioedema types I and II Set list of related panels to R341 Set panel types to: GMS Rare Disease |
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| Haemophagocytic syndrome with absent XIAP expression v0.0 |
Achchuthan Shanmugasundram Added Panel Haemophagocytic syndrome with absent XIAP expression Set list of related panels to R18 Set panel types to: GMS Rare Disease |
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| Haemophagocytic syndrome with absent perforin expression v0.0 |
Achchuthan Shanmugasundram Added Panel Haemophagocytic syndrome with absent perforin expression Set list of related panels to R232 Set panel types to: GMS Rare Disease |
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| Sickle cell, thalassaemia and other haemoglobinopathies trait or carrier testing v0.0 |
Achchuthan Shanmugasundram Added Panel Haemoglobinopathy trait or carrier testing Set list of related panels to R361 Set panel types to: GMS Rare Disease |
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| GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB v0.0 |
Achchuthan Shanmugasundram Added Panel GM1 Gangliosidosis and Mucopolysaccharidosis Type IVB Set list of related panels to R288 Set panel types to: GMS Rare Disease |
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| Glycogen storage disease V v0.0 |
Achchuthan Shanmugasundram Added Panel Glycogen storage disease V Set list of related panels to R273 Set panel types to: GMS Rare Disease |
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| Glucokinase-related fasting hyperglycaemia v0.0 |
Achchuthan Shanmugasundram Added Panel Glucokinase-related fasting hyperglycaemia Set list of related panels to R142 Set panel types to: GMS Rare Disease |
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| Generalised arterial calcification in infancy v0.0 |
Achchuthan Shanmugasundram Added Panel Generalised arterial calcification in infancy Set list of related panels to R384 Set panel types to: GMS Rare Disease |
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| Gaucher disease v0.0 |
Achchuthan Shanmugasundram Added Panel Gaucher disease Set list of related panels to R272 Set panel types to: GMS Rare Disease |
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| Fumarate hydratase-related tumour syndromes v0.0 |
Achchuthan Shanmugasundram Added Panel Fumarate hydratase-related tumour syndromes Set list of related panels to R365 Set panel types to: GMS Rare Disease |
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| Familial tumours of the nervous system v0.0 |
Achchuthan Shanmugasundram Added Panel Familial tumours of the nervous system Set list of related panels to R221 Set panel types to: GMS Rare Disease |
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| Familial dysalbuminaemic hyperthyroxinaemia v0.0 |
Achchuthan Shanmugasundram Added Panel Familial dysalbuminaemic hyperthyroxinaemia Set list of related panels to R329 Set panel types to: GMS Rare Disease |
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| Factor XIII deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor XIII deficiency Set list of related panels to R122 Set panel types to: GMS Rare Disease |
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| Factor XI deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor XI deficiency Set list of related panels to R120 Set panel types to: GMS Rare Disease |
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| Factor X deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor X deficiency Set list of related panels to R119 Set panel types to: GMS Rare Disease |
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| Factor VIII deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor VIII deficiency Set list of related panels to R117 Set panel types to: GMS Rare Disease |
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| Factor VII deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor VII deficiency Set list of related panels to R116 Set panel types to: GMS Rare Disease |
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| Factor V deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor V deficiency Set list of related panels to R115 Set panel types to: GMS Rare Disease |
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| Factor IX deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor IX deficiency Set list of related panels to R118 Set panel types to: GMS Rare Disease |
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| Factor II deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Factor II deficiency Set list of related panels to R112 Set panel types to: GMS Rare Disease |
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| Facioscapulohumeral muscular dystrophy - extended testing v0.0 |
Achchuthan Shanmugasundram Added Panel Facioscapulohumeral muscular dystrophy - extended testing Set list of related panels to R345 Set panel types to: GMS Rare Disease |
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| Fabry disease v0.0 |
Achchuthan Shanmugasundram Added Panel Fabry disease Set list of related panels to R335 Set panel types to: GMS Rare Disease |
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| Elastin-related phenotypes v0.0 |
Achchuthan Shanmugasundram Added Panel Elastin-related phenotypes Set list of related panels to R140 Set panel types to: GMS Rare Disease |
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| Duchenne or Becker muscular dystrophy v0.0 |
Achchuthan Shanmugasundram Added Panel Duchenne or Becker muscular dystrophy Set list of related panels to R73 Set panel types to: GMS Rare Disease |
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| DICER1-related cancer predisposition v0.0 |
Achchuthan Shanmugasundram Added Panel DICER1-related cancer predisposition Set list of related panels to R364 Set panel types to: GMS Rare Disease |
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| Cystinosis v0.0 |
Achchuthan Shanmugasundram Added Panel Cystinosis Set list of related panels to R334 Set panel types to: GMS Rare Disease |
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| Cystic fibrosis diagnostic test v0.0 |
Achchuthan Shanmugasundram Added Panel Cystic fibrosis diagnostic test Set list of related panels to R184 Set panel types to: GMS Rare Disease |
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| Congenital adrenal hyperplasia diagnostic test v0.0 |
Achchuthan Shanmugasundram Added Panel Congenital adrenal hyperplasia diagnostic test Set list of related panels to R180 Set panel types to: GMS Rare Disease |
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| Combined vitamin K-dependent clotting factor deficiency v0.0 |
Achchuthan Shanmugasundram Added Panel Combined vitamin K-dependent clotting factor deficiency Set list of related panels to R123 Set panel types to: GMS Rare Disease |
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| Cleidocranial Dysplasia v0.0 |
Achchuthan Shanmugasundram Added Panel Cleidocranial Dysplasia Set list of related panels to R415 Set panel types to: GMS Rare Disease |
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| Central congenital hypoventilation v0.0 |
Achchuthan Shanmugasundram Added Panel Central congenital hypoventilation Set list of related panels to R333 Set panel types to: GMS Rare Disease |
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| Carney complex v0.0 |
Achchuthan Shanmugasundram Added Panel Carney complex Set list of related panels to R156 Set panel types to: GMS Rare Disease |
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| Calcium-sensing receptor phenotypes v0.0 |
Achchuthan Shanmugasundram Added Panel Calcium-sensing receptor phenotypes Set list of related panels to R319 Set panel types to: GMS Rare Disease |
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| CADASIL v0.0 |
Achchuthan Shanmugasundram Added Panel CADASIL Set list of related panels to R337 Set panel types to: GMS Rare Disease |
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| Blepharophimosis ptosis and epicanthus inversus v0.0 |
Achchuthan Shanmugasundram Added Panel Blepharophimosis ptosis and epicanthus inversus Set list of related panels to R43 Set panel types to: GMS Rare Disease |
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| Beckwith-Wiedemann syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Beckwith-Wiedemann syndrome Set list of related panels to R49.3 Set panel types to: GMS Rare Disease |
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| Barth syndrome v0.0 |
Achchuthan Shanmugasundram Added Panel Barth syndrome Set list of related panels to R391 Set panel types to: GMS Rare Disease |
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| BAP1 associated tumour predisposition syndrome v0.1 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Autoimmune Polyendocrine Syndrome v0.1 | Achchuthan Shanmugasundram Panel types changed to GMS Rare Disease | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.62 | KDM6B |
Hannah Robinson gene: KDM6B was added gene: KDM6B was added to Early onset or syndromic epilepsy. Sources: NHS GMS Mode of inheritance for gene: KDM6B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: KDM6B were set to PMID: 37196654 Phenotypes for gene: KDM6B were set to Global developmental delay; Intellectual disability; Hypotonia; Joint hypermobility; seizures; Overgrowth Penetrance for gene: KDM6B were set to Incomplete Review for gene: KDM6B was set to GREEN gene: KDM6B was marked as current diagnostic Added comment: Information from Rots et al. 2023 (PMID:37196654): According to OMIM, heterozygous variants in KDM6B cause “neurodevelopmental disorder with coarse facies and mild distal skeletal abnormalities.” Here, by examining the molecular and clinical spectrum of 85 reported individuals with mostly de novo (likely) pathogenic KDM6B variants, we demonstrate that this description is inaccurate and potentially misleading. Cognitive deficits are seen consistently in all individuals, but the overall phenotype is highly variable. Notably, coarse facies and distal skeletal anomalies, as defined by OMIM, are rare in this expanded cohort while other features are unexpectedly common (e.g., hypotonia, psychosis, etc.). In this cohort, 9/69 (13%) of individuals had seizures. The majority of individuals had de novo variants but 9/85 individuals inherited the variant (five maternal, four paternal) from a mildly affected (developmental delay [DD], learning problems, autism spectrum disorder [ASD]) or clinically unaffected parent. Sources: NHS GMS |
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| Neuronal ceroid lipofuscinosis v2.2 | CLCN6 | Sarah Leigh edited their review of gene: CLCN6: Added comment: PMIDs: 16950870 & 21107136 report the characterization of CLCN6 deficient mouse model, which display some features of neuronal ceroid lipofuscinosis. PMID: 16950870 identifies two heterozygous CLCN6 variants (p.V580M, p.T628R) in 2/75 patients with late-onset neuronal ceroid lipofuscinosis, however, the authors concluded that there was insufficient evidence for these variants being responsible for the phenotype in the patients.; Changed rating: AMBER; Changed publications to: 21107136, 33217309, 16950870 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Neuronal ceroid lipofuscinosis v2.2 | CLCN6 | Sarah Leigh Publications for gene: CLCN6 were set to 29667327; 26658788; 25794116; 21107136; 33217309 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.78 | UBE3B | Achchuthan Shanmugasundram Classified gene: UBE3B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.78 | UBE3B | Achchuthan Shanmugasundram Gene: ube3b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.77 | UBE3B |
Achchuthan Shanmugasundram gene: UBE3B was added gene: UBE3B was added to Clefting. Sources: Literature Mode of inheritance for gene: UBE3B was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: UBE3B were set to 23200864; 23687348; 37010288 Phenotypes for gene: UBE3B were set to Kaufman oculocerebrofacial syndrome, OMIM:244450 Review for gene: UBE3B was set to AMBER Added comment: PMID:23687348 - One of two patients reported with biallelic variants in UBE3B in this study and one of four patients reported in PMID:23200864 and reviewed here had submucous cleft palate. DECIPHER database - One of three patients with homozygous sequence variants in UBE3B had median cleft palate. Sources: Literature |
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| Clefting v4.76 | TCF12 |
Achchuthan Shanmugasundram gene: TCF12 was added gene: TCF12 was added to Clefting. Sources: Literature Mode of inheritance for gene: TCF12 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TCF12 were set to 23354436; 31353793; 37010288 Phenotypes for gene: TCF12 were set to Craniosynostosis 3, OMIM:615314 Review for gene: TCF12 was set to RED Added comment: Clefting has only been rarely reported in patients with TCF12 variants and hence this gene should be rated red. PMID:23354436 - One of 73 individuals (from 38 families) reported with craniosynostosis and identified with heterozygous variants in TCF12 gene had cleft lip and cleft palate. PMID:31353793 - Of two cases reported with heterozygous TCF12 variants, one had hidden cleft palate. DECIPHER database - One of 11 patients with heterozygous sequence variants in TCF12 had bifid uvula. Sources: Literature |
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| Clefting v4.75 | SOX11 |
Achchuthan Shanmugasundram gene: SOX11 was added gene: SOX11 was added to Clefting. Sources: Literature Mode of inheritance for gene: SOX11 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SOX11 were set to 29437512; 37010288 Phenotypes for gene: SOX11 were set to Intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, OMIM:615866 Review for gene: SOX11 was set to RED Added comment: Cleft palate is a minor clinical indication that is only observed in <10% of patients with SOX11 variants. Hence, this gene should be rated red. PMID:29437512 - A 14-year-old boy with a phenotype resembling mild Coffin-Siris syndrome and identified with heterozygous SOX11 variant had cleft palate. However, cleft palate was not present in any of the previously reported patients (12 cases) reviewed in this publication. DECIPHER database - Of 12 patients with heterozygous sequence variants in SOX11 gene, only one patient had cleft soft palate. Sources: Literature |
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| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Classified gene: SMARCB1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are 3 unrelated cases in total, these represent only a minor fraction of patients (from total of 23) reported with SMARCB1 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Gene: smarcb1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Classified gene: SMARCB1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are 3 unrelated cases in total, these represent only a minor fraction of patients (from total of 23) reported with SMARCB1 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Gene: smarcb1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Classified gene: SMARCB1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are 3 unrelated cases in total, these represent only a minor fraction of patients (from total of 23) reported with SMARCB1 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Gene: smarcb1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Classified gene: SMARCB1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are 3 unrelated cases in total, these represent only a minor fraction of patients (from total of 23) reported with SMARCB1 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.74 | SMARCB1 | Achchuthan Shanmugasundram Gene: smarcb1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.73 | SMARCB1 | Achchuthan Shanmugasundram Classified gene: SMARCB1 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.73 | SMARCB1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are 3 unrelated cases in total, these represent only a minor fraction of patients (from total of 23) reported with SMARCB1 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.73 | SMARCB1 | Achchuthan Shanmugasundram Gene: smarcb1 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.72 | SMARCB1 |
Achchuthan Shanmugasundram gene: SMARCB1 was added gene: SMARCB1 was added to Clefting. Sources: Literature Mode of inheritance for gene: SMARCB1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SMARCB1 were set to 25168959; 37010288 Phenotypes for gene: SMARCB1 were set to Coffin-Siris syndrome 3, OMIM:614608 Review for gene: SMARCB1 was set to AMBER Added comment: PMID:25168959 - Two of ten patients reported with Coffin-Siris syndrome and heterozygous variants in SMARCB1 had cleft palate. DECIPHER database - One of 13 patients identified with heterozygous sequence variants in SMARCB1 had cleft palate. Sources: Literature |
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| Clefting v4.71 | SIN3A |
Achchuthan Shanmugasundram gene: SIN3A was added gene: SIN3A was added to Clefting. Sources: Literature Mode of inheritance for gene: SIN3A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SIN3A were set to 33437032; 37010288 Phenotypes for gene: SIN3A were set to Witteveen-Kolk syndrome, OMIM:613406 Review for gene: SIN3A was set to RED Added comment: Clefting was reported only in a minor fraction of patients (<10%) and hence should be rated red. PMID:33437032 - Of 28 patients with heterozugous variants in SIN3A gene, one patient had submucous cleft hard palate and another with deletion variant had orofacial cleft (both these are reported in DECIPHER database). DECIPHER database - In addition to the above mentioned patients, one with heterozygous sequence variant had submucous cleft soft panel (from 31 in total), while an additional patient with deletion had cleft hard palate (from 54 patients with CNV variants). Sources: Literature |
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| Clefting v4.70 | PUF60 |
Achchuthan Shanmugasundram changed review comment from: PMID:24140112 - One patient identified with heterozygous variant in PUF60 gene (p.His169Tyr) had cleft palate. PMID:27804958 - Five patients were reported with sequence variants in PUF60 gene and none of them had cleft lip/ palate as one of the clinical presentations. DECIPHER database - Of 27 patients with heterozygous sequence variants in PUF60, only one had submucous cleft hard palate. Sources: Literature; to: Clefting has only been identified in a minor fraction of patients with monoallelic variants in PUF60 gene and hence this gene should be rated red in this panel. PMID:24140112 - One patient identified with heterozygous variant in PUF60 gene (p.His169Tyr) had cleft palate. PMID:27804958 - Five patients were reported with sequence variants in PUF60 gene and none of them had cleft lip/ palate as one of the clinical presentations. DECIPHER database - Of 27 patients with heterozygous sequence variants in PUF60, only one had submucous cleft hard palate. Sources: Literature |
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| Clefting v4.70 | PUF60 |
Achchuthan Shanmugasundram gene: PUF60 was added gene: PUF60 was added to Clefting. Sources: Literature Mode of inheritance for gene: PUF60 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PUF60 were set to 24140112; 27804958; 37010288 Phenotypes for gene: PUF60 were set to Verheij syndrome, OMIM:615583 Review for gene: PUF60 was set to RED Added comment: PMID:24140112 - One patient identified with heterozygous variant in PUF60 gene (p.His169Tyr) had cleft palate. PMID:27804958 - Five patients were reported with sequence variants in PUF60 gene and none of them had cleft lip/ palate as one of the clinical presentations. DECIPHER database - Of 27 patients with heterozygous sequence variants in PUF60, only one had submucous cleft hard palate. Sources: Literature |
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| Clefting v4.69 | POLR2A |
Achchuthan Shanmugasundram gene: POLR2A was added gene: POLR2A was added to Clefting. Sources: Literature Mode of inheritance for gene: POLR2A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: POLR2A were set to 31353023; 37010288 Phenotypes for gene: POLR2A were set to Neurodevelopmental disorder with hypotonia and variable intellectual and behavioral abnormalities, OMIM:618603 Review for gene: POLR2A was set to RED Added comment: This gene should be rated red as clefting has only been reported in a minor fraction of patients with monoallelic variants in POLR2A. PMID:31353023 - 16 individuals were identified with heterozygous variants in POLR2A, of which only one patient had cleft lip. DECIPHER database - Of 14 patients with heterozygous sequence variants, one had cleft palate and another had bifid uvula. Sources: Literature |
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| Clefting v4.68 | POLA1 |
Achchuthan Shanmugasundram changed review comment from: PMID:3100651 - Nine patients from five unrelated families were identified with POLA1 variants, of which one patient from family C (has two reported patients) was reported with bifid uvula. DECIPHER database - One of two patients with hemizygous sequence variants had bifid uvula. Sources: Literature; to: Bifid uvula is a minor clinical indication that is only found in two patients with POLA1 variants and it is not fully penetrant in the family. Hence, this gene should be rated red. PMID:3100651 - Nine patients from five unrelated families were identified with POLA1 variants, of which one patient from family C (has two reported patients) was reported with bifid uvula. DECIPHER database - One of two patients with hemizygous sequence variants had bifid uvula. Sources: Literature |
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| Clefting v4.68 | POLA1 |
Achchuthan Shanmugasundram gene: POLA1 was added gene: POLA1 was added to Clefting. Sources: Literature Mode of inheritance for gene: POLA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: POLA1 were set to 31006512; 37010288 Review for gene: POLA1 was set to RED Added comment: PMID:3100651 - Nine patients from five unrelated families were identified with POLA1 variants, of which one patient from family C (has two reported patients) was reported with bifid uvula. DECIPHER database - One of two patients with hemizygous sequence variants had bifid uvula. Sources: Literature |
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| Clefting v4.67 | NOTCH2 | Achchuthan Shanmugasundram Publications for gene: NOTCH2 were set to 9188663; 30329210; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.67 | NOTCH2 | Achchuthan Shanmugasundram Publications for gene: NOTCH2 were set to 9188663; 30329210 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.66 | NOTCH2 | Achchuthan Shanmugasundram edited their review of gene: NOTCH2: Changed publications to: 9188663, 30329210, 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.66 | NOTCH2 | Achchuthan Shanmugasundram Classified gene: NOTCH2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.66 | NOTCH2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are three cases reported with cleft lip/ palate or cleft of uvula, these are reported only in a minor proportion of patients and hence this gene can only be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.66 | NOTCH2 | Achchuthan Shanmugasundram Gene: notch2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.65 | NOTCH2 |
Achchuthan Shanmugasundram gene: NOTCH2 was added gene: NOTCH2 was added to Clefting. Sources: Literature Mode of inheritance for gene: NOTCH2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: NOTCH2 were set to 9188663; 30329210 Phenotypes for gene: NOTCH2 were set to Hajdu-Cheney syndrome, OMIM:102500 Review for gene: NOTCH2 was set to AMBER Added comment: PMID:9188663 - An 8.5-year-old boy with NOTCH2 variant and Hajdu-Cheney syndrome was reported with cleft lip and palate. PMID:30329210 - A 32-year-old male patient with a de novo truncating variant in NOTCH2 and presenting with Hajdu-Cheney syndrome had high arched palate and cleft of uvula. DECIPHER database - One of seven patients with heterozygous sequence variants in NOTCH2 was identified with submucous cleft hard palate. Sources: Literature |
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| Intellectual disability v5.191 | PSMC3 |
Dmitrijs Rots gene: PSMC3 was added gene: PSMC3 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: PSMC3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PSMC3 were set to PMID: 37256937 Phenotypes for gene: PSMC3 were set to neurodevelopmental delay Mode of pathogenicity for gene: PSMC3 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: PSMC3 was set to GREEN Added comment: 23 individuals with NDD due to 15 different de novo missense variants in PMID: 37256937. Sources: Literature |
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| Clefting v4.64 | MAGEL2 |
Achchuthan Shanmugasundram gene: MAGEL2 was added gene: MAGEL2 was added to Clefting. Sources: Literature Mode of inheritance for gene: MAGEL2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: MAGEL2 were set to 31397880; 37010288 Phenotypes for gene: MAGEL2 were set to Schaaf-Yang syndrome, OMIM:615547 Review for gene: MAGEL2 was set to RED Added comment: Cleft palate is a minor feature of Schaaf-Yang syndrome and is present only in less than 10% of cases. Hence, this gene should be rated red. PMID:31397880 - One of five patients presented in this study with heterozygous variants in MAGEL2 gene had cleft palate. DECIPHER database - One of 20 patients with heterozygous sequence variants in MAGEL2 had cleft palate. Sources: Literature |
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| Clefting v4.63 | EP300 |
Achchuthan Shanmugasundram changed review comment from: This gene should be rated red as clefting has only been reported in a very small fraction of patients (<5%) identified with monoallleic variants in EP300. PMID:27648933 - One of 52 patients with Rubinstein-Taybi syndrome caused by monoallelic variants in EP300 gene had cleft lip and palate. DECIPHER database - Of 58 patients with heterozygous sequence variants in EP300, cleft palate, orofacial cleft and bifid uvula were found in one patient each. Sources: Literature; to: This gene should be rated red as clefting has only been reported in a very small fraction of patients (<5%) identified with monoallelic variants in EP300. PMID:27648933 - One of 52 patients with Rubinstein-Taybi syndrome caused by monoallelic variants in EP300 gene had cleft lip and palate. DECIPHER database - Of 58 patients with heterozygous sequence variants in EP300, cleft palate, orofacial cleft and bifid uvula were found in one patient each. Sources: Literature |
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| Clefting v4.63 | EP300 |
Achchuthan Shanmugasundram gene: EP300 was added gene: EP300 was added to Clefting. Sources: Literature Mode of inheritance for gene: EP300 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: EP300 were set to 27648933; 37010288 Phenotypes for gene: EP300 were set to Rubinstein-Taybi syndrome 2, OMIM:613684 Review for gene: EP300 was set to RED Added comment: This gene should be rated red as clefting has only been reported in a very small fraction of patients (<5%) identified with monoallleic variants in EP300. PMID:27648933 - One of 52 patients with Rubinstein-Taybi syndrome caused by monoallelic variants in EP300 gene had cleft lip and palate. DECIPHER database - Of 58 patients with heterozygous sequence variants in EP300, cleft palate, orofacial cleft and bifid uvula were found in one patient each. Sources: Literature |
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| Clefting v4.62 | CHD3 |
Achchuthan Shanmugasundram changed review comment from: Of 28 patients with heterozygous sequence variants in CHD3 gene from DECIPHER database, one patient had cleft palate and another had submucous cleft hard palate. Sources: Literature; to: Of 28 patients with heterozygous sequence variants in CHD3 gene from DECIPHER database, one patient had cleft palate and another had submucous cleft hard palate. Sources: Literature |
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| Clefting v4.62 | CHD3 |
Achchuthan Shanmugasundram gene: CHD3 was added gene: CHD3 was added to Clefting. Sources: Literature Mode of inheritance for gene: CHD3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CHD3 were set to 37010288 Phenotypes for gene: CHD3 were set to Snijders Blok-Campeau syndrome, OMIM:618205 Review for gene: CHD3 was set to RED Added comment: Of 28 patients with heterozygous sequence variants in CHD3 gene from DECIPHER database, one patient had cleft palate and another had submucous cleft hard palate. Sources: Literature |
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| Clefting v4.61 | AUTS2 | Achchuthan Shanmugasundram Classified gene: AUTS2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.61 | AUTS2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five cases reported with cleft lip/ palate. However, clefting has only been reported in less than 10% of patients with monoalellic variants in AUTS2 from the DECIPHER database. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.61 | AUTS2 | Achchuthan Shanmugasundram Gene: auts2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.60 | AUTS2 |
Achchuthan Shanmugasundram gene: AUTS2 was added gene: AUTS2 was added to Clefting. Sources: Literature Mode of inheritance for gene: AUTS2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: AUTS2 were set to 31788251; 37010288 Phenotypes for gene: AUTS2 were set to Intellectual developmental disorder, autosomal dominant 26, OMIM:615834 Review for gene: AUTS2 was set to AMBER Added comment: PMID:31788251 - A patient identified with a de novo heterozygous AUTS2 variant (c.1464_1467del ACTC/ p.Tyr488Ter) was reported with autism and cleft lip and palate. DECIPHER database - Of 44 patients reported with heterozygous sequence variants, 4 patients had cleft lip or cleft palate (2 - cleft palate; 1 - cleft soft palate; 1 - unilateral cleft lip). Sources: Literature |
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| Clefting v4.59 | ARID1A | Achchuthan Shanmugasundram Phenotypes for gene: ARID1A were changed from to Coffin-Siris syndrome 2, OMIM:614607 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.58 | ARID1A | Achchuthan Shanmugasundram edited their review of gene: ARID1A: Changed phenotypes to: Coffin-Siris syndrome 2, OMIM:614607 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.58 | ARID1A | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: Clefting is a minor feature on patients with monoallelic variants in ARID1A gene and it can be rated amber although there are three cases with clefting form a total of 34 cases.; to: Comment on list classification: Clefting is a minor feature on patients with monoallelic variants in ARID1A gene and it should be rated amber although there are three cases with clefting (from a total of 34 cases). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.58 | ARID1A | Achchuthan Shanmugasundram Classified gene: ARID1A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.58 | ARID1A | Achchuthan Shanmugasundram Added comment: Comment on list classification: Clefting is a minor feature on patients with monoallelic variants in ARID1A gene and it can be rated amber although there are three cases with clefting form a total of 34 cases. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.58 | ARID1A | Achchuthan Shanmugasundram Gene: arid1a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.57 | ARID1A |
Achchuthan Shanmugasundram gene: ARID1A was added gene: ARID1A was added to Clefting. Sources: Literature Mode of inheritance for gene: ARID1A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ARID1A were set to 25168959; 37010288 Review for gene: ARID1A was set to AMBER Added comment: PMID:25168959 - Two of eight patients with heterozygous variants in ARID1A gene had cleft palate. DECIPHER database - One of 26 patients with heterozygous sequence variants in ARID1A gene had cleft palate. Sources: Literature |
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| Clefting v4.56 | ADNP |
Achchuthan Shanmugasundram changed review comment from: PMID:29724491 - One child from a worldwide cohort of 78 individuals with variants in ADNP gene had submucous cleft palate. DECIPHER database - Of 66 patients identified with heterozygous sequence variants in ADNP gene, one each (three in total) was reported with cleft soft palate, submucous cleft hard palate and submucous cleft lip. Sources: Literature; to: Cleft lip/ palate has only been reported rarely in patients identified with monoallelic variants in ADNP gene. PMID:29724491 - One child from a worldwide cohort of 78 individuals with variants in ADNP gene had submucous cleft palate. DECIPHER database - Of 66 patients identified with heterozygous sequence variants in ADNP gene, one each (three in total) was reported with cleft soft palate, submucous cleft hard palate and submucous cleft lip. Sources: Literature |
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| Clefting v4.56 | ADNP |
Achchuthan Shanmugasundram gene: ADNP was added gene: ADNP was added to Clefting. Sources: Literature Mode of inheritance for gene: ADNP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ADNP were set to 29724491; 37010288 Phenotypes for gene: ADNP were set to Helsmoortel-van der Aa syndrome, OMIM:615873 Review for gene: ADNP was set to RED Added comment: PMID:29724491 - One child from a worldwide cohort of 78 individuals with variants in ADNP gene had submucous cleft palate. DECIPHER database - Of 66 patients identified with heterozygous sequence variants in ADNP gene, one each (three in total) was reported with cleft soft palate, submucous cleft hard palate and submucous cleft lip. Sources: Literature |
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| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | OTULIN | Boaz Palterer reviewed gene: OTULIN: Rating: ; Mode of pathogenicity: None; Publications: 35587511; Phenotypes: life-threatening staphylococcal disease; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.17 | DNAJC6 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: DNAJC6. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.17 | DNAJC6 | Sarah Leigh Classified gene: DNAJC6 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.17 | DNAJC6 | Sarah Leigh Gene: dnajc6 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | ARPC5 |
Boaz Palterer gene: ARPC5 was added gene: ARPC5 was added to Primary immunodeficiency or monogenic inflammatory bowel disease. Sources: Literature Mode of inheritance for gene: ARPC5 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ARPC5 were set to immunodeficiency; autoimmunity; inflammation; dysmorphisms; impaired wound healing; scoliosis; pneumatoceles; anemia Penetrance for gene: ARPC5 were set to unknown Review for gene: ARPC5 was set to GREEN Added comment: Nunes-Santos et al. described 2 unrelated patients from 2 kindreds woith germline biallelic null mutations in ARPC5 presenting with a complex actinopathy phenotype of increased susceptibility to infections, autoimmunity, inflammation, and dysmorphisms. There is strong biological rationale: ARPC5 is part of the Arp2/3 complex, related to WAS in Wiskott-Aldrich syndrome and ARPC1B deficiency. Strong functional ex vivo and in vitro data is presented. ( https://doi.org/10.1038/s41467-023-39272-0 ) Sources: Literature |
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| Early onset or syndromic epilepsy v4.62 | DNAJC6 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: DNAJC6. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.62 | DNAJC6 | Sarah Leigh Classified gene: DNAJC6 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.62 | DNAJC6 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.62 | DNAJC6 | Sarah Leigh Gene: dnajc6 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.16 | DNAJC6 | Sarah Leigh Classified gene: DNAJC6 as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.16 | DNAJC6 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.16 | DNAJC6 | Sarah Leigh Gene: dnajc6 has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.4 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to 26528954; 23211418; 27687717; 26703368; 22563501 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.28 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to 23211418; 27687717; 26528954; 22563501; 26703368 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Parkinson Disease and Complex Parkinsonism v1.116 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to 26528954; 27687717; 26703368; 22563501; 23211418 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.15 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to 34175496 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.14 | DNAJC6 | Sarah Leigh Phenotypes for gene: DNAJC6 were changed from to Parkinson disease 19b, early-onset, OMIM:615528; Parkinson disease 19a juvenile-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.13 | DNAJC6 | Sarah Leigh reviewed gene: DNAJC6: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.61 | DNAJC6 | Sarah Leigh edited their review of gene: DNAJC6: Added comment: DNAJC6 variants are associated with Parkinson disease 19b, early-onset (OMIM:615528), but not with a phenotype in Gen2Phen. At least nine variants have been reported in unrelated families. Seizures were reported in 5/9 families and dystonia was reported in 4/9 families reported (data review in PMID: 34175496.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | DOCK11 |
Boaz Palterer gene: DOCK11 was added gene: DOCK11 was added to Primary immunodeficiency or monogenic inflammatory bowel disease. Sources: Literature Mode of inheritance for gene: DOCK11 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females Publications for gene: DOCK11 were set to 36952639 Phenotypes for gene: DOCK11 were set to early-onset autoimmunity; cytopenia; systemic lupus erythematosus; dermatitis; enteropathy Penetrance for gene: DOCK11 were set to unknown Review for gene: DOCK11 was set to GREEN Added comment: Boussard et al. described 8 male patients, from 7 unrelated families, with hemizygous DOCK11 missense variants leading to reduced DOCK11 expression. The patients presented with early-onset autoimmunity, including cytopenia, systemic lupus erythematosus, skin, and digestive manifestations. Extensive ex vivo and in vitro functional validation. Sources: Literature |
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| Clefting v4.55 | ZC4H2 |
Achchuthan Shanmugasundram changed review comment from: PMID:31206972 - Of 42 families identified with variants in de novo and inherited heterozygous variants in ZC4H2 gene, eight patients had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with monoallelic sequence variants, three patients had cleft palate. Cleft palate has been recorded as one of the clinical presentations of female-restricted Wieacker-Wolff syndrome (MIM #301041) in OMIM. Sources: Literature; to: PMID:31206972 - Of 42 families identified with de novo and inherited variants in ZC4H2 gene, eight patients had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with sequence variants, three patients had cleft palate. Cleft palate has been recorded as one of the clinical presentations of female-restricted Wieacker-Wolff syndrome (MIM #301041) in OMIM. Sources: Literature |
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| Clefting v4.55 | ZC4H2 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZC4H2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.54 | ZC4H2 | Achchuthan Shanmugasundram edited their review of gene: ZC4H2: Changed mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.54 | ZC4H2 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are ten patients reported with cleft palate. Hence, this gene can be promoted to green rating in the next GMS update.; to: Comment on list classification: There are ten unrelated patients reported with cleft palate. Hence, this gene can be promoted to green rating in the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.54 | ZC4H2 |
Achchuthan Shanmugasundram changed review comment from: PMID:31206972 - Of 42 families identified with variants in de novo and inherited heterozygous variants in ZC4H2 gene, eight patients were had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with monoallelic sequence variants, three patients had cleft palate. Cleft palate has been recorded as one of the clinical presentations of female-restricted Wieacker-Wolff syndrome (MIM #301041) in OMIM. Sources: Literature; to: PMID:31206972 - Of 42 families identified with variants in de novo and inherited heterozygous variants in ZC4H2 gene, eight patients had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with monoallelic sequence variants, three patients had cleft palate. Cleft palate has been recorded as one of the clinical presentations of female-restricted Wieacker-Wolff syndrome (MIM #301041) in OMIM. Sources: Literature |
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| Adult onset dystonia, chorea or related movement disorder v3.3 | DNAJC6 | Sarah Leigh Phenotypes for gene: DNAJC6 were changed from Parkinson disease 19, juvenile-onset, OMIM:615528; Parkinson disease 19b, early-onset, OMIM:615528 to Parkinson disease 19b, early-onset, OMIM:615528; Parkinson disease 19a juvenile-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.27 | DNAJC6 | Sarah Leigh Phenotypes for gene: DNAJC6 were changed from Parkinson disease 19b, early-onset, OMIM:615528; Parkinson disease 19a, juvenile-onset, OMIM:615528 to Parkinson disease 19b, early-onset, OMIM:615528; Parkinson disease 19a juvenile-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Parkinson Disease and Complex Parkinsonism v1.115 | DNAJC6 | Sarah Leigh Phenotypes for gene: DNAJC6 were changed from Parkinson disease 19, juvenile-onset, 615528; Parkinson disease 19a, juvenile-onset; Parkinson disease 19b, early-onset to Parkinson disease 19b, early-onset, OMIM:615528; Parkinson disease 19a juvenile-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.61 | DNAJC6 | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.61 | DNAJC6 | Sarah Leigh Phenotypes for gene: DNAJC6 were changed from Parkinson disease 19b, early-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 to Parkinson disease 19b, early-onset, OMIM:615528; Parkinson disease 19a juvenile-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.60 | DNAJC6 | Sarah Leigh Mode of inheritance for gene: DNAJC6 was changed from to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.54 | ZC4H2 |
Achchuthan Shanmugasundram changed review comment from: PMID:31206972 - Of 42 families identified with variants in de novo and inherited heterozygous variants in ZC4H2 gene, eight patients were had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with monoallelic sequence variants, three patients had cleft palate. Sources: Literature; to: PMID:31206972 - Of 42 families identified with variants in de novo and inherited heterozygous variants in ZC4H2 gene, eight patients were had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with monoallelic sequence variants, three patients had cleft palate. Cleft palate has been recorded as one of the clinical presentations of female-restricted Wieacker-Wolff syndrome (MIM #301041) in OMIM. Sources: Literature |
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| Clefting v4.54 | ZC4H2 | Achchuthan Shanmugasundram Classified gene: ZC4H2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.54 | ZC4H2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are ten patients reported with cleft palate. Hence, this gene can be promoted to green rating in the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.54 | ZC4H2 | Achchuthan Shanmugasundram Gene: zc4h2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.53 | ZC4H2 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: ZC4H2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.53 | ZC4H2 |
Achchuthan Shanmugasundram gene: ZC4H2 was added gene: ZC4H2 was added to Clefting. Sources: Literature Mode of inheritance for gene: ZC4H2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ZC4H2 were set to 31206972; 37010288 Phenotypes for gene: ZC4H2 were set to Wieacker-Wolff syndrome, female-restricted, OMIM:301041 Review for gene: ZC4H2 was set to GREEN Added comment: PMID:31206972 - Of 42 families identified with variants in de novo and inherited heterozygous variants in ZC4H2 gene, eight patients were had cleft palate in addition to several other clinical presentations. These included one patient with cleft palate from the DDD study (DECIPHER database) DECIPHER database - Of 13 patients with monoallelic sequence variants, three patients had cleft palate. Sources: Literature |
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| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | SRP72 |
Lauma Freimane gene: SRP72 was added gene: SRP72 was added to Primary immunodeficiency or monogenic inflammatory bowel disease. Sources: Literature,Research Mode of inheritance for gene: SRP72 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SRP72 were set to 32098966 Phenotypes for gene: SRP72 were set to Familial MDS/AML; inherited bone marrow failure syndromes (IBMFS); congenital neutropenia; Shwachman-Diamond syndrome |
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| Early onset or syndromic epilepsy v4.59 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to 22563501; 23211418; 26528954; 34175496; 26703368 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.58 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to 23211418; 34175496 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.57 | DNAJC6 | Sarah Leigh Publications for gene: DNAJC6 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.56 | DNAJC6 | Sarah Leigh Added comment: Comment on phenotypes: OMIM:615528 also includes Parkinson disease 19a, juvenile-onset | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.56 | DNAJC6 | Sarah Leigh Phenotypes for gene: DNAJC6 were changed from to Parkinson disease 19b, early-onset, OMIM:615528; juvenile onset Parkinson disease 19A, MONDO:0014231 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.55 | SAMD12 | Sarah Leigh reviewed gene: SAMD12: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP |
Achchuthan Shanmugasundram changed review comment from: PMID:30827496 - Out of 13 unrelated individuals with a complex syndromic neurodevelopmental disorder comprising global developmental delay and intellectual disability and identified with monoallelic variants in TRRAP gene, five had cleft lip and palate. DECIPHER database - Out of 18 patients with heterozygous sequence variants in TRRAP gene, two were reported with cleft lip and palate. Sources: Literature; to: PMID:30827496 - Out of 13 unrelated individuals with a complex syndromic neurodevelopmental disorder comprising global developmental delay and intellectual disability and identified with monoallelic variants in TRRAP gene, five had cleft lip and palate. DECIPHER database - Out of 18 patients with heterozygous sequence variants in TRRAP gene, two were reported with cleft lip and palate. OMIM has also recorded cleft lip and palate as clinical presentations of the syndrome associated with dominant variants in TRRAP (MIM #618454). Sources: Literature |
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| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Classified gene: TRRAP as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Gene: trrap has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Classified gene: TRRAP as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be promoted green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.52 | TRRAP | Achchuthan Shanmugasundram Gene: trrap has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.51 | TRRAP | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: TRRAP. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.51 | TRRAP |
Achchuthan Shanmugasundram gene: TRRAP was added gene: TRRAP was added to Clefting. Sources: Literature Mode of inheritance for gene: TRRAP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TRRAP were set to 30827496; 37010288 Phenotypes for gene: TRRAP were set to Developmental delay with or without dysmorphic facies and autism, OMIM:618454 Review for gene: TRRAP was set to GREEN Added comment: PMID:30827496 - Out of 13 unrelated individuals with a complex syndromic neurodevelopmental disorder comprising global developmental delay and intellectual disability and identified with monoallelic variants in TRRAP gene, five had cleft lip and palate. DECIPHER database - Out of 18 patients with heterozygous sequence variants in TRRAP gene, two were reported with cleft lip and palate. Sources: Literature |
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| Early onset or syndromic epilepsy v4.55 | SAMD12 | Sarah Leigh Phenotypes for gene: SAMD12 were changed from Epilepsy, familial adult myoclonic, 1, MIM# 601068 to Epilepsy, familial adult myoclonic, 1, OMIM:601068; epilepsy, familial adult myoclonic, 1, MONDO:0010985 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.50 | TRAF7 | Achchuthan Shanmugasundram Classified gene: TRAF7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.50 | TRAF7 | Achchuthan Shanmugasundram Gene: traf7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.49 | TRAF7 | Achchuthan Shanmugasundram Publications for gene: TRAF7 were set to 32376980; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.49 | TRAF7 | Achchuthan Shanmugasundram Publications for gene: TRAF7 were set to 32376980 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.48 | TRAF7 | Achchuthan Shanmugasundram edited their review of gene: TRAF7: Changed publications to: 32376980, 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.48 | TRAF7 |
Achchuthan Shanmugasundram gene: TRAF7 was added gene: TRAF7 was added to Clefting. Sources: Literature Mode of inheritance for gene: TRAF7 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TRAF7 were set to 32376980 Phenotypes for gene: TRAF7 were set to Cardiac, facial, and digital anomalies with developmental delay, OMIM:618164 Review for gene: TRAF7 was set to AMBER Added comment: PMID:32376980 - 45 patients were identified with heterozygous variants in TRAF7 gene, of which one patient had cleft palate and three patients had submucous cleft palate. DECIPHER database - One of 15 patients with heterozygous sequence variants in TRAF7 gene had cleft palate as one of the clinical presentations. Sources: Literature |
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| Early onset or syndromic epilepsy v4.54 | SAMD12 | Sarah Leigh Publications for gene: SAMD12 were set to 30194086; 29507423 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.53 | SAMD12 | Sarah Leigh Classified gene: SAMD12 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.53 | SAMD12 | Sarah Leigh Gene: samd12 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.52 | SAMD12 | Sarah Leigh Tag STR tag was added to gene: SAMD12. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.47 | STAG2 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are ten cases identified with cleft lip/ palate, cleft soft palate or submucous cleft soft palate. Hence, this gene can be promoted to green rating at the next GMS review.; to: Comment on list classification: There are eight unrelated cases identified with cleft lip/ palate and two cases were identified with cleft soft palate or submucous cleft soft palate. Hence, this gene should be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.47 | STAG2 | Achchuthan Shanmugasundram Classified gene: STAG2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.47 | STAG2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are ten cases identified with cleft lip/ palate, cleft soft palate or submucous cleft soft palate. Hence, this gene can be promoted to green rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.47 | STAG2 | Achchuthan Shanmugasundram Gene: stag2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.46 | STAG2 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: STAG2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.46 | STAG2 |
Achchuthan Shanmugasundram gene: STAG2 was added gene: STAG2 was added to Clefting. Sources: Literature Mode of inheritance for gene: STAG2 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: STAG2 were set to 28296084; 29263825; 30158690; 31334757; 33014403; 37010288 Phenotypes for gene: STAG2 were set to Holoprosencephaly 13, X-linked, OMIM:301043; Mullegama-Klein-Martinez syndrome, OMIM:301022 Review for gene: STAG2 was set to GREEN Added comment: PMID:33014403 - Two female patients identified with de novo variants in STAG2. One had cleft lip/ palate and other had cleft palate. In addition, five additional cases with cleft lip/ palate were also reported from literature review in this publication. DECIPHER database - Of ten patients with sequence variants in STAG2 gene, one each was identified with cleft palate, cleft soft palate and submucous cleft soft palate (PMID:37010288). Sources: Literature |
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| Clefting v4.45 | SMARCA4 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: SMARCA4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.45 | SMARCA4 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.45 | SMARCA4 | Achchuthan Shanmugasundram Classified gene: SMARCA4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.45 | SMARCA4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated cases with cleft plate and one case each with submucous cleft palate and bifid uvula. This gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.45 | SMARCA4 | Achchuthan Shanmugasundram Gene: smarca4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.44 | SMARCA4 | Achchuthan Shanmugasundram Classified gene: SMARCA4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.44 | SMARCA4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated cases with cleft plate and one case each with submucous cleft palate and bifid uvula. This gene can be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.44 | SMARCA4 | Achchuthan Shanmugasundram Gene: smarca4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.43 | SMARCA4 |
Achchuthan Shanmugasundram gene: SMARCA4 was added gene: SMARCA4 was added to Clefting. Sources: Literature Mode of inheritance for gene: SMARCA4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SMARCA4 were set to 25168959; 37010288 Phenotypes for gene: SMARCA4 were set to Coffin-Siris syndrome 4, OMIM:614609 Review for gene: SMARCA4 was set to GREEN Added comment: PMID:25168959 - 4 of 12 patients with variants in SMARCA4 had cleft palate and another patient had submucous cleft palate. DECIPHER database - One of 22 patients with heterozygous sequence variants had cleft palate and another patient had bifid uvula (PMID:37010288) Sources: Literature |
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| Intellectual disability v5.191 | MKL2 |
Dmitrijs Rots gene: MKL2 was added gene: MKL2 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: MKL2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: MKL2 were set to PMID:37013900 Phenotypes for gene: MKL2 were set to neurodevelopmental phenotype with dysmorphic features Mode of pathogenicity for gene: MKL2 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: MKL2 was set to GREEN Added comment: 2 cases with de novo missense GoF variants in MRTFB (previously known as MKL2) + functional evidence Sources: Literature |
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| Clefting v4.42 | POGZ | Achchuthan Shanmugasundram Classified gene: POGZ as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.42 | POGZ | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three unrelated cases reported with either cleft palate or bifid uvula in total, this phenotype is not consistently present in patients with monoallelic variants in POGZ gene. Hence, this gene should only be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.42 | POGZ | Achchuthan Shanmugasundram Gene: pogz has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.41 | POGZ | Achchuthan Shanmugasundram Publications for gene: POGZ were set to 26739615; 31782611 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.40 | POGZ |
Achchuthan Shanmugasundram changed review comment from: PMID:26739615 - Five unrelated individuals were identified with de novo truncating variants in POGZ gene, of which one individual had cleft palate and another one had bifid uvula. PMID:31782611 - In this cohort of 22 individuals with 21 different loss of function variants in POGZ, two patients were reported with bifid uvula. DECIPHER database - Of 42 patients with heterozygous sequence variants, one had cleft palate and another one had bifid uvula. The OMIM entry for White-Sutton syndrome (MIM #616364) does not currently include cleft lip/ palate as one of the clinical manifestations of this syndrome. Sources: Literature; to: PMID:26739615 - Five unrelated individuals were identified with de novo truncating variants in POGZ gene, of which one individual had cleft palate and another one had bifid uvula. PMID:31782611 - In this cohort of 22 individuals with 21 different loss of function variants in POGZ, two patients were reported with bifid uvula. DECIPHER database - Of 42 patients with heterozygous sequence variants, one had cleft palate and another one had bifid uvula (PMID:37010288). The OMIM entry for White-Sutton syndrome (MIM #616364) does not currently include cleft lip/ palate as one of the clinical manifestations of this syndrome. Sources: Literature |
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| Clefting v4.40 | POGZ | Achchuthan Shanmugasundram edited their review of gene: POGZ: Changed publications to: 26739615, 31782611, 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.40 | POGZ |
Achchuthan Shanmugasundram gene: POGZ was added gene: POGZ was added to Clefting. Sources: Literature Mode of inheritance for gene: POGZ was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: POGZ were set to 26739615; 31782611 Phenotypes for gene: POGZ were set to White-Sutton syndrome, OMIM:616364 Review for gene: POGZ was set to AMBER Added comment: PMID:26739615 - Five unrelated individuals were identified with de novo truncating variants in POGZ gene, of which one individual had cleft palate and another one had bifid uvula. PMID:31782611 - In this cohort of 22 individuals with 21 different loss of function variants in POGZ, two patients were reported with bifid uvula. DECIPHER database - Of 42 patients with heterozygous sequence variants, one had cleft palate and another one had bifid uvula. The OMIM entry for White-Sutton syndrome (MIM #616364) does not currently include cleft lip/ palate as one of the clinical manifestations of this syndrome. Sources: Literature |
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| Hereditary neuropathy or pain disorder v3.35 | ITPR3 | Sarah Leigh Classified gene: ITPR3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.35 | ITPR3 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.35 | ITPR3 | Sarah Leigh Gene: itpr3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.34 | ITPR3 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: ITPR3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.34 | ITPR3 | Sarah Leigh reviewed gene: ITPR3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.34 | ITPR3 | Sarah Leigh Phenotypes for gene: ITPR3 were changed from Charcot-Marie-Tooth disease to Charcot-Marie-Tooth disease, demyelinating, type 1J, OMIM:620111 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.33 | ITPR3 | Sarah Leigh Publications for gene: ITPR3 were set to 32949214 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.32 | ITPR3 | Sarah Leigh Classified gene: ITPR3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.32 | ITPR3 | Sarah Leigh Gene: itpr3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.52 | EIF4A2 | Sarah Leigh Classified gene: EIF4A2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.52 | EIF4A2 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rating Green at the major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.52 | EIF4A2 | Sarah Leigh Gene: eif4a2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.191 | EIF4A2 | Sarah Leigh Classified gene: EIF4A2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.191 | EIF4A2 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rating Green at the major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.191 | EIF4A2 | Sarah Leigh Gene: eif4a2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.51 | EIF4A2 |
Sarah Leigh gene: EIF4A2 was added gene: EIF4A2 was added to Early onset or syndromic epilepsy. Sources: Literature Q3_23_promote_green tags were added to gene: EIF4A2. Mode of inheritance for gene: EIF4A2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: EIF4A2 were set to 36528028 Phenotypes for gene: EIF4A2 were set to Neurodevelopmental disorder Review for gene: EIF4A2 was set to GREEN Added comment: EIF4A2 has not been associated with a phenotype in OMIM, Gen2Phen or Mondo at the time of reporting. PMID: 36528028 reports the findings of an international collaboration through Matchmaker Exchange, where EIF4A2 variants are found in cases with neurodevelopmental disorder characterized by intellectual disability, hypotonia, and epilepsy. A total of 15 EIF4A2 variants have been reported in PMID: 36528028, with 12 variants occurring as de novo monoallelic in 12 individuals and 3 as biallelic in two unrelated cases (one as homozygote and the other as compound heterozygous). Severe intellectual was seen in 6/10 unrelated cases where an assessment was made, epilepsy was evident in 10/14 unrelated cases and 13/14 cases had hyptonia. Functional studies were also presented and it would appear that both loss and gain functions maybe associated with EIF4A2 variants. Sources: Literature |
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| Intellectual disability v5.190 | EIF4A2 |
Sarah Leigh gene: EIF4A2 was added gene: EIF4A2 was added to Intellectual disability - microarray and sequencing. Sources: Literature Q3_23_promote_green tags were added to gene: EIF4A2. Mode of inheritance for gene: EIF4A2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: EIF4A2 were set to 36528028 Phenotypes for gene: EIF4A2 were set to Neurodevelopmental disorder Review for gene: EIF4A2 was set to GREEN Added comment: EIF4A2 has not been associated with a phenotype in OMIM, Gen2Phen or Mondo at the time of reporting. PMID: 36528028 reports the findings of an international collaboration through Matchmaker Exchange, where EIF4A2 variants are found in cases with neurodevelopmental disorder characterized by intellectual disability, hypotonia, and epilepsy. A total of 15 EIF4A2 variants have been reported in PMID: 36528028, with 12 variants occurring as de novo monoallelic in 12 individuals and 3 as biallelic in two unrelated cases (one as homozygote and the other as compound heterozygous). Severe intellectual was seen in 6/10 unrelated cases where an assessment was made, epilepsy was evident in 10/14 unrelated cases and 13/14 cases had hyptonia. Functional studies were also presented and it would appear that both loss and gain functions maybe associated with EIF4A2 variants. Sources: Literature |
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| Clefting v4.39 | PGM1 | Achchuthan Shanmugasundram Classified gene: PGM1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.39 | PGM1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>10 unrelated cases) for this gene to be rated green at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.39 | PGM1 | Achchuthan Shanmugasundram Gene: pgm1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.38 | PGM1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PGM1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.38 | PGM1 | Achchuthan Shanmugasundram Phenotypes for gene: PGM1 were changed from Cleft palate to Congenital disorder of glycosylation, type It, OMIM:14921 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.37 | PGM1 | Achchuthan Shanmugasundram Publications for gene: PGM1 were set to 24499211; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.37 | PGM1 | Achchuthan Shanmugasundram Publications for gene: PGM1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.36 | PGM1 | Achchuthan Shanmugasundram Mode of inheritance for gene: PGM1 was changed from to BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.35 | PGM1 |
Achchuthan Shanmugasundram changed review comment from: PMID:24499211 - 19 patients from 16 families with biallelic variants in PGM1 and presenting with CGG1T. Of these, 16 patients from 13 different families had cleft palate and/ or bifid uvula. DECIPHER database - Only one patient reported with compound heterozygous variant in PGM1 gene and this patient had cleft palate (PMID:37010288); to: PMID:24499211 - 19 patients from 16 families with biallelic variants in PGM1 and presenting with CGG1T. Of these, 16 patients from 13 different families had cleft palate and/ or bifid uvula. DECIPHER database - Only one patient reported with compound heterozygous variant in PGM1 gene and this patient had cleft palate (PMID:37010288) OMIM associated autosomal recessive PGM1 variants to congenital disorder of glycosylation, type It (MIM #14921) and cleft palate and bifid uvula have been recorded as clinical presentations of this disorder. |
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| Clefting v4.35 | PGM1 | Achchuthan Shanmugasundram reviewed gene: PGM1: Rating: GREEN; Mode of pathogenicity: None; Publications: 24499211, 37010288; Phenotypes: Congenital disorder of glycosylation, type It, OMIM:14921; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.35 | PGAP3 | Achchuthan Shanmugasundram Classified gene: PGAP3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.35 | PGAP3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>10 unrelated cases) available for promoting this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.35 | PGAP3 | Achchuthan Shanmugasundram Gene: pgap3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.34 | PGAP3 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: PGAP3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.34 | PGAP3 |
Achchuthan Shanmugasundram gene: PGAP3 was added gene: PGAP3 was added to Clefting. Sources: Literature Mode of inheritance for gene: PGAP3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PGAP3 were set to 28390064; 37010288 Phenotypes for gene: PGAP3 were set to Hyperphosphatasia with impaired intellectual development syndrome 4, OMIM:615716 Review for gene: PGAP3 was set to GREEN Added comment: PMID:28390064 - 10 patients from eight families presented with developmental delay, severe intellectual disability, distinct facial dysmorphism and increased alkaline phosphatase. Nine patients from seven families were homozygous for the same variant (c.402dupC/ p.M135Hfs*28), while one patient had a different homozygous variant ( c.817_820delGACT/ p.D273Sfs*37). Of nine patients with p.M135Hfs*28 variant, eight patients from seven families (except one of the two patients from family 7) had cleft palate. But, the only patient with the different variant did not have cleft palate. DECIPHER database - Of seven patients reported with biallelic sequence variants, three patents with homozygous variants were reported with cleft palate and two patients with compound heterozygous variants were reported with cleft soft palate (PMID:37010288). OMIM associated patients with autosomal recessive variants in PGAP3 to hyperphosphatasia with impaired intellectual development syndrome 4 (MIM #615716) and cleft palate has been recorded as one of the clinical manifestations occurring in some patients. Sources: Literature |
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| Clefting v4.33 | MED13L |
Achchuthan Shanmugasundram changed review comment from: PMID:25137640 - Cleft palate was present in the patient reported with intellectual disability and dysmorphic facial features. PMID:25712080 - Cleft palate was reported in a single case (patient 1) of MED13L haploinsufficiency. PMID:29159987 - One of the two patients reported with de novo variants had repaired posterior cleft palate and the other had only high palate. PMID:29511999 - One of 36 patients with monoallelic variants had posterior cleft palate. DECIPHER database - Of 72 patients reported with heterozygous sequence variants, cleft palate was reported in two patients, cleft soft palate in one and submucous cleft hard palate in one patient (PMID:37010288).; to: Although there are more than three cases reported with clefting, this feature is not consistently found in patients with monoallelic variants in MED13L gene. PMID:25137640 - Cleft palate was present in the patient reported with intellectual disability and dysmorphic facial features. PMID:25712080 - Cleft palate was reported in a single case (patient 1) of MED13L haploinsufficiency. PMID:29159987 - One of the two patients reported with de novo variants had repaired posterior cleft palate and the other had only high palate. PMID:29511999 - One of 36 patients with monoallelic variants had posterior cleft palate. DECIPHER database - Of 72 patients reported with heterozygous sequence variants, cleft palate was reported in two patients, cleft soft palate in one and submucous cleft hard palate in one patient (PMID:37010288). |
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| Clefting v4.33 | MED13L | Achchuthan Shanmugasundram Publications for gene: MED13L were set to 25137640; 25712080; 29159987; 29511999; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.33 | MED13L | Achchuthan Shanmugasundram Publications for gene: MED13L were set to 25137640; 25712080; 29159987; 29511999; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.33 | MED13L | Achchuthan Shanmugasundram Publications for gene: MED13L were set to 25137640; 25712080 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.32 | MED13L |
Achchuthan Shanmugasundram changed review comment from: PMID:25137640 - Cleft palate was present in the patient reported with intellectual disability and dysmorphic facial features. PMID:25712080 - Cleft palate was reported in a single case (patient 1) of MED13L haploinsufficiency. PMID:29159987 - One of the two patients reported with de novo variants had repaired posterior cleft palate and the other had only high palate. PMID:29511999 - One of 36 patients with monoallelic variants had posterior cleft palate. DECIPHER database - Of 72 patients reported with heterozygous sequence variants, cleft palate was reported in two patients, cleft soft palate in one and submucous cleft hard palate in one patient.; to: PMID:25137640 - Cleft palate was present in the patient reported with intellectual disability and dysmorphic facial features. PMID:25712080 - Cleft palate was reported in a single case (patient 1) of MED13L haploinsufficiency. PMID:29159987 - One of the two patients reported with de novo variants had repaired posterior cleft palate and the other had only high palate. PMID:29511999 - One of 36 patients with monoallelic variants had posterior cleft palate. DECIPHER database - Of 72 patients reported with heterozygous sequence variants, cleft palate was reported in two patients, cleft soft palate in one and submucous cleft hard palate in one patient (PMID:37010288). |
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| Clefting v4.32 | MED13L | Achchuthan Shanmugasundram edited their review of gene: MED13L: Changed publications to: 25137640, 25712080, 29159987, 29511999, 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.32 | MED13L | Achchuthan Shanmugasundram reviewed gene: MED13L: Rating: AMBER; Mode of pathogenicity: None; Publications: 25712080, 29159987, 29511999; Phenotypes: Impaired intellectual development and distinctive facial features with or without cardiac defects, OMIM:616789; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.32 | KMT2A | Achchuthan Shanmugasundram Classified gene: KMT2A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.32 | KMT2A | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three cases reported with clefting, it is only present in a very small subsection of patients with KMT2A monoallelic variants. Hence, this gene can only be rated amber with current evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.32 | KMT2A | Achchuthan Shanmugasundram Gene: kmt2a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.31 | KMT2A |
Achchuthan Shanmugasundram gene: KMT2A was added gene: KMT2A was added to Clefting. Sources: Literature Mode of inheritance for gene: KMT2A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: KMT2A were set to 25929198; 30305169; 31710778; 37010288 Phenotypes for gene: KMT2A were set to Wiedemann-Steiner syndrome, OMIM:605130 Review for gene: KMT2A was set to AMBER Added comment: PMID:25929198 - De novo KMT2A variant (p.Arg1083Ter) in monozygotic twins and they had submucosal cleft palate. PMID:30305169 - Two of 14 patients with KMT2A variants and presenting with Wiedemann–Steiner syndrome had cleft palate. PMID:31710778 - Both patients reported with KMT2A variants had only high arched palate and not cleft palate. DECIPHER database - None of the reported patients had cleft lip/ palate and only one of 115 had bifid uvula (PMID:37010288) Sources: Literature |
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| Clefting v4.30 | KAT6B | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: KAT6B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.30 | KAT6B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.30 | KAT6B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.30 | KAT6B | Achchuthan Shanmugasundram Classified gene: KAT6B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.30 | KAT6B | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although clefting is a minor feature in patients reported with monoallelic KAT6B variants, it has been reported in more than 20 cases so far. Hence, this gene should be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.30 | KAT6B | Achchuthan Shanmugasundram Gene: kat6b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.29 | KAT6B | Achchuthan Shanmugasundram Classified gene: KAT6B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.29 | KAT6B | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although clefting is a minor feature in patients reported with monoallelic KAT6B variants, it has been reported in more than 20 cases so far. Hence, this gene should be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.29 | KAT6B | Achchuthan Shanmugasundram Gene: kat6b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.29 | KAT6B | Achchuthan Shanmugasundram Classified gene: KAT6B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.29 | KAT6B | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although clefting is a minor feature in patients reported with monoallelic KAT6B variants, it has been reported in more than 20 cases so far. Hence, this gene should be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.29 | KAT6B | Achchuthan Shanmugasundram Gene: kat6b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.28 | GLI2 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: Although cleating is a minor feature in patients reported with monoallelic GLI2 variants, it has been reported in more than 15 cases. Hence, this gene should be promoted to green rating in the next GMS review.; to: Comment on list classification: Although clefting is a minor feature in patients reported with monoallelic GLI2 variants, it has been reported in more than 15 cases. Hence, this gene should be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.28 | KAT6B | Achchuthan Shanmugasundram Phenotypes for gene: KAT6B were changed from Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 to Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.28 | KAT6B | Achchuthan Shanmugasundram Phenotypes for gene: KAT6B were changed from Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 to Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.28 | KAT6B | Achchuthan Shanmugasundram Phenotypes for gene: KAT6B were changed from Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 to Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.27 | KAT6B | Achchuthan Shanmugasundram Phenotypes for gene: KAT6B were changed from Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 to Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.27 | KAT6B | Achchuthan Shanmugasundram Phenotypes for gene: KAT6B were changed from Genitopatellar syndrome, 606170; GTPTS to Genitopatellar syndrome, OMIM:606170; SBBYSS syndrome, OMIM:603736 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.26 | KAT6B | Achchuthan Shanmugasundram Publications for gene: KAT6B were set to 20182757; 27031267; 32424177; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.26 | KAT6B | Achchuthan Shanmugasundram Publications for gene: KAT6B were set to 20182757; 27031267 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.25 | KAT6B | Achchuthan Shanmugasundram reviewed gene: KAT6B: Rating: AMBER; Mode of pathogenicity: None; Publications: 32424177, 37010288; Phenotypes: Genitopatellar syndrome, OMIM:606170, SBBYSS syndrome, OMIM:603736; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.25 | HNRNPK | Achchuthan Shanmugasundram Classified gene: HNRNPK as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.25 | HNRNPK | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available to promote this gene to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.25 | HNRNPK | Achchuthan Shanmugasundram Gene: hnrnpk has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.24 | HNRNPK | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: HNRNPK. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.24 | HNRNPK | Achchuthan Shanmugasundram Phenotypes for gene: HNRNPK were changed from Au-Kline syndrome, OMIM:616580 to Au-Kline syndrome, OMIM:616580 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.24 | HNRNPK | Achchuthan Shanmugasundram Phenotypes for gene: HNRNPK were changed from to Au-Kline syndrome, OMIM:616580 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.23 | HNRNPK |
Achchuthan Shanmugasundram changed review comment from: PMID:29904177 reported six new cases and reviewed additional cases from literature with Au-Kline syndrome and monoallelic variants in HNRNPK gene. Of 12 patients reported and reviewed in this publication, five had cleft palate and two others had bifid uvula. Three out of six patients reported with heterozygous sequence variants in HNRNPK gene had cleft palate as one of the phenotypes (PMID:37010288). OMIM reported that patients with Au-Kline syndrome (MIM #616580) caused by autosomal dominant variants in HNRNPK gene has cleft palate/ bifid uvula as clinical manifestations. Sources: Literature; to: PMID:29904177 reported six new cases and reviewed additional cases from literature with Au-Kline syndrome and monoallelic variants in HNRNPK gene. Of 12 patients reported and reviewed in this publication, five had cleft palate and two others had bifid uvula. Three out of six patients reported with heterozygous sequence variants in HNRNPK gene in the DECIPHER database had cleft palate as one of the phenotypes (PMID:37010288). OMIM reported that patients with Au-Kline syndrome (MIM #616580) caused by autosomal dominant variants in HNRNPK gene has cleft palate/ bifid uvula as clinical manifestations. Sources: Literature |
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| Clefting v4.23 | HNRNPK | Achchuthan Shanmugasundram edited their review of gene: HNRNPK: Changed phenotypes to: Au-Kline syndrome, OMIM:616580 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.23 | HNRNPK |
Achchuthan Shanmugasundram gene: HNRNPK was added gene: HNRNPK was added to Clefting. Sources: Literature Mode of inheritance for gene: HNRNPK was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: HNRNPK were set to 29904177; 37010288 Review for gene: HNRNPK was set to GREEN Added comment: PMID:29904177 reported six new cases and reviewed additional cases from literature with Au-Kline syndrome and monoallelic variants in HNRNPK gene. Of 12 patients reported and reviewed in this publication, five had cleft palate and two others had bifid uvula. Three out of six patients reported with heterozygous sequence variants in HNRNPK gene had cleft palate as one of the phenotypes (PMID:37010288). OMIM reported that patients with Au-Kline syndrome (MIM #616580) caused by autosomal dominant variants in HNRNPK gene has cleft palate/ bifid uvula as clinical manifestations. Sources: Literature |
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| Autoinflammatory disorders v1.1 | SEC23B |
Lauma Freimane gene: SEC23B was added gene: SEC23B was added to Autoinflammatory disorders. Sources: Literature Mode of inheritance for gene: SEC23B was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SEC23B were set to 32098966 Phenotypes for gene: SEC23B were set to Dyserythropoietic anemia, congenital, type II Review for gene: SEC23B was set to GREEN Added comment: Sources: Literature |
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| Autoinflammatory disorders v1.1 | PRF1 |
Lauma Freimane gene: PRF1 was added gene: PRF1 was added to Autoinflammatory disorders. Sources: Literature Mode of inheritance for gene: PRF1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PRF1 were set to 32098966 Phenotypes for gene: PRF1 were set to Familial hemophagocytic lymphohistiocytosis-2 (FHL2) (OMIM: 603553) |
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| Autoinflammatory disorders v1.1 | GP6 |
Lauma Freimane gene: GP6 was added gene: GP6 was added to Autoinflammatory disorders. Sources: Expert Review,Literature Mode of inheritance for gene: GP6 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GP6 were set to 32098966 Phenotypes for gene: GP6 were set to Platlet-type bleeding disorder-11 Review for gene: GP6 was set to GREEN Added comment: Sources: Expert Review, Literature |
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| Autoinflammatory disorders v1.1 | IL17RA |
Lauma Freimane gene: IL17RA was added gene: IL17RA was added to Autoinflammatory disorders. Sources: Literature Mode of inheritance for gene: IL17RA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: IL17RA were set to 32098966 Phenotypes for gene: IL17RA were set to Immunodeficiency-51 Review for gene: IL17RA was set to GREEN Added comment: Sources: Literature |
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| Autoinflammatory disorders v1.1 | ADA |
Lauma Freimane gene: ADA was added gene: ADA was added to Autoinflammatory disorders. Sources: Literature Mode of inheritance for gene: ADA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ADA were set to 32098966 Phenotypes for gene: ADA were set to T(-), B(-), NK(-) severe combin immunodeficiency Review for gene: ADA was set to GREEN Added comment: Sources: Literature |
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| Haematological malignancies cancer susceptibility v4.2 | NAPRT |
Lauma Freimane gene: NAPRT was added gene: NAPRT was added to Haematological malignancies cancer susceptibility. Sources: Literature Mode of inheritance for gene: NAPRT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NAPRT were set to 32098966 Phenotypes for gene: NAPRT were set to MDS/AML; inherited bone marrow failure series Review for gene: NAPRT was set to GREEN Added comment: Sources: Literature |
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| Haematological malignancies cancer susceptibility v4.2 | DNAH9 |
Lauma Freimane gene: DNAH9 was added gene: DNAH9 was added to Haematological malignancies cancer susceptibility. Sources: Literature Mode of inheritance for gene: DNAH9 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DNAH9 were set to 32098966 Phenotypes for gene: DNAH9 were set to MDS/AML; inherited bone marrow failure (IBMF) Review for gene: DNAH9 was set to GREEN Added comment: Sources: Literature |
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| Haematological malignancies cancer susceptibility v4.2 | ADA |
Lauma Freimane gene: ADA was added gene: ADA was added to Haematological malignancies cancer susceptibility. Sources: Literature Mode of inheritance for gene: ADA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ADA were set to 32098966 Phenotypes for gene: ADA were set to severe combined immunodeficiency Added comment: A causative factor of T cell-negative, B cell-negative, natural killer cell-negative severe combined immunodeficiency. Sources: Literature |
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| Clefting v4.22 | GLI2 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: GLI2. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.22 | GLI2 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.22 | GLI2 | Achchuthan Shanmugasundram Classified gene: GLI2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.22 | GLI2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although cleating is a minor feature in patients reported with monoallelic GLI2 variants, it has been reported in more than 15 cases. Hence, this gene should be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.22 | GLI2 | Achchuthan Shanmugasundram Gene: gli2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.21 | GLI2 | Achchuthan Shanmugasundram Classified gene: GLI2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.21 | GLI2 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although cleating is a minor feature in patients reported with monoallelic GLI2 variants, it has been reported in more than 15 cases. Hence, this gene should be promoted to green rating in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.21 | GLI2 | Achchuthan Shanmugasundram Gene: gli2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.20 | GLI2 |
Achchuthan Shanmugasundram gene: GLI2 was added gene: GLI2 was added to Clefting. Sources: Literature Mode of inheritance for gene: GLI2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: GLI2 were set to 24744436; 37010288 Phenotypes for gene: GLI2 were set to Culler-Jones syndrome, OMIM:615849; Holoprosencephaly 9, OMIM:610829 Review for gene: GLI2 was set to GREEN Added comment: In ~400 screened individuals with HPE spectrum disorders, 112 individuals were identified with variants in GLI2 gene, of which 16 cases had cleft lip/ palate (PMID:24744436). Three out of 17 patients reported with heterozygous GLI2 sequence variants in the DECIPHER database presented with cleft lip/ palate as one of the phenotypes (PMID:37010288). OMIM reported cleft lip/ palate as one of the clinical presentations in a subset of patients with Culler-Jones syndrome (MIM #615849) and holoprosencephaly 9 (MIM #610829). These are diseases associated with autosomal dominant variants in GLI2 gene. Sources: Literature |
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| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Classified gene: FGFR3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three unrelated cases reported with cleft lip and/or palate, this is not consistently found in patients with monoallelic variants in FGFR3 gene. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Gene: fgfr3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Classified gene: FGFR3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three unrelated cases reported with cleft lip and/or palate, this is not consistently found in patients with monoallelic variants in FGFR3 gene. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.19 | FGFR3 | Achchuthan Shanmugasundram Gene: fgfr3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.18 | FGFR3 | Achchuthan Shanmugasundram Classified gene: FGFR3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.18 | FGFR3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three unrelated cases reported with cleft lip and/or palate, this is not consistently found in patients with monoallelic variants in FGFR3 gene. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.18 | FGFR3 | Achchuthan Shanmugasundram Gene: fgfr3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.18 | FGFR3 | Achchuthan Shanmugasundram Classified gene: FGFR3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.18 | FGFR3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are more than three unrelated cases reported with cleft lip and/or palate, this is not consistently found in patients with monoallelic variants in FGFR3 gene. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.18 | FGFR3 | Achchuthan Shanmugasundram Gene: fgfr3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital muscular dystrophy v4.9 | COL4A1 | Gavin Ryan reviewed gene: COL4A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 18160688, 20818663; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.17 | FGFR3 |
Achchuthan Shanmugasundram gene: FGFR3 was added gene: FGFR3 was added to Clefting. Sources: Literature Mode of inheritance for gene: FGFR3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: FGFR3 were set to 22565872; 29150894; 37010288 Phenotypes for gene: FGFR3 were set to Muenke syndrome, OMIM:602849; Hypochondroplasia, OMIM:146000 Review for gene: FGFR3 was set to AMBER Added comment: PMID:22565872 included 21 patients with variants in FGFR3 and presenting with Muenke syndrome in this study, of which 16 patients had structural anomaly of the palate. However, only one patient had cleft lip and palate. PMID:29150894 reported a father and two children with FGFR3 variant and presenting with hypochondroplasia, of which only the daughter had cleft palate. 2 out of 15 patients reported in DECIPHER database with monoallelic sequence variants had cleft palate. Sources: Literature |
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| Clefting v4.16 | CNTNAP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - There is one patient reported with compound heterozygous stop gain variants in CNTNAP1 (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature; to: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - There is one patient reported with compound heterozygous stop gain variants in CNTNAP1 (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature |
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| Clefting v4.16 | CNTNAP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - A patient with compound heterozygous stop gain variants in CNTNAP1 gene (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature; to: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - There is one patient reported with compound heterozygous stop gain variants in CNTNAP1 (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature |
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| Clefting v4.16 | CNTNAP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - Of seven patients reported with biallelic variants in CNTNAP1 gene, single patient with compound heterozygous stop gain variants (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature; to: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - A patient with compound heterozygous stop gain variants in CNTNAP1 gene (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature |
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| Clefting v4.16 | CNTNAP1 | Achchuthan Shanmugasundram edited their review of gene: CNTNAP1: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.16 | CNTNAP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - There is one patient reported with compound heterozygous stop gain variants in CNTNAP1 (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature; to: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - Of seven patients reported with biallelic variants in CNTNAP1 gene, single patient with compound heterozygous stop gain variants (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature |
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| Clefting v4.16 | CNTNAP1 | Achchuthan Shanmugasundram edited their review of gene: CNTNAP1: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.16 | ARID1B | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: Although there are three unrelated cases reported, clefting is not consistently present in patients with monoallelic variants in this gene. Hence, this gene should be rated amber.; to: Comment on list classification: Although there are more than three unrelated cases reported, clefting is not consistently present in patients with monoallelic variants in this gene. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.16 | ARID1B |
Achchuthan Shanmugasundram changed review comment from: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. One patient with ARID1B variant (c.3183_3184insT/ p.Tyr1062LeufsTer10) was reported with submucous cleft soft palate and two patients with ARID1B variants (c.4155_4156insA/ p.Asn1386LysfsTer18 & c.2620+5G>A) were reported with bifid uvula in DECIPHER database. Sources: Literature; to: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. Of >100 patients with ARID1B variants in the DECIPHER database, only one patient (c.3183_3184insT/ p.Tyr1062LeufsTer10) was reported with submucous cleft soft palate and two patients (c.4155_4156insA/ p.Asn1386LysfsTer18 & c.2620+5G>A) were reported with bifid uvula. Sources: Literature |
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| Clefting v4.16 | ARID1B | Achchuthan Shanmugasundram Classified gene: ARID1B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.16 | ARID1B | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are three unrelated cases reported, clefting is not consistently present in patients with monoallelic variants in this gene. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.16 | ARID1B | Achchuthan Shanmugasundram Gene: arid1b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | ARID1B | Achchuthan Shanmugasundram Tag Q3_23_promote_green was removed from gene: ARID1B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | ARID1B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | ARID1B | Achchuthan Shanmugasundram edited their review of gene: ARID1B: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | CHD4 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | CHD4 | Achchuthan Shanmugasundram Classified gene: CHD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | CHD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are four unrelated cases presenting with either cleft palate and/or bifid uvula, this phenotype is not consistently found in patients with monoallelic CHD4 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.15 | CHD4 | Achchuthan Shanmugasundram Gene: chd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.14 | CHD4 | Achchuthan Shanmugasundram Classified gene: CHD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.14 | CHD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: Although there are four unrelated cases presenting with either cleft palate and/or bifid uvula, this phenotype is not consistently found in patients with monoallelic CHD4 variants. Hence, this gene should be rated amber. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.14 | CHD4 | Achchuthan Shanmugasundram Gene: chd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.13 | CHD4 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.13 | CHD4 | Achchuthan Shanmugasundram Tag Q3_23_promote_green was removed from gene: CHD4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.13 | CHD4 | Achchuthan Shanmugasundram edited their review of gene: CHD4: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.13 | CHD4 |
Achchuthan Shanmugasundram changed review comment from: PMID:31388190 reported a patient with heterozygous variant (p.Gln715Ter) in CHD4 that had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, DDD study reported two patients with likely pathogenic heterozygous variants who had cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288). Sources: Literature; to: PMID:31388190 reported 32 patients with heterozygous variants in CHD4 gene, of which one patient (p.Gln715Ter) had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, 2 out of 10 patients with pathogenic/ likely pathogenic heterozygous variants from the DDD study were reported with cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288). Sources: Literature |
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| Clefting v4.13 | CHD4 |
Achchuthan Shanmugasundram changed review comment from: PMID:3138819 reported a patient with heterozygous variant (p.Gln715Ter) in CHD4 that had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, DDD study reported two patients with likely pathogenic heterozygous variants who had cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288). Sources: Literature; to: PMID:31388190 reported a patient with heterozygous variant (p.Gln715Ter) in CHD4 that had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, DDD study reported two patients with likely pathogenic heterozygous variants who had cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288). Sources: Literature |
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| Clefting v4.13 | B4GALT7 | Achchuthan Shanmugasundram Publications for gene: B4GALT7 were set to 24755949 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | B4GALT7 | Achchuthan Shanmugasundram Tag Q3_23_promote_green was removed from gene: B4GALT7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | B4GALT7 |
Achchuthan Shanmugasundram changed review comment from: PMID:24755949 - One of 22 patients identified with homozygous p.Arg270Cys variant in B4GALT7 gene had a cleft palate. PMID:26940150 - One of two patients reported in this publication from DDD study with compound heterozygous variants (p.His93Profds*73 & p.Cys2145Tyr) had cleft palate. PMID:31278392 - One patient and affected third pregnancy with compound heterozygous variants (p.Gln133Arg & p.Arg270Cys) and cleft palate was reported in this family.; to: Cleft palate is not a consistent feature that is reported in patients with biallelic variants in B4GALT7 gene. However, there are three unrelated cases reported with cleft palate. PMID:24755949 - One of 22 patients identified with homozygous p.Arg270Cys variant in B4GALT7 gene had a cleft palate. PMID:26940150 - One of two patients reported in this publication from DDD study with compound heterozygous variants (p.His93Profds*73 & p.Cys2145Tyr) had cleft palate. PMID:31278392 - One patient and affected third pregnancy with compound heterozygous variants (p.Gln133Arg & p.Arg270Cys) and cleft palate was reported in this family. |
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| Clefting v4.12 | B4GALT7 | Achchuthan Shanmugasundram edited their review of gene: B4GALT7: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | B4GALT7 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | B4GALT7 |
Achchuthan Shanmugasundram changed review comment from: PMID:24755949 - One of 22 patients identified with with homozygous p.Arg270Cys variant in B4GALT7 gene had a cleft palate. PMID:26940150 - One of two patients reported in this publication from DDD study with compound heterozygous variants (p.His93Profds*73 & p.Cys2145Tyr) had cleft palate. PMID:31278392 - One patient and affected third pregnancy with compound heterozygous variants (p.Gln133Arg & p.Arg270Cys) and cleft palate was reported in this family.; to: PMID:24755949 - One of 22 patients identified with homozygous p.Arg270Cys variant in B4GALT7 gene had a cleft palate. PMID:26940150 - One of two patients reported in this publication from DDD study with compound heterozygous variants (p.His93Profds*73 & p.Cys2145Tyr) had cleft palate. PMID:31278392 - One patient and affected third pregnancy with compound heterozygous variants (p.Gln133Arg & p.Arg270Cys) and cleft palate was reported in this family. |
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| Clefting v4.12 | DDX3X |
Achchuthan Shanmugasundram changed review comment from: PMID:26235985 - Patients with DDX3X variants reported from multiple studies including the Deciphering Developmental Disorders (DDD) study, of which three females had cleft lip and/ or palate (one from the DDD study) and one male had bifid uvula. PMID:27159028 - A female patient with DDX3X variant (c.856G>A/ p.Gly286Ser) and reported with severe ID and ataxic gait also had cleft uvula.; to: PMID:26235985 - 38 female and three male patients with DDX3X variants were reported from multiple studies including the Deciphering Developmental Disorders (DDD) study, of which three females had cleft lip and/ or palate (one from the DDD study) and one male had bifid uvula. PMID:27159028 - Two female patients were reported with DDX3X variants, of which one of them reported with severe ID and ataxic gait (c.856G>A/ p.Gly286Ser) also had cleft uvula. |
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| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram edited their review of gene: DDX3X: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Tag Q3_23_promote_green was removed from gene: DDX3X. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ehlers Danlos syndrome with a likely monogenic cause v3.3 | COL12A1 | Sarah Leigh Publications for gene: COL12A1 were set to 28306229; 28306225; 24334769; 24334604; 27348394 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ehlers Danlos syndrome with a likely monogenic cause v3.2 | COL12A1 | Sarah Leigh reviewed gene: COL12A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 35019233; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ehlers Danlos syndrome with a likely monogenic cause v3.2 | COL12A1 | Sarah Leigh Phenotypes for gene: COL12A1 were changed from Bethlem myopathy 2, OMIM:616471 to Bethlem myopathy 2, OMIM:616471; Bethlem myopathy 2, MONDO:0034022 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Haematological malignancies cancer susceptibility v4.2 | DHX34 |
Lauma Freimane gene: DHX34 was added gene: DHX34 was added to Haematological malignancies cancer susceptibility. Sources: Literature Mode of inheritance for gene: DHX34 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DHX34 were set to 32098966 Phenotypes for gene: DHX34 were set to Thrombocytopenia; Neutropenia; Pancytopenia; AML Penetrance for gene: DHX34 were set to Complete Review for gene: DHX34 was set to GREEN Added comment: PMID: 32098966 - "[..] functionally validated heterozygous variants in the RNA helicase DHX34, detected in four families, all of which impacted activity of the NMD (nonsense-mediated mRNA decay) pathway. [..]" Sources: Literature |
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| Haematological malignancies cancer susceptibility v4.2 | SH2B3 | Lauma Freimane reviewed gene: SH2B3: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Classified gene: DDX3X as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated cases associating this gene with cleft lip and/ or palate. Hence, this gene can be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Gene: ddx3x has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Classified gene: DDX3X as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are five unrelated cases associating this gene with cleft lip and/ or palate. Hence, this gene can be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.12 | DDX3X | Achchuthan Shanmugasundram Gene: ddx3x has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.11 | DDX3X | Achchuthan Shanmugasundram Publications for gene: DDX3X were set to 26235985; 27159028; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.11 | DDX3X | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: DDX3X. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.11 | DDX3X | Achchuthan Shanmugasundram Publications for gene: DDX3X were set to 26235985; 27159028; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.11 | DDX3X | Achchuthan Shanmugasundram Publications for gene: DDX3X were set to 26235985; 27159028; 37010288 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.11 | DDX3X | Achchuthan Shanmugasundram Publications for gene: DDX3X were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.10 | DDX3X | Achchuthan Shanmugasundram reviewed gene: DDX3X: Rating: GREEN; Mode of pathogenicity: None; Publications: 26235985, 27159028, 37010288; Phenotypes: Intellectual developmental disorder, X-linked syndromic, Snijders Blok type, OMIM:300958; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.10 | CNTNAP1 | Achchuthan Shanmugasundram Classified gene: CNTNAP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.10 | CNTNAP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated cases) for the association of biallelic variants from this gene with cleft palate. Hence, it can be promoted to green rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.10 | CNTNAP1 | Achchuthan Shanmugasundram Gene: cntnap1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.9 | CNTNAP1 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: CNTNAP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.9 | CNTNAP1 |
Achchuthan Shanmugasundram gene: CNTNAP1 was added gene: CNTNAP1 was added to Clefting. Sources: Literature Mode of inheritance for gene: CNTNAP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CNTNAP1 were set to 28374019; 29511323; 29882456; 37010288 Phenotypes for gene: CNTNAP1 were set to Hypomyelinating neuropathy, congenital, 3, OMIM:618186 Review for gene: CNTNAP1 was set to GREEN Added comment: PMID:28374019 - Cleft palate was reported in two children from a large Israeli consanguineous family of Palestinian ancestry with a homozygous stop-gain variant in CNTNAP1(c.2015G>A/ p.Trp672Ter). PMID:29511323/ 37010288 - There is one patient reported with compound heterozygous stop gain variants in CNTNAP1 (c.2687G>A/ p.Trp896Ter & c.1861C>T/ p.Arg621Ter) had cleft palate from DECIPHER database. PMID:29882456 - An eight year old American male patient with a homozygous CNTNAP1 variant (c.1163G>C/ p.Arg388Pro) had cleft palate. Sources: Literature |
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| Clefting v4.8 | ARID1B | Achchuthan Shanmugasundram Classified gene: ARID1B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.8 | ARID1B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (at least three unrelated cases) for this gene to be promoted to green rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.8 | ARID1B | Achchuthan Shanmugasundram Gene: arid1b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.7 | ARID1B | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: ARID1B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.7 | ARID1B | Achchuthan Shanmugasundram edited their review of gene: ARID1B: Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.7 | ARID1B |
Achchuthan Shanmugasundram changed review comment from: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. One patient was reported with submucous cleft soft palate and two patients were reported with bifid uvula in DECIPHER database. Sources: Literature; to: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. One patient with ARID1B variant (c.3183_3184insT/ p.Tyr1062LeufsTer10) was reported with submucous cleft soft palate and two patients with ARID1B variants (c.4155_4156insA/ p.Asn1386LysfsTer18 & c.2620+5G>A) were reported with bifid uvula in DECIPHER database. Sources: Literature |
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| Clefting v4.7 | ARID1B |
Achchuthan Shanmugasundram changed review comment from: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. There is only one patient reported with pathogenic variant in ARID1B gene and submucous cleft soft palate in DECIPHER database. Sources: Literature; to: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. One patient was reported with submucous cleft soft palate and two patients were reported with bifid uvula in DECIPHER database. Sources: Literature |
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| Clefting v4.7 | ARID1B |
Achchuthan Shanmugasundram gene: ARID1B was added gene: ARID1B was added to Clefting. Sources: Literature Mode of inheritance for gene: ARID1B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ARID1B were set to 30349098; 37010288 Phenotypes for gene: ARID1B were set to Coffin-Siris syndrome 1, OMIM:135900 Review for gene: ARID1B was set to AMBER Added comment: PMID:30349098 - On this web-based survey based on previously reported features of patients with variants in ARID1B gene (143 patients in total), which also included submissions to DECIPHER database, two patients were identified with cleft palate, one with cleft uvula, two with bifid uvula and three with sub mucous cleft. Although variants identified in these patients are reported in this publication, there is no association of individual patients to phenotypes available. There is only one patient reported with pathogenic variant in ARID1B gene and submucous cleft soft palate in DECIPHER database. Sources: Literature |
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| Clefting v4.6 | CHD4 |
Achchuthan Shanmugasundram changed review comment from: PMID:3138819 reported a patient with heterozygous variant (p.Gln715Ter) in CHD4 that had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, DDD study reported two patients with likely pathogenic heterozygous variants who had cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288) Sources: Literature; to: PMID:3138819 reported a patient with heterozygous variant (p.Gln715Ter) in CHD4 that had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, DDD study reported two patients with likely pathogenic heterozygous variants who had cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288). Sources: Literature |
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| Clefting v4.6 | CHD4 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: CHD4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.6 | CHD4 | Achchuthan Shanmugasundram Classified gene: CHD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.6 | CHD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are four unrelated cases presenting with either cleft palate and/or bifid uvula. Hence, this gene can be promoted to green at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.6 | CHD4 | Achchuthan Shanmugasundram Gene: chd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.5 | CHD4 |
Achchuthan Shanmugasundram gene: CHD4 was added gene: CHD4 was added to Clefting. Sources: Literature Mode of inheritance for gene: CHD4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CHD4 were set to 31388190; 37010288 Phenotypes for gene: CHD4 were set to Sifrim-Hitz-Weiss syndrome, OMIM:617159 Review for gene: CHD4 was set to GREEN Added comment: PMID:3138819 reported a patient with heterozygous variant (p.Gln715Ter) in CHD4 that had cleft palate and pierre robin. In addition, another patient identified with heterozygous variant p.Arg1127Gln was reported with bifid uvula. In addition, DDD study reported two patients with likely pathogenic heterozygous variants who had cleft palate in addition to several other clinical presentations including global developmental delay (PMID:37010288) Sources: Literature |
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| Clefting v4.4 | B4GALT7 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.4 | B4GALT7 | Achchuthan Shanmugasundram Classified gene: B4GALT7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.4 | B4GALT7 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated cases) for this gene to be promoted to Green rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.4 | B4GALT7 | Achchuthan Shanmugasundram Gene: b4galt7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.3 | B4GALT7 | Achchuthan Shanmugasundram Classified gene: B4GALT7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.3 | B4GALT7 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated cases) for this gene to be promoted to Green rating at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.3 | B4GALT7 | Achchuthan Shanmugasundram Gene: b4galt7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.2 | B4GALT7 | Achchuthan Shanmugasundram Tag Q3_23_promote_green tag was added to gene: B4GALT7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Clefting v4.2 | B4GALT7 | Achchuthan Shanmugasundram reviewed gene: B4GALT7: Rating: GREEN; Mode of pathogenicity: None; Publications: 24755949, 26940150, 31278392; Phenotypes: Ehlers-Danlos syndrome, spondylodysplastic type, 1, OMIM:130070; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.189 | TTI1 | Sarah Leigh Classified gene: TTI1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.189 | TTI1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.189 | TTI1 | Sarah Leigh Gene: tti1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.27 | TTI1 | Sarah Leigh Classified gene: TTI1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.27 | TTI1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.27 | TTI1 | Sarah Leigh Gene: tti1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.26 | TTI1 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: TTI1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.188 | TTI1 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: TTI1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.26 | TTI1 |
Sarah Leigh gene: TTI1 was added gene: TTI1 was added to Severe microcephaly. Sources: Literature Mode of inheritance for gene: TTI1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TTI1 were set to 36724785 Phenotypes for gene: TTI1 were set to neurodevelopmental disorder with microcephaly Review for gene: TTI1 was set to GREEN Added comment: TTI1 has not previously been associated with a phenotype in OMIM, Gen2Phen or MONDO. At least 2 variants have been reported. PMID: 36724785 reported 15 TTI1 variants as either homozygotes (2 families) or compound heterozygotes (7 families) in cases with a neurodevelopmental disorder with microcephaly. In all cases the parents were heterozygous carriers of the TTI1 variant identified in the affected child. Development delay was observed in all of the families (9/9), moderate to severe intellectual disability was evident in all families where it could be assessed (8/8) and severe microcephaly was present in members of 5/9 families. Supportive functional results were also presented. Sources: Literature |
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| Intellectual disability v5.188 | TTI1 |
Sarah Leigh gene: TTI1 was added gene: TTI1 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: TTI1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TTI1 were set to 36724785 Phenotypes for gene: TTI1 were set to neurodevelopmental disorder with microcephaly Review for gene: TTI1 was set to GREEN Added comment: TTI1 has not previously been associated with a phenotype in OMIM, Gen2Phen or MONDO. At least 2 variants have been reported. PMID: 36724785 reported 15 TTI1 variants as either homozygotes (2 families) or compound heterozygotes (7 families) in cases with a neurodevelopmental disorder with microcephaly. In all cases the parents were heterozygous carriers of the TTI1 variant identified in the affected child. Development delay was observed in all of the families (9/9), moderate to severe intellectual disability was evident in all families where it could be assessed (8/8) and severe microcephaly was present in members of 5/9 families. Supportive functional results were also presented. Sources: Literature |
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| Intellectual disability v5.187 | TSPOAP1 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: TSPOAP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.13 | TSPOAP1 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: TSPOAP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.187 | TSPOAP1 | Sarah Leigh Entity copied from Childhood onset dystonia, chorea or related movement disorder v3.13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.187 | TSPOAP1 |
Sarah Leigh gene: TSPOAP1 was added gene: TSPOAP1 was added to Intellectual disability - microarray and sequencing. Sources: Literature,Expert Review Amber Mode of inheritance for gene: TSPOAP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TSPOAP1 were set to 33539324 Phenotypes for gene: TSPOAP1 were set to Dystonia, intellectual disability and cerebellar atrophy |
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| Childhood onset dystonia, chorea or related movement disorder v3.13 | TSPOAP1 | Sarah Leigh Tag Q3_23_promote_green was removed from TSPOAP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least TSPOAP1 three variants have been reported in three unrelated families. Family members carrying homozygous TSPOAP1 variants have dystonia, intellectual disability and cerebellar atrophy to varying degrees. Motor symptoms were apparent between 11 and 13 years of age for NM_004758: c.2449_2450delinsTG, p.Gln817* and c.538delG, p.Ala180Profs*8, while NM_004758: c.5422G>A, p.Gly1808Ser was from 58 years through to the 60s. Similarly, cognitive impairment was apparent from school age and progressed to moderate to extensive, in the carries of the two terminating TSPOAP1 variants, while those with the missense variant were diagnosed with mild cognitive impairment (PMID: 33539324). In vitro functional studies and mouse models support the association of the TSPOAP1 variants and phenotypes seen in the cases (PMID: 33539324).; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least three TSPOAP1variants have been reported in three unrelated families. Family members carrying homozygous TSPOAP1 variants have dystonia, intellectual disability and cerebellar atrophy to varying degrees. Motor symptoms were apparent between 11 and 13 years of age for NM_004758: c.2449_2450delinsTG, p.Gln817* and c.538delG, p.Ala180Profs*8, while NM_004758: c.5422G>A, p.Gly1808Ser was from 58 years through to the 60s. Similarly, cognitive impairment was apparent from school age and progressed to moderate to extensive, in the carries of the two terminating TSPOAP1 variants, while those with the missense variant were diagnosed with mild cognitive impairment (PMID: 33539324). In vitro functional studies and mouse models support the association of the TSPOAP1 variants and phenotypes seen in the cases (PMID: 33539324). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least TSPOAP1 three variants have been reported in three unrelated families. Family members carrying homozygous TSPOAP1 variants have dystonia, intellectual disability and cerebellar atrophy to varying degrees (PMID: 33539324). In vitro functional studies and mouse models support the association of the TSPOAP1 variants and phenotypes seen in the cases (PMID: 33539324).; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least TSPOAP1 three variants have been reported in three unrelated families. Family members carrying homozygous TSPOAP1 variants have dystonia, intellectual disability and cerebellar atrophy to varying degrees. Motor symptoms were apparent between 11 and 13 years of age for NM_004758: c.2449_2450delinsTG, p.Gln817* and c.538delG, p.Ala180Profs*8, while NM_004758: c.5422G>A, p.Gly1808Ser was from 58 years through to the 60s. Similarly, cognitive impairment was apparent from school age and progressed to moderate to extensive, in the carries of the two terminating TSPOAP1 variants, while those with the missense variant were diagnosed with mild cognitive impairment (PMID: 33539324). In vitro functional studies and mouse models support the association of the TSPOAP1 variants and phenotypes seen in the cases (PMID: 33539324). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: TSPOAP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh edited their review of gene: TSPOAP1: Added comment: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least TSPOAP1 three variants have been reported in three unrelated families. Family members carrying homozygous TSPOAP1 variants have dystonia, intellectual disability and cerebellar atrophy to varying degrees (PMID: 33539324). In vitro functional studies and mouse models support the association of the TSPOAP1 variants and phenotypes seen in the cases (PMID: 33539324).; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh Classified gene: TSPOAP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.12 | TSPOAP1 | Sarah Leigh Gene: tspoap1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.186 | SRRM2 | Sarah Leigh Added comment: Comment on publications: www.hindawi.com/journals/humu/2023/6633248 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.186 | SRRM2 | Sarah Leigh Publications for gene: SRRM2 were set to 35567594; 33057194 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.12 | FGF14_GAA | Eleanor Williams changed review comment from: Comment on list classification: Promoting to amber but there is sufficient evidence to promote to green following GMS review, and configuration in the Rare Disease analysis pipeline.; to: Comment on list classification: Promoting to amber but there is sufficient evidence to promote to green following GMS review, and configuration in the Rare Disease analysis pipeline. GMS expert review is required to confirm that the normal and pathogenic thresholds set are appropriate. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Haematological malignancies cancer susceptibility v4.2 | TCF3 |
Lauma Freimane gene: TCF3 was added gene: TCF3 was added to Haematological malignancies cancer susceptibility. Sources: Literature Mode of inheritance for gene: TCF3 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: TCF3 were set to 36576946 Phenotypes for gene: TCF3 were set to B-cell acute lymphoblastic leukemia Penetrance for gene: TCF3 were set to unknown Review for gene: TCF3 was set to GREEN gene: TCF3 was marked as current diagnostic Added comment: Autors hypothesize that variants in TCF3 gene alter B-cell maturation which may increase the risk for preleukemic clone emergence (PMID: 36576946). Sources: Literature |
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| Early onset or syndromic epilepsy v4.50 | PNPO | Achchuthan Shanmugasundram Publications for gene: PNPO were set to 24658933; 28818555; 22196487; 21704546; 25296925; 26535729; 15772097; 24266778; 36106796 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.49 | PNPO | Achchuthan Shanmugasundram Publications for gene: PNPO were set to 24658933; 28818555; 22196487; 21704546; 25296925; 26535729; 15772097; 24266778; 36106796 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.49 | PNPO | Achchuthan Shanmugasundram Publications for gene: PNPO were set to 24658933; 28818555; 22196487; 21704546; 25296925; 26535729; 15772097; 24266778 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Dilated and arrhythmogenic cardiomyopathy v2.10 | PPA2 |
Matthew Edwards gene: PPA2 was added gene: PPA2 was added to Dilated and arrhythmogenic cardiomyopathy. Sources: Expert Review Mode of inheritance for gene: PPA2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PPA2 were set to PMID: 34400813 Phenotypes for gene: PPA2 were set to Sudden cardiac failure, infantile; Sudden cardiac failure, alcohol-induced Penetrance for gene: PPA2 were set to unknown Review for gene: PPA2 was set to GREEN gene: PPA2 was marked as current diagnostic Added comment: Now a well established gene causing infantile sudden death, but can also manifest at a later age as alcohol-induced sudden death. Our lab and others have found several bi-allelic pathogenic variants in such SCD cases (see above ref). Is currently on syndromic/paediatric cardiomyopathy panel (R135) and mitochindrial panels, but wholly appropriate for this panel as well Sources: Expert Review |
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| Adult onset hereditary spastic paraplegia v3.10 | PRNP | Sarah Leigh edited their review of gene: PRNP: Added comment: Amongst the variable phenotypes seen in carriers of PRNP variants, features of Gerstmann-Straussler disease (OMIM: 137440) have been associated with eight PRNP variants in unrelated cases (p.P105L, p.D178N, p.P102L, p.A117V, p.F198S, p.Q217R, p.G131V, p.H187R (PMIDs: 7902971, 1699173, 1363810, 11709001, 7902972, 19228673).; Changed rating: GREEN; Changed phenotypes to: Gerstmann-Straussler disease, OMIM: 137440 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.10 | PRNP | Sarah Leigh Publications for gene: PRNP were set to 30240140; 8250529; 34746379; 28195350; 16227536; 19228673; 1699173; 7902971; 11709001; 10581485; 10953183; 1363810 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.9 | PRNP | Sarah Leigh Publications for gene: PRNP were set to 30240140; 8250529; 34746379; 28195350; 16227536; 19228673; 1699173; 7902971; 11709001; 10581485; 10953183 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.8 | PRNP | Sarah Leigh Phenotypes for gene: PRNP were changed from Gerstmann-Straussler disease, OMIM: 137440 to Gerstmann-Straussler disease, OMIM: 137440; Gerstmann-Straussler-Scheinker syndrome, MONDO:0007656 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.7 | PRNP | Sarah Leigh Classified gene: PRNP as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.7 | PRNP | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.7 | PRNP | Sarah Leigh Gene: prnp has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.6 | PRNP | Sarah Leigh Publications for gene: PRNP were set to 30240140; 8250529; 34746379; 28195350; 16227536; 19228673 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.5 | PRNP | Sarah Leigh Tag Q3_23_promote_green tag was added to gene: PRNP. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.5 | PRNP | Sarah Leigh Publications for gene: PRNP were set to 30240140; 8250529; 34746379; 28195350 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.29 | UNC45B | Eleanor Williams commented on gene: UNC45B | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.29 | UNC45B | Eleanor Williams Tag to_be_confirmed_NHSE was removed from gene: UNC45B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.29 | KY | Eleanor Williams changed review comment from: Removed the to_be_confirmed_NHSE tag because this gene has been re-reviewed by an NHSE clinician Anna Sarkozy. Tag added in March 2022, re-reviewed in Nov 2022, removed June 2023.; to: Removed the to_be_confirmed_NHSE tag because this gene has been re-reviewed by an NHSE clinician Anna Sarkozy and so should be included in the next data review. Tag added in March 2022, re-reviewed in Nov 2022, removed June 2023. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.29 | KY | Eleanor Williams changed review comment from: Removed the to_be_confirmed_NHSE tag because this gene has been re-reviewed by an NHSE clinician.; to: Removed the to_be_confirmed_NHSE tag because this gene has been re-reviewed by an NHSE clinician Anna Sarkozy. Tag added in March 2022, re-reviewed in Nov 2022, removed June 2023. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.29 | KY | Eleanor Williams commented on gene: KY | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Congenital myopathy v4.29 | KY | Eleanor Williams Tag to_be_confirmed_NHSE was removed from gene: KY. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.4 | PRNP | Sarah Leigh Phenotypes for gene: PRNP were changed from HSP; Gerstmann–Sträussler–Scheinker disease to Gerstmann-Straussler disease, OMIM: 137440 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.25 | GRM7 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: GRM7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.25 | GRM7 | Achchuthan Shanmugasundram Classified gene: GRM7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.25 | GRM7 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (three unrelated cases with severe microcephaly) for this gene to be promoted to GREEN rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.25 | GRM7 | Achchuthan Shanmugasundram Gene: grm7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.24 | GRM7 | Achchuthan Shanmugasundram Publications for gene: GRM7 were set to 2248644; 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.23 | GRM7 | Achchuthan Shanmugasundram edited their review of gene: GRM7: Changed publications to: 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.23 | GRM7 |
Achchuthan Shanmugasundram changed review comment from: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising severe to profound global developmental delays, intellectual disability, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel). Sources: Literature; to: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising severe to profound global developmental delays, intellectual disability, seizures, hypotonia, microcephaly and brain abnormalities. Head circumference measurements at time of last visit were available in eight individuals (from six families) and were consistent with microcephaly (−3.8 to −2.7 SD from mean for age). Of these four individuals from three families had severe microcephaly (head circumference beyond 3 SD from mean for age). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel). Sources: Literature |
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| Severe microcephaly v4.23 | GRM7 | Achchuthan Shanmugasundram edited their review of gene: GRM7: Changed publications to: 32248644, 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.185 | GRM7 | Achchuthan Shanmugasundram Classified gene: GRM7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.185 | GRM7 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (six unrelated cases and supporting mouse model) for this gene to be promoted to GREEN rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.185 | GRM7 | Achchuthan Shanmugasundram Gene: grm7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.184 | GRM7 | Achchuthan Shanmugasundram Publications for gene: GRM7 were set to 32248644; 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.184 | GRM7 | Achchuthan Shanmugasundram edited their review of gene: GRM7: Changed publications to: 32248644, 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.184 | GRM7 | Achchuthan Shanmugasundram Publications for gene: GRM7 were set to 32248644; 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.184 | GRM7 | Achchuthan Shanmugasundram Publications for gene: GRM7 were set to 2248644; 32286009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.183 | GRM7 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: GRM7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.23 | GRM7 |
Achchuthan Shanmugasundram gene: GRM7 was added gene: GRM7 was added to Severe microcephaly. Sources: Literature Mode of inheritance for gene: GRM7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GRM7 were set to 2248644; 32286009 Phenotypes for gene: GRM7 were set to Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities, OMIM:618922 Review for gene: GRM7 was set to GREEN Added comment: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising severe to profound global developmental delays, intellectual disability, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel). Sources: Literature |
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| Intellectual disability v5.183 | GRM7 |
Achchuthan Shanmugasundram gene: GRM7 was added gene: GRM7 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: GRM7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GRM7 were set to 2248644; 32286009 Phenotypes for gene: GRM7 were set to Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities, OMIM:618922 Review for gene: GRM7 was set to GREEN Added comment: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising severe to profound global developmental delays, intellectual disability, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel). Sources: Literature |
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| Early onset or syndromic epilepsy v4.48 | GRM7 |
Achchuthan Shanmugasundram changed review comment from: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising global developmental delay/ intellectual impairment, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel).; to: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising severe to profound global developmental delays, intellectual disability, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel). |
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| Early onset or syndromic epilepsy v4.48 | GRM7 |
Achchuthan Shanmugasundram changed review comment from: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmentakl disorder comprising global developmental delay/ intellectual impairment, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel).; to: PMID:32286009 reported eleven individuals from six unrelated families identified with three different biallelic variants and presenting with a neurodevelopmental disorder comprising global developmental delay/ intellectual impairment, seizures, hypotonia, microcephaly and brain abnormalities. This is also supported by functional evidence from knockout mouse models, where absence of metabotropic glutamate receptor 7 alters the phenotypes within the domains of social behavior, associative learning, motor function, epilepsy and sleep (PMID:32248644). This gene has also been associated with relevant phenotypes in both OMIM (MIM #618922) and in Gene2Phenotype (with 'strong' rating in the DD panel). |
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| Early onset or syndromic epilepsy v4.48 | GRM7 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: GRM7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.48 | GRM7 | Achchuthan Shanmugasundram Classified gene: GRM7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.48 | GRM7 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (6 unrelated cases and supporting mouse model) for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.48 | GRM7 | Achchuthan Shanmugasundram Gene: grm7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.47 | GRM7 | Achchuthan Shanmugasundram Phenotypes for gene: GRM7 were changed from Epilepsy, microcephaly, developmental delay to Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities, OMIM:618922 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.46 | GRM7 | Achchuthan Shanmugasundram reviewed gene: GRM7: Rating: GREEN; Mode of pathogenicity: None; Publications: 32248644, 32286009; Phenotypes: Neurodevelopmental disorder with seizures, hypotonia, and brain abnormalities, OMIM:618922; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.10 | CCDC82 | Achchuthan Shanmugasundram Classified gene: CCDC82 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.10 | CCDC82 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases and hence this gene should be rated AMBER. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.10 | CCDC82 | Achchuthan Shanmugasundram Gene: ccdc82 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset hereditary spastic paraplegia v4.9 | CCDC82 |
Achchuthan Shanmugasundram gene: CCDC82 was added gene: CCDC82 was added to Childhood onset hereditary spastic paraplegia. Sources: Literature Mode of inheritance for gene: CCDC82 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CCDC82 were set to 35118659; 35373332 Phenotypes for gene: CCDC82 were set to neurodevelopmental disorder, MONDO:0700092; hereditary spastic paraplegia, MONDO:0019064 Review for gene: CCDC82 was set to AMBER Added comment: PMID: 35118659 reported two siblings presenting with global global developmental delay (last evaluation at 4 years and 9 months) and spasticity. They also had a common history of infantile spasms with the elder developing GTC convulsions with spontaneous resolution and both presented with microcephaly (<-2 and <-3SD). They harboured homozygous variant c.535C>T ( p.Arg179Ter). PMID: 35373332 reported a 21 years old male who presented with features included short stature, intellectual disability, spastic paraparesis (at the age of 3 years). Gelastic seizures were suspected but not confirmed (repeated normal EEGs). This patient harboured a homozygous frameshift CCDC82 variant c.183del (p.Phe61Leufs*27) and the parents were heterozygous carriers. There was another homozygous variant, albeit classified as VUS and not thought to fit the clinical presentation. Sources: Literature |
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| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram changed review comment from: As reviewed by Konstantinos Varvagiannis, there is more than three unrelated cases with biallelic variants in CCDC82 presenting with a neurodevelopmental disorder comprising intellectual disability/ global developmental delay. Hence, this gene should be rated GREEN at the next GMS review.; to: As reviewed by Konstantinos Varvagiannis, there are more than three unrelated cases with biallelic variants in CCDC82 presenting with a neurodevelopmental disorder comprising intellectual disability/ global developmental delay. Hence, this gene should be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: CCDC82. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram Classified gene: CCDC82 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram Gene: ccdc82 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram Classified gene: CCDC82 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram Gene: ccdc82 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.181 | CCDC82 | Achchuthan Shanmugasundram Phenotypes for gene: CCDC82 were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.182 | CCDC82 | Achchuthan Shanmugasundram Phenotypes for gene: CCDC82 were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.181 | CCDC82 | Achchuthan Shanmugasundram Phenotypes for gene: CCDC82 were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.181 | CCDC82 | Achchuthan Shanmugasundram Phenotypes for gene: CCDC82 were changed from Global developmental delay; Intellectual disability; Spastic paraparesis to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.180 | CCDC82 | Achchuthan Shanmugasundram commented on gene: CCDC82: As reviewed by Konstantinos Varvagiannis, there is more than three unrelated cases with biallelic variants in CCDC82 presenting with a neurodevelopmental disorder comprising intellectual disability/ global developmental delay. Hence, this gene should be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.180 | CCDC82 | Achchuthan Shanmugasundram reviewed gene: CCDC82: Rating: GREEN; Mode of pathogenicity: None; Publications: 27457812, 28397838, 35118659, 35373332; Phenotypes: neurodevelopmental disorder, MONDO:0700092, intellectual disability, MONDO:0001071; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.180 | FLNA | Sarah Leigh edited their review of gene: FLNA: Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.180 | FLNA | Sarah Leigh reviewed gene: FLNA: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.180 | FLNA | Sarah Leigh Tag Q2_23_demote_red tag was added to gene: FLNA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.180 | FLNA | Sarah Leigh Publications for gene: FLNA were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Tag Q2_23_promote_green was removed from gene: UBE3C. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Classified gene: UBE3C as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases associating biallelic variants in UBE3C gene with intellectual disability. Hence, this gene should be rated AMBER. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Gene: ube3c has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Classified gene: UBE3C as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases associating biallelic variants in UBE3C gene with intellectual disability. Hence, this gene should be rated AMBER. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.179 | UBE3C | Achchuthan Shanmugasundram Gene: ube3c has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.178 | UBE3C | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: UBE3C. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.178 | UBE3C |
Achchuthan Shanmugasundram gene: UBE3C was added gene: UBE3C was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: UBE3C was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: UBE3C were set to 36401616 Phenotypes for gene: UBE3C were set to Neurodevelopmental disorder with absent speech and movement and behavioral abnormalities, OMIM:620270 Review for gene: UBE3C was set to AMBER Added comment: PMID:36401616 reported three patients from two unrelated families with homozygous variants in UBE3C gene and presenting with syndromic neurodevelopmental, seizure, and movement disorders and neurobehavioral phenotypes. All three patients had severe intellectual disability. The RNA studies in some patients with LoF variants provided evidence for the LoF effect. Sources: Literature |
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| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Classified gene: HECTD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Gene: hectd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Classified gene: HECTD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Gene: hectd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Classified gene: HECTD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.177 | HECTD4 | Achchuthan Shanmugasundram Gene: hectd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.176 | HECTD4 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: HECTD4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.176 | HECTD4 | Achchuthan Shanmugasundram Classified gene: HECTD4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.176 | HECTD4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.176 | HECTD4 | Achchuthan Shanmugasundram Gene: hectd4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.175 | HECTD4 |
Achchuthan Shanmugasundram gene: HECTD4 was added gene: HECTD4 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: HECTD4 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: HECTD4 were set to 36401616 Phenotypes for gene: HECTD4 were set to Neurodevelopmental disorder with seizures, spasticity, and complete or partial agenesis of the corpus callosum, OMIM:620250 Review for gene: HECTD4 was set to GREEN Added comment: PMID:36401616 reported seven patients from five unrelated families with either homozygous (3 families) or compound heterozygous variants (2 families) in HECTD4 gene and presenting with syndromic neurodevelopmental, seizure, and movement disorders and neurobehavioral phenotypes. All seven patients had severe (4 cases) or moderate (3 cases) intellectual disability. Sources: Literature |
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| Severe microcephaly v4.22 | FILIP1 | Achchuthan Shanmugasundram Tag watchlist tag was added to gene: FILIP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.22 | FILIP1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are two unrelated cases reported with severe microcephaly and three additional cases with microcephaly. Hence, this gene should be rated amber in this panel with the current evidence. 'watchlist' tag has been added to review the rating in the future new evidence.; to: Comment on list classification: There are two unrelated cases reported with severe microcephaly and three additional cases with microcephaly. Hence, this gene should be rated amber in this panel with the current evidence. The 'watchlist' tag has been added to review the rating in the future with any new evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.22 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.22 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases reported with severe microcephaly and three additional cases with microcephaly. Hence, this gene should be rated amber in this panel with the current evidence. 'watchlist' tag has been added to review the rating in the future new evidence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.22 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.21 | FILIP1 |
Achchuthan Shanmugasundram gene: FILIP1 was added gene: FILIP1 was added to Severe microcephaly. Sources: Literature Mode of inheritance for gene: FILIP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FILIP1 were set to 36943452; 37163662 Phenotypes for gene: FILIP1 were set to microcephaly, MONDO:0001149 Review for gene: FILIP1 was set to AMBER Added comment: PMID:36943452 reported five individuals from three unrelated families with three different biallelic variants in FILIP1 gene (including the variant reported in the patient from PMID:36344539) and presenting with an overlapping phenotype with congenital contractures affecting shoulder, elbow, hand, hip, knee and foot as well as scoliosis, reduced palmar and plantar skin folds, microcephaly and facial dysmorphism. Of these five patients, two unrelated patients had severe microcephaly (head circumference beyond 3 SD below the mean for age) and one patient from the family with three patients also had microcephaly (head circumference beyond 2 SD below the mean for age). PMID:37163662 reported five individuals from four unrelated families with four different biallelic variants in FILIP1 gene. The main symptoms in childhood included delayed motor milestones (all four families), delayed speech development (three families), intellectual disability (three families), contractures (2 families), clubfeet (2 families) and microcephaly (2 families). One of these cases only had borderline microcephaly (3rd percentile) and the other had OFC below 3rd percentile. Sources: Literature |
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| Childhood onset dystonia, chorea or related movement disorder v3.11 | NUP54 |
Achchuthan Shanmugasundram changed review comment from: PMID:36333996 reported three unrelated patients with early-onset dystonia with striatal lesions identified with biallelic variants in NUP54 gene. One patient (patient A) had homozygous variant c.1073T>G (p.Ile358Ser), while other two patients had compound heterozygous variants (patient B: c.1073T>G (p.Ile358Ser) & c.1126A>G (p.Lys376Glu); patient C: c.1410_1412del (p.Gln471del) and two missense variants c.1414G>A (p.Glu472Lys) & c.1420C>T (p.Leu474Phe)). The age of onset was between 12 months and five years and all had progressive neurological deterioration with dystonia, ataxia, dysarthria, dysphagia, hypotonia. This gene has been associated with relevant phenotypes in Gene2Phenotype (NUP54-related early-onset dystonia with striatal lesions with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature; to: PMID:36333996 reported three unrelated patients with early-onset dystonia with striatal lesions identified with biallelic variants in NUP54 gene. One patient (patient A) had homozygous variant c.1073T>G (p.Ile358Ser), while other two patients had compound heterozygous variants (patient B: c.1073T>G (p.Ile358Ser) & c.1126A>G (p.Lys376Glu); patient C: c.1410_1412del (p.Gln471del) and two missense variants c.1414G>A (p.Glu472Lys) & c.1420C>T (p.Leu474Phe)). The age of onset was between 12 months and five years and all had progressive neurological deterioration with dystonia, ataxia, dysarthria, dysphagia, hypotonia. Western blots showed reduced expression of NUP54 and its interaction partners NUP62/NUP58 in patient fibroblasts. This gene has been associated with relevant phenotypes in Gene2Phenotype (NUP54-related early-onset dystonia with striatal lesions with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Childhood onset dystonia, chorea or related movement disorder v3.11 | NUP54 | Achchuthan Shanmugasundram Classified gene: NUP54 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.11 | NUP54 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated cases) for rating this gene as GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.11 | NUP54 | Achchuthan Shanmugasundram Gene: nup54 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.10 | NUP54 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: NUP54. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.10 | NUP54 |
Achchuthan Shanmugasundram gene: NUP54 was added gene: NUP54 was added to Childhood onset dystonia, chorea or related movement disorder. Sources: Literature Mode of inheritance for gene: NUP54 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: NUP54 were set to 36333996 Phenotypes for gene: NUP54 were set to Early-onset dystonia Review for gene: NUP54 was set to GREEN Added comment: PMID:36333996 reported three unrelated patients with early-onset dystonia with striatal lesions identified with biallelic variants in NUP54 gene. One patient (patient A) had homozygous variant c.1073T>G (p.Ile358Ser), while other two patients had compound heterozygous variants (patient B: c.1073T>G (p.Ile358Ser) & c.1126A>G (p.Lys376Glu); patient C: c.1410_1412del (p.Gln471del) and two missense variants c.1414G>A (p.Glu472Lys) & c.1420C>T (p.Leu474Phe)). The age of onset was between 12 months and five years and all had progressive neurological deterioration with dystonia, ataxia, dysarthria, dysphagia, hypotonia. This gene has been associated with relevant phenotypes in Gene2Phenotype (NUP54-related early-onset dystonia with striatal lesions with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Ectodermal dysplasia v3.3 | TUFT1 | Achchuthan Shanmugasundram Classified gene: TUFT1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ectodermal dysplasia v3.3 | TUFT1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: This gene should be rated AMBER despite having three unrelated cases, as the variant found in two families is a founder variant in the Irish population. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ectodermal dysplasia v3.3 | TUFT1 | Achchuthan Shanmugasundram Gene: tuft1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ectodermal dysplasia v3.2 | TUFT1 |
Achchuthan Shanmugasundram gene: TUFT1 was added gene: TUFT1 was added to Ectodermal dysplasia. Sources: Literature Mode of inheritance for gene: TUFT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TUFT1 were set to 36689522 Phenotypes for gene: TUFT1 were set to ectodermal dysplasia syndrome, MONDO:0019287 Review for gene: TUFT1 was set to AMBER Added comment: PMID:36689522 reported nine individuals from three different families with biallelic variants in TUFT1 gene and presenting with woolly hair and skin fragility. One donor splice-site variant, c.60+1G>A, was present in two families, while a frameshift variant, p.Gln189Asnfs*49, was found in the third family. Haplotype analysis showed the c.60+1G>A variant is a founder variant in the Irish population. This is also supported by functional studies, mainly expression studies. This gene has not yet been associated with any phenotypes in OMIM or in Gene2Phenotype. Sources: Literature |
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| Lysosomal storage disorder v3.1 | VPS16 | Sarah Leigh changed review comment from: The rating of this gene has been updated following NHS Genomic Medicine Serviceapproval.; to: The rating of this gene has been updated following NHS Genomic Medicine Service approval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.2 | VPS16 | Sarah Leigh changed review comment from: The rating of this gene has been updated followingNHS Genomic Medicine Serviceapproval.; to: The rating of this gene has been updated following NHS Genomic Medicine Serviceapproval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.20 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.20 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are only two unrelated cases with severe microcephaly. Hence, this gene should be rated AMBER. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.20 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.19 | TRA2B | Achchuthan Shanmugasundram Phenotypes for gene: TRA2B were changed from neurodevelopmental disorder, MONDO:0700092; epilepsy, MONDO:0005027 to neurodevelopmental disorder, MONDO:0700092; microcephaly, MONDO:0001149 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.18 | TRA2B |
Achchuthan Shanmugasundram changed review comment from: This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature; to: PMID:36549593 reported 12 individuals from 11 unrelated families identified with 11 different heterozygous variants in TRA2B gene. The variants arose de novo in 10 families, while the variant was inherited from father to son in one family. 6 variants were expected to disrupt the translation start site in exon 1 (start-loss variants), 3 were expected to disrupt the splicing process at the exon 2/3 boundary (splice-affecting variants), and the remaining 2 were expected to produce a premature stop codon (truncating variants). These patients presented with a neurodevelopmental disorder comprising developmental delay/ intellectual disability (in all patients), axial or global hypotonia (10 patients), delayed motor milestones (all patients), behavioural issues (8 patients), speech impairment (9 patients), epilepsy (7 patients, initial presentation as infantile spasms in 6 and unclassified epileptic encephalopathy in 1), brain abnormalities (10 patients) and microcephaly (5 patients). Of 5 unrelated cases with microcephaly, only two cases had severe microcephaly (head circumference beyond 3 standard deviations below the mean for the age). In addition, functional studies in mice showed that heterozygous knockout mice developed normal, while complete knockout mice cannot develop embryonically. This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Severe microcephaly v4.18 | TRA2B | Achchuthan Shanmugasundram edited their review of gene: TRA2B: Changed rating: AMBER; Changed phenotypes to: neurodevelopmental disorder, MONDO:0700092, microcephaly, MONDO:0001149 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (11 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (11 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (11 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (11 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.174 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.173 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.173 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (11 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.173 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.173 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.173 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (11 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.173 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.172 | TRA2B | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TRA2B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.172 | TRA2B | Achchuthan Shanmugasundram Phenotypes for gene: TRA2B were changed from neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.172 | TRA2B | Achchuthan Shanmugasundram Phenotypes for gene: TRA2B were changed from neurodevelopmental disorder, MONDO:0700092; epilepsy, MONDO:0005027 to neurodevelopmental disorder, MONDO:0700092; intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.171 | TRA2B | Achchuthan Shanmugasundram edited their review of gene: TRA2B: Changed phenotypes to: neurodevelopmental disorder, MONDO:0700092, intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.171 | TRA2B |
Achchuthan Shanmugasundram changed review comment from: This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature; to: PMID:36549593 reported 12 individuals from 11 unrelated families identified with 11 different heterozygous variants in TRA2B gene. The variants arose de novo in 10 families, while the variant was inherited from father to son in one family. 6 variants were expected to disrupt the translation start site in exon 1 (start-loss variants), 3 were expected to disrupt the splicing process at the exon 2/3 boundary (splice-affecting variants), and the remaining 2 were expected to produce a premature stop codon (truncating variants). These patients presented with a neurodevelopmental disorder comprising developmental delay/ intellectual disability (in all patients), axial or global hypotonia (10 patients), delayed motor milestones (all patients), behavioural issues (8 patients), speech impairment (9 patients), epilepsy (7 patients, initial presentation as infantile spasms in 6 and unclassified epileptic encephalopathy in 1), brain abnormalities (10 patients) and microcephaly (5 patients). The degree of ID was severe to profound for 6 individuals, moderate to severe for 2 and mild to moderate for 3. In addition, functional studies in mice showed that heterozygous knockout mice developed normal, while complete knockout mice cannot develop embryonically. This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Early onset or syndromic epilepsy v4.46 | TRA2B | Achchuthan Shanmugasundram Classified gene: TRA2B as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.46 | TRA2B | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for rating this gene as GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.46 | TRA2B | Achchuthan Shanmugasundram Gene: tra2b has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.45 | TRA2B | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TRA2B. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.45 | TRA2B |
Achchuthan Shanmugasundram changed review comment from: This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature; to: PMID:36549593 reported 12 individuals from 11 unrelated families identified with 11 different heterozygous variants in TRA2B gene. The variants arose de novo in 10 families, while the variant was inherited from father to son in one family. 6 variants were expected to disrupt the translation start site in exon 1 (start-loss variants), 3 were expected to disrupt the splicing process at the exon 2/3 boundary (splice-affecting variants), and the remaining 2 were expected to produce a premature stop codon (truncating variants). These patients presented with a neurodevelopmental disorder comprising developmental delay/ intellectual disability (in all patients), axial or global hypotonia (10 patients), delayed motor milestones (all patients), behavioural issues (8 patients), speech impairment (9 patients), epilepsy (7 patients, initial presentation as infantile spasms in 6 and unclassified epileptic encephalopathy in 1), brain abnormalities (10 patients) and microcephaly (5 patients). In addition, functional studies in mice showed that heterozygous knockout mice developed normal, while complete knockout mice cannot develop embryonically. This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Severe microcephaly v4.18 | TRA2B |
Achchuthan Shanmugasundram gene: TRA2B was added gene: TRA2B was added to Severe microcephaly. Sources: Literature Mode of inheritance for gene: TRA2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TRA2B were set to 36549593 Phenotypes for gene: TRA2B were set to neurodevelopmental disorder, MONDO:0700092; epilepsy, MONDO:0005027 Review for gene: TRA2B was set to GREEN Added comment: This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Intellectual disability v5.171 | TRA2B |
Achchuthan Shanmugasundram gene: TRA2B was added gene: TRA2B was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: TRA2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TRA2B were set to 36549593 Phenotypes for gene: TRA2B were set to neurodevelopmental disorder, MONDO:0700092; epilepsy, MONDO:0005027 Review for gene: TRA2B was set to GREEN Added comment: This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Early onset or syndromic epilepsy v4.45 | TRA2B |
Achchuthan Shanmugasundram gene: TRA2B was added gene: TRA2B was added to Early onset or syndromic epilepsy. Sources: Literature Mode of inheritance for gene: TRA2B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: TRA2B were set to 36549593 Phenotypes for gene: TRA2B were set to neurodevelopmental disorder, MONDO:0700092; epilepsy, MONDO:0005027 Review for gene: TRA2B was set to GREEN Added comment: This gene has already been associated with phenotypes in Gene2Phenotype (with 'moderate' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Mitochondrial disorder with complex II deficiency v2.6 | SDHA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorder with complex II deficiency v2.6 | SDHA | Achchuthan Shanmugasundram commented on gene: SDHA: Test | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorder with complex II deficiency v2.5 | SDHB | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorder with complex II deficiency v2.5 | SDHA | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorder with complex II deficiency v2.5 | SDHB | Achchuthan Shanmugasundram commented on gene: SDHB: The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorder with complex II deficiency v2.5 | SDHA | Achchuthan Shanmugasundram commented on gene: SDHA: The mode of inheritance of this gene has been updated to 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal' following NHS Genomic Medicine Service approval. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | ZMYND8 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | ZMYND8 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | ZMYND8 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.14 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.14 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.14 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.13 | CLDN5 |
Achchuthan Shanmugasundram changed review comment from: PMID: 36477332 identified de novo heterozygous missense variants in CLDN5 in fifteen unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. Sources: Literature; to: PMID:36477332 reported the identification of de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a number of clinical features including developmental delay including intellectual disability, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognisable pattern of pontine atrophy and brain calcifications. All patients except one (patient 2 who had a single MRI taken at 4 days of age) showed pontine atrophy and brain calcifications from neuroimaging. In addition, functional studies from zebrafish model also provided parallel evidence that CLDN5 variants cause a neurodevelopmental disorder involving disruption of the blood brain barrier and impaired neuronal function. This gene has been associated with relevant phenotypes in Gene2Phenotype (CLDN5-related neurodevelopmental disorder with 'limited' rating in the DD panel), but not in OMIM. Sources: Literature |
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| White matter disorders and cerebral calcification - narrow panel v3.13 | CLDN5 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: CLDN5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.13 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from Brain calcifications to Brain calcifications | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.12 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from Brain calcifications to Brain calcifications | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.12 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from epilepsy, MONDO:0005027 to Brain calcifications | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| White matter disorders and cerebral calcification - narrow panel v3.11 | CLDN5 | Achchuthan Shanmugasundram edited their review of gene: CLDN5: Changed phenotypes to: Brain calcifications | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | ATG4D |
Dmitrijs Rots gene: ATG4D was added gene: ATG4D was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: ATG4D was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ATG4D were set to 36765070 Phenotypes for gene: ATG4D were set to neurodevelopmental disorder characterized by speech and motor impairment Review for gene: ATG4D was set to GREEN Added comment: Morimoto et al., described 3 cases from 2 families with ATG4D biallelic variants and provided some functional evidence. No data about homozygous or compound heterozygous with two rare variants in ATG4D in gnomAD database. Sources: Literature |
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| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: CLDN5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.170 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN in the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.169 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.168 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.168 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.168 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.167 | CLDN5 | Achchuthan Shanmugasundram Phenotypes for gene: CLDN5 were changed from epilepsy, MONDO:0005027 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.166 | CLDN5 | Achchuthan Shanmugasundram edited their review of gene: CLDN5: Changed phenotypes to: intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.166 | CLDN5 |
Achchuthan Shanmugasundram changed review comment from: PMID: 36477332 identified de novo heterozygous missense variants in CLDN5 in fifteen unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. Sources: Literature; to: PMID:36477332 reported the identification of de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a number of clinical features including developmental delay including intellectual disability, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognisable pattern of pontine atrophy and brain calcifications. All seven living patients over four years of age were reported to have intellectual disability. In addition, functional studies from zebrafish model also provided parallel evidence that CLDN5 variants cause a neurodevelopmental disorder involving disruption of the blood brain barrier and impaired neuronal function. This gene has been associated with relevant phenotypes in Gene2Phenotype (CLDN5-related neurodevelopmental disorder with 'limited' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Early onset or syndromic epilepsy v4.44 | CLDN5 |
Achchuthan Shanmugasundram changed review comment from: PMID:36477332 reported the identification of de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a number of clinical features including developmental delay including intellectual disability, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognisable pattern of pontine atrophy and brain calcifications. All 15 patients had seizures. In addition, functional studies from zebrafish model also provided parallel evidence that CLDN5 variants cause a neurodevelopmental disorder involving disruption of the blood brain barrier and impaired neuronal function. This gene has been associated with relevant phenotypes in Gene2Phenotype (CLDN5-related neurodevelopmental disorder with 'limited' rating in the DD panel), but not in OMIM. Sources: Literature; to: PMID:36477332 reported the identification of de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a number of clinical features including developmental delay including intellectual disability, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognisable pattern of pontine atrophy and brain calcifications. All 15 patients had seizures. In addition, functional studies from zebrafish model also provided parallel evidence that CLDN5 variants cause a neurodevelopmental disorder involving disruption of the blood brain barrier and impaired neuronal function. This gene has been associated with relevant phenotypes in Gene2Phenotype (CLDN5-related neurodevelopmental disorder with 'limited' rating in the DD panel), but not in OMIM. Sources: Literature |
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| Intellectual disability v5.166 | CLDN5 | Achchuthan Shanmugasundram edited their review of gene: CLDN5: Changed phenotypes to: intellectual disability, MONDO:0001071tual | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.44 | CLDN5 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: CLDN5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.8 |
Arina Puzriakova Panel types changed to GMS Rare Disease Virtual; GMS Rare Disease; GMS signed-off Panel version 1.7 has been signed off on 2023-05-31 |
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| Early onset or syndromic epilepsy v4.44 | CLDN5 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.44 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.44 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.44 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.43 | CLDN5 | Achchuthan Shanmugasundram Classified gene: CLDN5 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.43 | CLDN5 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.43 | CLDN5 | Achchuthan Shanmugasundram Gene: cldn5 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.42 | CLDN5 |
Achchuthan Shanmugasundram changed review comment from: PMID: 36477332 identified de novo heterozygous missense variants in CLDN5 in fifteen unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. Sources: Literature; to: PMID:36477332 reported the identification of de novo heterozygous missense variants in CLDN5 in 15 unrelated patients who presented with a number of clinical features including developmental delay including intellectual disability, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognisable pattern of pontine atrophy and brain calcifications. All 15 patients had seizures. In addition, functional studies from zebrafish model also provided parallel evidence that CLDN5 variants cause a neurodevelopmental disorder involving disruption of the blood brain barrier and impaired neuronal function. This gene has been associated with relevant phenotypes in Gene2Phenotype (CLDN5-related neurodevelopmental disorder with 'limited' rating in the DD panel), but not in OMIM. Sources: Literature |
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| White matter disorders and cerebral calcification - narrow panel v3.11 | CLDN5 |
Achchuthan Shanmugasundram gene: CLDN5 was added gene: CLDN5 was added to White matter disorders and cerebral calcification - narrow panel. Sources: Literature Mode of inheritance for gene: CLDN5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CLDN5 were set to 36477332 Phenotypes for gene: CLDN5 were set to epilepsy, MONDO:0005027 Review for gene: CLDN5 was set to GREEN Added comment: PMID: 36477332 identified de novo heterozygous missense variants in CLDN5 in fifteen unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. Sources: Literature |
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| Intellectual disability v5.166 | CLDN5 |
Achchuthan Shanmugasundram gene: CLDN5 was added gene: CLDN5 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: CLDN5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CLDN5 were set to 36477332 Phenotypes for gene: CLDN5 were set to epilepsy, MONDO:0005027 Review for gene: CLDN5 was set to GREEN Added comment: PMID: 36477332 identified de novo heterozygous missense variants in CLDN5 in fifteen unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. Sources: Literature |
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| Early onset or syndromic epilepsy v4.42 | CLDN5 |
Achchuthan Shanmugasundram gene: CLDN5 was added gene: CLDN5 was added to Early onset or syndromic epilepsy. Sources: Literature Mode of inheritance for gene: CLDN5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CLDN5 were set to 36477332 Phenotypes for gene: CLDN5 were set to epilepsy, MONDO:0005027 Review for gene: CLDN5 was set to GREEN Added comment: PMID: 36477332 identified de novo heterozygous missense variants in CLDN5 in fifteen unrelated patients who presented with a shared constellation of features including developmental delay, seizures (primarily infantile onset focal epilepsy), microcephaly and a recognizable pattern of pontine atrophy and brain calcifications. Sources: Literature |
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| Intellectual disability v5.165 | KDM2B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | KDM2B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | KDM2B | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Classified gene: TCEAL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Gene: tceal1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Classified gene: TCEAL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.165 | TCEAL1 | Achchuthan Shanmugasundram Gene: tceal1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Classified gene: TCEAL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Gene: tceal1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Classified gene: TCEAL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Gene: tceal1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Classified gene: TCEAL1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (7 unrelated cases) for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.164 | TCEAL1 | Achchuthan Shanmugasundram Gene: tceal1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.163 | TCEAL1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TCEAL1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.163 | TCEAL1 |
Achchuthan Shanmugasundram changed review comment from: PMID:36368327 reported seven unrelated individuals with de novo variants (2 nonsense, 2 frameshift, 2 CNVs & 1 missense variants) in TCEAL1 gene and presenting with an X-linked dominant neurodevelopmental disorder. All these seven individuals had intellectual disability (mild to severe). The other major clinical presentations include hypotonia, abnormal gait, speech impairment, autistic-like behavior, and mildly dysmorphic facial features. This gene is associated with relevant phenotypes in OMIM (MIM #301094), but not in Gene2Phenotype. Sources: Literature; to: PMID:36368327 reported seven unrelated individuals with de novo variants (2 nonsense, 2 frameshift, 2 CNVs & 1 missense variants) in TCEAL1 gene and presenting with an X-linked dominant neurodevelopmental disorder. All these seven individuals had intellectual disability (mild to severe). The other major clinical presentations include hypotonia, abnormal gait, speech impairment, autistic-like behaviour, and mildly dysmorphic facial features. This gene is associated with relevant phenotypes in OMIM (MIM #301094), but not in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.163 | TCEAL1 |
Achchuthan Shanmugasundram gene: TCEAL1 was added gene: TCEAL1 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: TCEAL1 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: TCEAL1 were set to 36368327 Phenotypes for gene: TCEAL1 were set to Neurodevelopmental disorder with gait disturbance, dysmorphic facies and behavioral abnormalities, X-linked, OMIM:301094 Review for gene: TCEAL1 was set to GREEN Added comment: PMID:36368327 reported seven unrelated individuals with de novo variants (2 nonsense, 2 frameshift, 2 CNVs & 1 missense variants) in TCEAL1 gene and presenting with an X-linked dominant neurodevelopmental disorder. All these seven individuals had intellectual disability (mild to severe). The other major clinical presentations include hypotonia, abnormal gait, speech impairment, autistic-like behavior, and mildly dysmorphic facial features. This gene is associated with relevant phenotypes in OMIM (MIM #301094), but not in Gene2Phenotype. Sources: Literature |
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| Ataxia and cerebellar anomalies - narrow panel v4.13 | FEM1C | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: FEM1C. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.13 | FEM1C | Achchuthan Shanmugasundram Classified gene: FEM1C as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.13 | FEM1C | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases (one in literature and another from Diagnostic Discovery initiative) and functional evidence from animal models in support of the association of this gene to ataxia. Hence, this gene can be rated Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.13 | FEM1C | Achchuthan Shanmugasundram Gene: fem1c has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.12 | FEM1C |
Achchuthan Shanmugasundram commented on gene: FEM1C: PMID:36336956 reported a 9 year-old boy with severe global developmental delay, lack of speech, pyramidal signs and limb ataxia and identified with a heterozygous de novo missense variant c.376G>C (p.Asp126His) in the FEM1C gene. The introduction of the equivalent variant in C. elegans resulted in disabled locomotion caused by synaptic abnormalities and not by muscle dysfunction. An additional case with a diagnostically reported de novo variant in this gene and a compatible phenotype including intellectual disability and ataxia was identified in the internal Genomics England Clinical Variant Archive (CVA) by the Diagnostic Discovery initiative. This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype. |
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| Ataxia and cerebellar anomalies - narrow panel v4.12 | FEM1C |
Achchuthan Shanmugasundram gene: FEM1C was added gene: FEM1C was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature Mode of inheritance for gene: FEM1C was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: FEM1C were set to 36336956 Phenotypes for gene: FEM1C were set to Ataxia, HP:0001251 Review for gene: FEM1C was set to GREEN Added comment: Sources: Literature |
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| Intellectual disability v5.162 | FEM1C | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: This gene should be rated AMBER as there are two unrelated cases of intellectual disability reported (one in literature and another from Diagnostic Discovery initiative).; to: Comment on list classification: This gene should be rated AMBER as there are two unrelated cases of intellectual disability (one in literature and another from Diagnostic Discovery initiative). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.162 | FEM1C | Achchuthan Shanmugasundram Classified gene: FEM1C as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.162 | FEM1C | Achchuthan Shanmugasundram Added comment: Comment on list classification: This gene should be rated AMBER as there are two unrelated cases of intellectual disability reported (one in literature and another from Diagnostic Discovery initiative). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.162 | FEM1C | Achchuthan Shanmugasundram Gene: fem1c has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | FEM1C |
Achchuthan Shanmugasundram changed review comment from: This gene should be rated RED as there is only one clear case of intellectual disability reported in literature. PMID:36336956 reported a 9 year-old boy with severe global developmental delay, lack of speech, pyramidal signs and limb ataxia and identified with a heterozygous de novo missense variant c.376G>C (p.Asp126His) in the FEM1C gene. Cognitive assessment performed at 9 years of age showed that he has moderate intellectual disability. De novo variant in the same residue (p.Asp126Val) has also been associated with an uncharacterised developmental disorder in PMID:28135719. An additional case with a diagnostically reported de novo variant in this gene and a compatible phenotype including intellectual disability and ataxia was identified in the internal Genomics England Clinical Variant Archive (CVA) by the Diagnostic Discovery initiative. This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype. Sources: Literature; to: PMID:36336956 reported a 9 year-old boy with severe global developmental delay, lack of speech, pyramidal signs and limb ataxia and identified with a heterozygous de novo missense variant c.376G>C (p.Asp126His) in the FEM1C gene. Cognitive assessment performed at 9 years of age showed that he has moderate intellectual disability. De novo variant in the same residue (p.Asp126Val) has also been associated with an uncharacterised developmental disorder in PMID:28135719. An additional case with a diagnostically reported de novo variant in this gene and a compatible phenotype including intellectual disability and ataxia was identified in the internal Genomics England Clinical Variant Archive (CVA) by the Diagnostic Discovery initiative. This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.161 | FEM1C |
Achchuthan Shanmugasundram changed review comment from: This gene should be rated RED as there is only one clear case of intellectual disability reported in literature. PMID:36336956 reported a 9 year-old boy with severe global developmental delay, lack of speech, pyramidal signs and limb ataxia and identified with a heterozygous de novo missense variant c.376G>C (p.Asp126His) in the FEM1C gene. Cognitive assessment performed at 9 years of age showed that he has moderate intellectual disability. De novo variant in the same residue (p.Asp126Val) has also been associated with an uncharacterised developmental disorder in PMID:28135719. This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype. Sources: Literature; to: This gene should be rated RED as there is only one clear case of intellectual disability reported in literature. PMID:36336956 reported a 9 year-old boy with severe global developmental delay, lack of speech, pyramidal signs and limb ataxia and identified with a heterozygous de novo missense variant c.376G>C (p.Asp126His) in the FEM1C gene. Cognitive assessment performed at 9 years of age showed that he has moderate intellectual disability. De novo variant in the same residue (p.Asp126Val) has also been associated with an uncharacterised developmental disorder in PMID:28135719. An additional case with a diagnostically reported de novo variant in this gene and a compatible phenotype including intellectual disability and ataxia was identified in the internal Genomics England Clinical Variant Archive (CVA) by the Diagnostic Discovery initiative. This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.161 | FEM1C | Achchuthan Shanmugasundram edited their review of gene: FEM1C: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset hereditary spastic paraplegia v3.3 | PRNP |
James Polke gene: PRNP was added gene: PRNP was added to Adult onset hereditary spastic paraplegia. Sources: NHS GMS Mode of inheritance for gene: PRNP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PRNP were set to 30240140; 8250529; 34746379; 28195350 Phenotypes for gene: PRNP were set to HSP; Gerstmann–Sträussler–Scheinker disease Penetrance for gene: PRNP were set to Complete Mode of pathogenicity for gene: PRNP was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments Review for gene: PRNP was set to GREEN gene: PRNP was marked as current diagnostic Added comment: HSP can be a rare presenting phenotype for some individuals with inherited prion disease. Sources: NHS GMS |
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| Severe microcephaly v4.17 | ARPC4 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: ARPC4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.17 | ARPC4 | Achchuthan Shanmugasundram Classified gene: ARPC4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.17 | ARPC4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be rated GREEN at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.17 | ARPC4 | Achchuthan Shanmugasundram Gene: arpc4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.16 | ARPC4 | Achchuthan Shanmugasundram Phenotypes for gene: ARPC4 were changed from Microcephaly; mild motor delays; significant speech impairment to Developmental delay, language impairment, and ocular abnormalities, OMIM:620141; microcephaly, MONDO:0001149 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.15 | ARPC4 | Achchuthan Shanmugasundram Publications for gene: ARPC4 were set to DOI:https://doi.org/10.1016/j.xhgg.2021.100072 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.14 | ARPC4 |
Achchuthan Shanmugasundram commented on gene: ARPC4: As reviewed by Zornitza Stark, PMID:35047857 reported seven cases from six unrelated families with the same missense variant (p.Arg158Cys) and presenting with developmental and speech delays, of which six individuals from five families presented with microcephaly. Three individuals from two of these families had severe microcephaly with occipitofrontal circumference (OFC) beyond 3 standard deviations below the mean for age. In addition, functional studies showed that the variant is associated with a decreased amount of F-actin in cells from two affected individuals. This gene has been associated with relevant phenotypes in both OMIM (MIM #620141) and Gene2Phenotype (ARPC4-related microcephaly and developmental delay with 'strong' rating in the DD panel). |
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| Early onset or syndromic epilepsy v4.41 | RHEB | Arina Puzriakova Tag Q2_23_promote_green tag was added to gene: RHEB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.41 | RHEB | Arina Puzriakova changed review comment from: At least 2 additional cases reported (PMID: 33434304; 37015817) with a spectrum of cortical malformations and brain mosaic RHEB variants. This now meets the diagnostic-grade criteria and therefore this gene should be rated Green.; to: At least 2 additional cases reported (PMID: 33434304; 37015817) with seizures, a spectrum of cortical malformations and brain mosaic RHEB variants. This now meets the diagnostic-grade criteria and therefore this gene should be rated Green. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.41 | RHEB | Arina Puzriakova Classified gene: RHEB as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.41 | RHEB | Arina Puzriakova Gene: rheb has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.40 | RHEB | Arina Puzriakova changed review comment from: Comment on list classification: There is sufficient evidence to support an association with epilepsy; however, it is worth noting that variants are brain-specific somatic. Still adding to this panel as other somatic mosaic genes (e.g. GNAQ, MTOR, TSC1, TSC2) are included.; to: Comment on list classification: There is sufficient evidence to support an association with epilepsy; however, it is worth noting that variants are brain-specific somatic. Still adding to this panel as other somatic mosaic genes are included (e.g. GNAQ, MTOR, TSC1, TSC2). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.40 | RHEB | Arina Puzriakova changed review comment from: Comment on list classification: The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.; to: Comment on list classification: There is sufficient evidence to support an association with epilepsy; however, it is worth noting that variants are brain-specific somatic. Still adding to this panel as other somatic mosaic genes (e.g. GNAQ, MTOR, TSC1, TSC2) are included. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.40 | RHEB | Arina Puzriakova Tag mosaicism tag was added to gene: RHEB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.40 | RHEB | Arina Puzriakova Entity copied from Mosaic brain disorders - deep sequencing v0.116 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.40 | RHEB |
Arina Puzriakova gene: RHEB was added gene: RHEB was added to Early onset or syndromic epilepsy. Sources: Expert Review Green,Expert list somatic tags were added to gene: RHEB. Mode of inheritance for gene: RHEB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: RHEB were set to 29051493; 30414531; 33434304; 37015817 Phenotypes for gene: RHEB were set to Epilepsy and cortical dysplasia Mode of pathogenicity for gene: RHEB was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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| Severe microcephaly v4.14 | ARPC4 | Achchuthan Shanmugasundram reviewed gene: ARPC4: Rating: GREEN; Mode of pathogenicity: None; Publications: 35047857; Phenotypes: Developmental delay, language impairment, and ocular abnormalities, OMIM:620141, microcephaly, MONDO:0001149; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.8 | NPC1 | Achchuthan Shanmugasundram Tag watchlist tag was added to gene: NPC1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.26 | VRK1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: VRK1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.26 | VRK1 | Achchuthan Shanmugasundram Classified gene: VRK1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.26 | VRK1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (five unrelated cases) for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.26 | VRK1 | Achchuthan Shanmugasundram Gene: vrk1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.25 | VRK1 | Achchuthan Shanmugasundram Phenotypes for gene: VRK1 were changed from Pontocerebellar hypoplasia 1A (#607596) to Pontocerebellar hypoplasia type 1A, OMIM:607596; spinal muscular atrophy, MONDO:0001516; distal hereditary motor neuropathy, MONDO:0018894; familial amyotrophic lateral sclerosis, MONDO:0005144 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.24 | VRK1 | Achchuthan Shanmugasundram Publications for gene: VRK1 were set to 26583493 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.23 | VRK1 | Achchuthan Shanmugasundram reviewed gene: VRK1: Rating: GREEN; Mode of pathogenicity: None; Publications: 26583493, 31837156, 34169149; Phenotypes: Pontocerebellar hypoplasia type 1A, OMIM:607596, spinal muscular atrophy, MONDO:0001516, distal hereditary motor neuropathy, MONDO:0018894, familial amyotrophic lateral sclerosis, MONDO:0005144; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.8 | NPC1 | Achchuthan Shanmugasundram edited their review of gene: NPC1: Changed rating: AMBER | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.8 | NPC1 | Achchuthan Shanmugasundram Classified gene: NPC1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.8 | NPC1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are two unrelated cases associating NPC1 with white matter abnormalities in adulthood. However, there are several other cases with childhood-onset and functional evidence from animal models. This gene should be rated AMBER and 'watchlist' tag should be added. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.8 | NPC1 | Achchuthan Shanmugasundram Gene: npc1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | POU3F2 | Sarah Leigh Classified gene: POU3F2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | POU3F2 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | POU3F2 | Sarah Leigh Gene: pou3f2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | POU3F2 | Sarah Leigh Classified gene: POU3F2 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | POU3F2 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.161 | POU3F2 | Sarah Leigh Gene: pou3f2 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.7 | NPC1 | Achchuthan Shanmugasundram Publications for gene: NPC1 were set to 26910362; 29406968 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.6 | NPC1 | Achchuthan Shanmugasundram reviewed gene: NPC1: Rating: GREEN; Mode of pathogenicity: None; Publications: 26910362, 27900365, 29406968, 31254056; Phenotypes: Niemann-Pick disease, type C1, OMIM:257220, Niemann-Pick disease, type D, OMIM:257220; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.160 | POU3F2 |
Sarah Leigh gene: POU3F2 was added gene: POU3F2 was added to Intellectual disability - microarray and sequencing. Sources: Literature Q2_23_promote_green tags were added to gene: POU3F2. Mode of inheritance for gene: POU3F2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: POU3F2 were set to 37207645 Phenotypes for gene: POU3F2 were set to neurodevelopmental delay with hyperphagic obesity Review for gene: POU3F2 was set to GREEN Added comment: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. PMID: 37207645 reports eight POU3F2 variants in the unrelated cases of neurodevelopmental delay with hyperphagic obesity, with no other variants detected in other candidate genes. Intellectual disability was apparent in 6/7 of these cases from infancy to early childhood. The remaining variant : NM_005604.4 c.135C>A, p.Tyr45* was found in a mother and son, where the son was classified as having intellectual disability, the mother did not. Excluding the mother and son, all of the remaining cases carrying POU3F2 variants had neurodevelopmental delay. Sources: Literature |
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| Possible mitochondrial disorder - nuclear genes v3.30 | IDH3A | Sarah Leigh Tag Q2_23_promote_green tag was added to gene: IDH3A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | IDH3A | Sarah Leigh Tag Q2_23_promote_green was removed from gene: IDH3A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | IDH3A | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.51 | IDH3A | Sarah Leigh Classified gene: IDH3A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.51 | IDH3A | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.51 | IDH3A | Sarah Leigh Gene: idh3a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | IDH3A | Sarah Leigh Classified gene: IDH3A as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | IDH3A | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.30 | IDH3A | Sarah Leigh Gene: idh3a has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.29 | IDH3A | Sarah Leigh Tag Q2_23_promote_green tag was added to gene: IDH3A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.12 | IDH3A | Sarah Leigh reviewed gene: IDH3A: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.29 | IDH3A | Sarah Leigh reviewed gene: IDH3A: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.50 | IDH3A | Sarah Leigh Tag Q2_23_promote_green tag was added to gene: IDH3A. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.50 | IDH3A | Sarah Leigh edited their review of gene: IDH3A: Added comment: Associated with relevant phenotype in OMIM and as strong Gen2Phen gene. At least nine IDH3A variants have been reported in six unrelated cases of Retinitis pigmentosa 90, OMIM:619007. Mice homozygous for p.E229K variant exhibited signs of retinal stress, those who were compound heterozygous for p.E229K and Idh3a knockout, had more severe retinal degeneration and embryonic lethality was seen in Idh3a knockout mice; reduced mitochondrial function was seen in the equivalent cell lines (PMID: 30478029).; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.50 | IDH3A | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.12 | IDH3A | Sarah Leigh Publications for gene: IDH3A were set to 28412069; 30478029 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.29 | IDH3A | Sarah Leigh Publications for gene: IDH3A were set to 28412069; 28058510 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.50 | IDH3A | Sarah Leigh Publications for gene: IDH3A were set to 28412069; 28058510 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Retinal disorders v4.11 | IDH3A | Sarah Leigh Phenotypes for gene: IDH3A were changed from Retinitis Pigmentosa; Pseudocoloboma to Retinitis pigmentosa 90, OMIM:619007; retinitis pigmentosa 90, MONDO:0033563 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Possible mitochondrial disorder - nuclear genes v3.28 | IDH3A | Sarah Leigh Phenotypes for gene: IDH3A were changed from Infantile encephalopathy; Retinitis pigmentosa with macular pseudocoloboma to Retinitis pigmentosa 90, OMIM:619007; retinitis pigmentosa 90, MONDO:0033563 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.49 | IDH3A | Sarah Leigh Added comment: Comment on phenotypes: Retinitis pigmentosa with macular pseudocoloboma; Infantile encephalopathy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.49 | IDH3A | Sarah Leigh Phenotypes for gene: IDH3A were changed from Retinitis pigmentosa with macular pseudocoloboma; Infantile encephalopathy to Retinitis pigmentosa 90, OMIM:619007; retinitis pigmentosa 90, MONDO:0033563 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.48 | IDH3A | Sarah Leigh Added comment: Comment on phenotypes: Retinitis pigmentosa 90, OMIM:619007;retinitis pigmentosa 90, MONDO:0033563 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.48 | IDH3A | Sarah Leigh Phenotypes for gene: IDH3A were changed from Retinitis pigmentosa with macular pseudocoloboma; Infantile encephalopathy to Retinitis pigmentosa with macular pseudocoloboma; Infantile encephalopathy | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.47 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 7912128; 12815589 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.17 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 27081516 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.159 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 30847515; 11980892; 25778941; 24360804; 27021474; 28489334; 30089828; 36495139 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.6 | ETFB | Sarah Leigh Publications for gene: ETFB were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.90 | ETFB | Sarah Leigh Publications for gene: ETFB were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.158 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.7 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 25929793; 32550677 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.41 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.5 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 25929793 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.591 | ETFB | Sarah Leigh Publications for gene: ETFB were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.590 | ETFB | Sarah Leigh Added comment: Comment on phenotypes: Electron transfer flavoprotein deficiency, beta chain (Disorders of mitochondrial fatty acid oxidation);Glutaric acidemia IIB | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.590 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from Electron transfer flavoprotein deficiency, beta chain (Disorders of mitochondrial fatty acid oxidation); Glutaric acidemia IIB to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.40 | ETFB | Sarah Leigh Added comment: Comment on phenotypes: Electron transfer flavoprotein deficiency, beta chain (Disorders of mitochondrial fatty acid oxidation) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.40 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from Glutaric acidemia IIB; Electron transfer flavoprotein deficiency, beta chain (Disorders of mitochondrial fatty acid oxidation) to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.6 | MAN2B1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green was removed from gene: MAN2B1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.6 | MAN2B1 | Achchuthan Shanmugasundram Classified gene: MAN2B1 as Red List (low evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.6 | MAN2B1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is only one family with white matter abnormalities confirmed in adulthood. All other reported cases with white matter abnormalities detected by MRI are during childhood/ adolescence. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.6 | MAN2B1 | Achchuthan Shanmugasundram Gene: man2b1 has been classified as Red List (Low Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.4 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from Glutaric acidemia IIB 231680 to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.6 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from Glutaric acidemia IIB, OMIM:231680 to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.157 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from GLUTARIC ACIDURIA TYPE 2B to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.5 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from GLUTARIC ACIDURIA TYPE 2B 231680 to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 | Achchuthan Shanmugasundram edited their review of gene: MAN2B1: Changed rating: RED | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.89 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from GLUTARIC ACIDURIA TYPE 2B to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.16 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from Glutaric acidemia IIB 231680 to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 |
Achchuthan Shanmugasundram changed review comment from: PMID:15534274 reported that MRI from three adult siblings with alpha-mannosidosis (AM) showed cerebellar atrophy and periventricular white matter changes. PMID:26212233 reported that five of ten patients who have had MRI from the cohort of 34 patients with AM had occipital white matter signal abnormalities. PMID:33317989 reported cerebral white matter signal abnormalities in 11 (85%) out of 13 untreated AM patients. In addition, cortical atrophy (62%), corpus callosum thinning (23%) and enlargement of perivascular spaces in white matter (38%) was observed. This gene has been associated with alpha-mannosidosis in both OMIM (MIM #248500) and Gene2Phenotype ('Definitive' rating).; to: PMID:15534274 reported that MRI from three adult siblings with alpha-mannosidosis (AM) showed cerebellar atrophy and periventricular white matter changes. PMID:26212233 reported that five of ten patients who have had MRI from the cohort of 34 patients with AM had occipital white matter signal abnormalities. However the age of these patients ranged from 7 to 17 years. PMID:33317989 reported cerebral white matter signal abnormalities in 11 (85%) out of 13 untreated AM patients. In addition, cortical atrophy (62%), corpus callosum thinning (23%) and enlargement of perivascular spaces in white matter (38%) was observed. The age of onset (first symptom) of AM ranged from neonatal period to 4 years. However, four patients were currently adults with MRI taken during their adulthood. This gene has been associated with alpha-mannosidosis in both OMIM (MIM #248500) and Gene2Phenotype ('Definitive' rating). |
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| Mitochondrial disorders v4.46 | ETFB | Sarah Leigh Publications for gene: ETFB were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.45 | ETFB | Sarah Leigh Tag Q2_23_promote_green tag was added to gene: ETFB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.45 | ETFB | Sarah Leigh edited their review of gene: ETFB: Added comment: Associated with relevant phenotype in OMIM and as definitive Gen2Phen gene. At least three ETFB variants have been reported in at least three cases.; Changed rating: GREEN; Changed publications to: 7912128, 12815589 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.45 | ETFB | Sarah Leigh Phenotypes for gene: ETFB were changed from Glutaric acidemia IIB ,231680 to Glutaric acidemia IIB, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.44 | ETFB | Sarah Leigh Classified gene: ETFB as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.44 | ETFB | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.44 | ETFB | Sarah Leigh Gene: etfb has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: MAN2B1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 | Achchuthan Shanmugasundram Classified gene: MAN2B1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to Green at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.5 | MAN2B1 | Achchuthan Shanmugasundram Gene: man2b1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.4 | MAN2B1 | Achchuthan Shanmugasundram Phenotypes for gene: MAN2B1 were changed from Mannosidosis, alpha-, types I and II, MIM# 248500 to Mannosidosis, alpha-, types I and II, OMIM:248500 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.3 | MAN2B1 | Achchuthan Shanmugasundram Publications for gene: MAN2B1 were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset leukodystrophy v3.2 | MAN2B1 | Achchuthan Shanmugasundram reviewed gene: MAN2B1: Rating: GREEN; Mode of pathogenicity: None; Publications: 15534274, 26212233, 33317989; Phenotypes: Mannosidosis, alpha-, types I and II, OMIM:248500; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.39 | ETFA | Sarah Leigh Added comment: Comment on phenotypes: Electron transfer flavoprotein deficiency, alpha chain (Disorders of mitochondrial fatty acid oxidation);Glutaric acidemia IIA | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.39 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Acute rhabdomyolysis v1.5 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Glutaric acidemia IIA, OMIM:231680 to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.156 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from GLUTARIC ACIDURIA TYPE 2A to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.4 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from GLUTARIC ACIDURIA TYPE 2A 231680 to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.88 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from GLUTARIC ACIDURIA TYPE 2A to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.38 | ETFA | Sarah Leigh Added comment: Comment on phenotypes: Electron transfer flavoprotein deficiency, alpha chain (Disorders of mitochondrial fatty acid oxidation) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.38 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Electron transfer flavoprotein deficiency, alpha chain (Disorders of mitochondrial fatty acid oxidation); Glutaric acidemia IIA to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.37 | ETFA | Sarah Leigh edited their review of gene: ETFA: Added comment: Associated with phenotype in OMIM and as a definitive Developmental Disorder Gene / G2P. At least five ETFA variants have been reported, two in homozygous and compound heterozygous cases and three as compound heterozygotes (at least eight unrelated cases).; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.589 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Electron transfer flavoprotein deficiency, alpha chain (Disorders of mitochondrial fatty acid oxidation); Glutaric acidemia IIA to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Rhabdomyolysis and metabolic muscle disorders v3.3 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Glutaric acidemia IIA 231680 to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hyperammonaemia v1.15 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Glutaric acidemia IIA 231680 to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.43 | ETFA | Sarah Leigh Tag Q2_23_promote_green tag was added to gene: ETFA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.43 | ETFA | Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as definitive Gen2Phen gene. At least ETFA five variants have been reported in at least five unrelated cases.; to: Associated with phenotype in OMIM and as a definitive Developmental Disorder Gene / G2P. At least five ETFA variants have been reported, two in homozygous and compound heterozygous cases and three as compound heterozygotes (at least eight unrelated cases). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.43 | ETFA | Sarah Leigh Classified gene: ETFA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.43 | ETFA | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.43 | ETFA | Sarah Leigh Gene: etfa has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.42 | ETFA | Sarah Leigh edited their review of gene: ETFA: Added comment: Associated with relevant phenotype in OMIM and as definitive Gen2Phen gene. At least ETFA five variants have been reported in at least five unrelated cases.; Changed rating: GREEN | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Undiagnosed metabolic disorders v1.588 | ETFA | Sarah Leigh Publications for gene: ETFA were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.37 | ETFA | Sarah Leigh Publications for gene: ETFA were set to 27604308 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.42 | ETFA | Sarah Leigh Publications for gene: ETFA were set to 1882842; 12815589 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.41 | ETFA | Sarah Leigh Phenotypes for gene: ETFA were changed from Glutaric acidemia IIA ,231680 to Glutaric acidemia IIA, OMIM:231680; multiple acyl-CoA dehydrogenase deficiency, MONDO:0009282 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.40 | ETFA | Sarah Leigh Publications for gene: ETFA were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Childhood onset dystonia, chorea or related movement disorder v3.9 | COASY | Sarah Leigh Publications for gene: COASY were set to 27021474; 24360804 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset dystonia, chorea or related movement disorder v3.2 | COASY | Sarah Leigh Publications for gene: COASY were set to 24360804; 27021474 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.12 | COASY | Sarah Leigh Publications for gene: COASY were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| DDG2P v3.3 | COASY | Sarah Leigh Publications for gene: COASY were set to 24360804 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.87 | COASY | Sarah Leigh Publications for gene: COASY were set to | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.36 | COASY | Sarah Leigh Publications for gene: COASY were set to 30089828 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Adult onset neurodegenerative disorder v4.23 | COASY | Sarah Leigh Publications for gene: COASY were set to 27021474; 28489334; 24360804 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cerebellar hypoplasia v1.73 | COASY | Sarah Leigh Publications for gene: COASY were set to 30089828; 24360804 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.14 | COASY | Sarah Leigh Publications for gene: COASY were set to 30089828; 24360804; 27892483 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.10 | FGF9 | Eleanor Williams Phenotypes for gene: FGF9 were changed from ?Multiple synostoses syndrome type 3 612961 to Multiple synostoses syndrome 3, OMIM:612961; multiple synostoses syndrome 3, MONDO:0013064 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.9 | FGF9 | Eleanor Williams Publications for gene: FGF9 were set to 19589401 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.8 | FGF9 | Eleanor Williams Classified gene: FGF9 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.8 | FGF9 | Eleanor Williams Added comment: Comment on list classification: Promoting this gene from red to amber but with a recommendation for GREEN rating following GMS review as 4 unrelated cases with variants in FGF9 and a phenotype of multiple synostoses syndrome. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.8 | FGF9 | Eleanor Williams Gene: fgf9 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.7 | FGF9 |
Eleanor Williams Tag watchlist was removed from gene: FGF9. Tag Q2_23_promote_green tag was added to gene: FGF9. |
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| Skeletal dysplasia v4.7 | EN1 | Eleanor Williams Classified gene: EN1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.7 | EN1 |
Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber. One patient with a loss of function variant in this gene and a skeletal phenotype reported, plus mouse model with this gene knocked out also shows a skeletal phenotype. A further 3 patients with 27 and 63Kb deletions 300Kb upstream of this gene also show a skeletal phenotype and this appears to be due to ablation of a long non-coding RNA loci (in mice). However, at this distance it is unlikely to be detected by the Genomics England rare disease pipeline as being associated with EN1, and there are currently no regions on Skeletal dysplasia panel covering that area of chr 2. Therefore, at the present time this gene should be rated amber, following confirmation by the clinical team. |
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| Skeletal dysplasia v4.7 | EN1 | Eleanor Williams Gene: en1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.6 | EN1 | Eleanor Williams commented on gene: EN1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.3 | FAN1 | Eleanor Williams Phenotypes for gene: FAN1 were changed from interstitial nephritis; chronic kidney disease; Interstitial nephritis, karyomegalic 614817 to interstitial nephritis; chronic kidney disease; Interstitial nephritis, karyomegalic, OMIM:614817; karyomegalic interstitial nephritis, MONDO:0013898 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.2 | FAN1 | Eleanor Williams Publications for gene: FAN1 were set to 22772369 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unexplained young onset end-stage renal disease v3.1 | FAN1 | Eleanor Williams commented on gene: FAN1: Mouse model data added by reviewer Yu Leng Phua provides functional data to support this gene-disease association from PMID: 35931300 Airik et al 2022. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.6 | DZIP1L | Eleanor Williams commented on gene: DZIP1L | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.6 | DZIP1L | Eleanor Williams Phenotypes for gene: DZIP1L were changed from ARPKD; Polycystic kidney disease 5 617610 to Polycystic kidney disease 5, OMIM:617610; polycystic kidney disease 5, MONDO_0033281 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.5 | DZIP1L | Eleanor Williams Publications for gene: DZIP1L were set to 28530676 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | NUP214 | Eleanor Williams Tag Q2_23_promote_green tag was added to gene: NUP214. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | NUP214 | Eleanor Williams commented on gene: NUP214: After consultation with the Genomics England clinical team it has been decided that there is just enough evidence to promote this gene to green as there are 4 unrelated families and developmental delay is reported in all. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.39 | CPA6 | Eleanor Williams commented on gene: CPA6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Early onset or syndromic epilepsy v4.39 | CPA6 |
Eleanor Williams Tag Q2_23_NHS_review tag was added to gene: CPA6. Tag Q2_23_expert_review tag was added to gene: CPA6. |
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| Early onset or syndromic epilepsy v4.39 | CPA6 |
Eleanor Williams Tag to_be_confirmed_NHSE was removed from gene: CPA6. Tag Q2_23_demote_red tag was added to gene: CPA6. |
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| Skeletal dysplasia v4.6 | GPX4 | Achchuthan Shanmugasundram Classified gene: GPX4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.6 | GPX4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Zornitza Stark, there is sufficient evidence (>3 unrelated cases) available for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.6 | GPX4 | Achchuthan Shanmugasundram Gene: gpx4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.5 | GPX4 | Achchuthan Shanmugasundram Publications for gene: GPX4 were set to 24706940; 32827718; 34931062 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.5 | GPX4 | Achchuthan Shanmugasundram Publications for gene: GPX4 were set to 24706940 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.4 | GPX4 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: GPX4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.4 | GPX4 | Achchuthan Shanmugasundram reviewed gene: GPX4: Rating: GREEN; Mode of pathogenicity: None; Publications: 24706940, 32827718, 34931062; Phenotypes: Spondylometaphyseal dysplasia, Sedaghatian type, OMIM:250220; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.4 | NMNAT1 | Achchuthan Shanmugasundram Publications for gene: NMNAT1 were set to 32533184; 33668384 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.4 | NMNAT1 | Achchuthan Shanmugasundram Publications for gene: NMNAT1 were set to 32533184; 33668384 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.4 | NMNAT1 | Achchuthan Shanmugasundram Publications for gene: NMNAT1 were set to 32533184 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.3 | NMNAT1 | Achchuthan Shanmugasundram Classified gene: NMNAT1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.3 | NMNAT1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As two of the three reported families were distantly related, this gene should only be rated AMBER with the current evidence. However, 'watchlist' tag was added to review the rating in light of new evidence in the future. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.3 | NMNAT1 | Achchuthan Shanmugasundram Gene: nmnat1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.2 | NMNAT1 | Achchuthan Shanmugasundram commented on gene: NMNAT1: The 'cnv' tag was added as two of the reported cases harboured duplication variants in homozygous state and the third case harboured duplication variant together with a splicing variant. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v4.2 | NMNAT1 |
Achchuthan Shanmugasundram Tag watchlist tag was added to gene: NMNAT1. Tag cnv tag was added to gene: NMNAT1. |
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| Skeletal dysplasia v4.2 | NMNAT1 | Achchuthan Shanmugasundram reviewed gene: NMNAT1: Rating: AMBER; Mode of pathogenicity: None; Publications: 32533184, 33668384; Phenotypes: Spondyloepiphyseal dysplasia, sensorineural hearing loss, intellectual developmental disorder, and Leber congenital amaurosis, OMIM:619260; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Inherited polyposis and early onset colorectal cancer - germline testing v2.4 | GREM1 | Kate Downes reviewed gene: GREM1: Rating: GREEN; Mode of pathogenicity: Other; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | INTU | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are three unrelated cases and supporting functional evidence from mouse model to support the promotion of this gene to GREEN rating at the next GMS review.; to: Comment on list classification: As reviewed by Zornitza Stark, there are three unrelated cases and supporting functional evidence from mouse model to support the promotion of this gene to GREEN rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | INTU | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: INTU. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | INTU | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are three unrelated cases and supporting functional evidence from mouse model to support the promotion of this gene to GREEN rating at the next GMS update.; to: Comment on list classification: There are three unrelated cases and supporting functional evidence from mouse model to support the promotion of this gene to GREEN rating at the next GMS review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | INTU | Achchuthan Shanmugasundram Classified gene: INTU as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | INTU | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are three unrelated cases and supporting functional evidence from mouse model to support the promotion of this gene to GREEN rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.9 | INTU | Achchuthan Shanmugasundram Gene: intu has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.8 | INTU | Achchuthan Shanmugasundram Phenotypes for gene: INTU were changed from ?Short-rib thoracic dysplasia 20 with polydactyly, OMIM:617925; ?Orofaciodigital syndrome XVII, OMIM:617926 to ?Short-rib thoracic dysplasia 20 with polydactyly, OMIM:617925; ?Orofaciodigital syndrome XVII, OMIM:617926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.8 | INTU | Achchuthan Shanmugasundram Phenotypes for gene: INTU were changed from ?Short-rib thoracic dysplasia 20 with polydactyly, OMIM:617925; ?Orofaciodigital syndrome XVII, OMIM:617926 to ?Short-rib thoracic dysplasia 20 with polydactyly, OMIM:617925; ?Orofaciodigital syndrome XVII, OMIM:617926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.8 | INTU | Achchuthan Shanmugasundram Phenotypes for gene: INTU were changed from Orofaciodigital syndrome XVII MIM#617926; Short-rib thoracic dysplasia 20 with polydactyly MIM#617925 to ?Short-rib thoracic dysplasia 20 with polydactyly, OMIM:617925; ?Orofaciodigital syndrome XVII, OMIM:617926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.7 | INTU | Achchuthan Shanmugasundram Publications for gene: INTU were set to 27158779; 29451301; 20067783 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.6 | INTU | Achchuthan Shanmugasundram reviewed gene: INTU: Rating: GREEN; Mode of pathogenicity: None; Publications: 20067783, 27158779, 29451301; Phenotypes: ?Short-rib thoracic dysplasia 20 with polydactyly, OMIM:617925, ?Orofaciodigital syndrome XVII, OMIM:617926; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: FILIP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:36344539 reported a single male with biallelic variant in FILIP1 (c.2665C > T/ p.Arg889Ter) gene and presenting with distal arthrogryposis and mild learning disability. PMID:37163662 reported five individuals from four unrelated families with four different biallelic variants in FILIP1 gene. The main symptoms in childhood included delayed motor milestones (all four families), delayed speech development (three families), intellectual disability (three families), contractures (2 families), clubfeet (2 families) and microcephaly (2 families). As one of the patients died at the age of 13 months, intellectual disability and speech delay were not evaluated. This gene has not been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. Sources: Literature; to: PMID:36344539 reported a single male with biallelic variant in FILIP1 (c.2665C > T/ p.Arg889Ter) gene and presenting with distal arthrogryposis and mild learning disability. PMID:37163662 reported five individuals from four unrelated families with four different biallelic variants in FILIP1 gene. The main symptoms in childhood included delayed motor milestones (all four families), delayed speech development (three families), intellectual disability (three families), contractures (2 families), clubfeet (2 families) and microcephaly (2 families). As one of the patients died at the age of 13 months, intellectual disability and speech delay were not evaluated. This gene has not yet been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. Sources: Literature |
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| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.155 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (3 unrelated families) for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.154 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.153 | FILIP1 |
Achchuthan Shanmugasundram changed review comment from: Sources: Literature; to: PMID:36344539 reported a single male with biallelic variant in FILIP1 (c.2665C > T/ p.Arg889Ter) gene and presenting with distal arthrogryposis and mild learning disability. PMID:37163662 reported five individuals from four unrelated families with four different biallelic variants in FILIP1 gene. The main symptoms in childhood included delayed motor milestones (all four families), delayed speech development (three families), intellectual disability (three families), contractures (2 families), clubfeet (2 families) and microcephaly (2 families). As one of the patients died at the age of 13 months, intellectual disability and speech delay were not evaluated. This gene has not been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. Sources: Literature |
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| Arthrogryposis v5.13 | FILIP1 | Achchuthan Shanmugasundram Publications for gene: FILIP1 were set to 36943452; 36344539; 37163662 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.153 | FILIP1 |
Achchuthan Shanmugasundram gene: FILIP1 was added gene: FILIP1 was added to Intellectual disability - microarray and sequencing. Sources: Literature Mode of inheritance for gene: FILIP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FILIP1 were set to 36344539; 37163662 Phenotypes for gene: FILIP1 were set to intellectual disability, MONDO:0001071 Review for gene: FILIP1 was set to GREEN Added comment: Sources: Literature |
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| Arthrogryposis v5.12 | FILIP1 | Achchuthan Shanmugasundram Tag Q2_23_NHS_review tag was added to gene: FILIP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.12 | FILIP1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: FILIP1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.12 | FILIP1 | Achchuthan Shanmugasundram Classified gene: FILIP1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.12 | FILIP1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (6 unrelated cases) for this gene to be promoted to GREEN rating in the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.12 | FILIP1 | Achchuthan Shanmugasundram Gene: filip1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.11 | FILIP1 | Achchuthan Shanmugasundram Publications for gene: FILIP1 were set to PubMed: 36344539; PubMed: 36943452; PMID: 37163662 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.10 | FILIP1 |
Achchuthan Shanmugasundram changed review comment from: PMID:36344539 reported a single male with biallelic variant in FILIP1 (c.2665C > T/ p.Arg889Ter) gene and presenting with distal arthrogryposis with contractures of the knees and elbows, congenital clubfoot, muscular hypotonia, and mild learning disability. PMID:36943452 reported five individuals from three unrelated families with three different biallelic variants in FILIP1 gene (including the variant reported in the patient from PMID:36344539) and presenting with an overlapping phenotype with congenital contractures affecting shoulder, elbow, hand, hip, knee and foot as well as scoliosis, reduced palmar and plantar skin folds, microcephaly and facial dysmorphism.; to: PMID:36344539 reported a single male with biallelic variant in FILIP1 (c.2665C > T/ p.Arg889Ter) gene and presenting with distal arthrogryposis with contractures of the knees and elbows, congenital clubfoot, muscular hypotonia, and mild learning disability. PMID:36943452 reported five individuals from three unrelated families with three different biallelic variants in FILIP1 gene (including the variant reported in the patient from PMID:36344539) and presenting with an overlapping phenotype with congenital contractures affecting shoulder, elbow, hand, hip, knee and foot as well as scoliosis, reduced palmar and plantar skin folds, microcephaly and facial dysmorphism. PMID:37163662 reported five individuals from four unrelated families with four different biallelic variants, out of which three individuals from two different families presented with congenital onset of contractures. This gene has not yet been associated with relevant phenotypes either in OMIM or in Gene2Phenotype. |
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| Arthrogryposis v5.10 | FILIP1 | Achchuthan Shanmugasundram edited their review of gene: FILIP1: Changed publications to: 36943452, 36344539, 37163662 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.10 | FILIP1 | Achchuthan Shanmugasundram Phenotypes for gene: FILIP1 were changed from neurodevelopmental delay; arthrogryposis; muscular hypotonia; mild learning difficulties to arthrogryposis multiplex congenita, MONDO:0015168 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.9 | FILIP1 | Achchuthan Shanmugasundram reviewed gene: FILIP1: Rating: GREEN; Mode of pathogenicity: None; Publications: 36943452, 36344539; Phenotypes: arthrogryposis multiplex congenita, MONDO:0015168; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.22 | TULP3 | Achchuthan Shanmugasundram Classified gene: TULP3 as Green List (high evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.22 | TULP3 | Achchuthan Shanmugasundram Gene: tulp3 has been classified as Green List (High Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.21 | TULP3 | Achchuthan Shanmugasundram Publications for gene: TULP3 were set to 36460032; 36276950; 35397207 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.20 | TULP3 | Achchuthan Shanmugasundram Phenotypes for gene: TULP3 were changed from cystic kidney disease; ductal plate malformation; congentital hepatic fibrosis; cardiomyopathy to Hepatorenocardiac degenerative fibrosis, OMIM:619902 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ductal plate malformation v1.19 | TULP3 | Achchuthan Shanmugasundram reviewed gene: TULP3: Rating: GREEN; Mode of pathogenicity: None; Publications: 35397207, 36276950, 36460032; Phenotypes: Hepatorenocardiac degenerative fibrosis, OMIM:619902; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | FLNA | Tracy Lester reviewed gene: FLNA: Rating: RED; Mode of pathogenicity: None; Publications: 20301392; Phenotypes: Skeletal dysplasia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.4 | TULP3 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There are three cases with cardiac hypertrophy and hence this gene can be promoted to GREEN rating at the next major update.; to: Comment on list classification: There are three cases reported with cardiac phenotype and hence this gene can be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.4 | TULP3 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TULP3. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.4 | TULP3 | Achchuthan Shanmugasundram Phenotypes for gene: TULP3 were changed from hypertrophic cardiomyopathy; cystic kidney disease; congenital hepatic fibrosis to Hepatorenocardiac degenerative fibrosis, OMIM:619902 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.3 | TULP3 | Achchuthan Shanmugasundram Publications for gene: TULP3 were set to 35397207 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.2 | TULP3 | Achchuthan Shanmugasundram Classified gene: TULP3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.2 | TULP3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are three cases with cardiac hypertrophy and hence this gene can be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.2 | TULP3 | Achchuthan Shanmugasundram Gene: tulp3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.1 | TULP3 |
Achchuthan Shanmugasundram changed review comment from: PMID:35397207 reported 15 individuals from eight unrelated families with biallelic variants in TULP3 gene, out of which three individuals from two different families were reported with hypertrophic non-obstructive cardiomyopathy. In addition, experiments in TULP3 knockout zebrafish models showed that no aberrant morphological features were found in the heart tissue, and histological examination found no indication of fibrosis or underlying cellular disruptions.; to: PMID:35397207 reported 15 individuals from eight unrelated families with biallelic variants in TULP3 gene, out of which three individuals from two different families were reported with hypertrophic non-obstructive cardiomyopathy. In addition, experiments in TULP3 knockout zebrafish models showed that no aberrant morphological features were found in the heart tissue, and histological examination found no indication of fibrosis or underlying cellular disruptions. PMID:36460032 reported an individual with compound heterozygous variants in TULP3 gene and with left ventricular hypertrophy in addition to kidney cysts and liver fibrosis. |
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| Hypertrophic cardiomyopathy v4.1 | TULP3 | Achchuthan Shanmugasundram edited their review of gene: TULP3: Changed publications to: 35397207, 36460032 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.1 | TULP3 | Achchuthan Shanmugasundram changed review comment from: PMID:35397207 reported 15 individuals from eight unrelated families with biallelic variants in TULP3 gene, out of which three individuals from two different families were reported with hypertrophic non-obstructive cardiomyopathy. In addition, experiments in TULP3 knockout zebrafish models recapitulated the phenotypes observed in patients including the kidney cysts.; to: PMID:35397207 reported 15 individuals from eight unrelated families with biallelic variants in TULP3 gene, out of which three individuals from two different families were reported with hypertrophic non-obstructive cardiomyopathy. In addition, experiments in TULP3 knockout zebrafish models showed that no aberrant morphological features were found in the heart tissue, and histological examination found no indication of fibrosis or underlying cellular disruptions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There is sufficient evidence (8 unrelated cases and supporting functional evidence from animal models) for this gene to be promoted to GREEN rating at the next GMS update.; to: Comment on list classification: As reviewed by John Sayer, there is sufficient evidence (8 unrelated cases and supporting functional evidence from animal models) for this gene to be promoted to GREEN rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hypertrophic cardiomyopathy v4.1 | TULP3 | Achchuthan Shanmugasundram reviewed gene: TULP3: Rating: GREEN; Mode of pathogenicity: None; Publications: 35397207; Phenotypes: Hepatorenocardiac degenerative fibrosis, OMIM:619902; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 |
Achchuthan Shanmugasundram changed review comment from: PMID:35397207 reported individuals from eight unrelated families with biallelic variants in TULP3 gene, out of which individuals from six families had kidney abnormalities including presentation of kidney cysts in at least an individual from five families. In addition, experiments in TULP3 knockout zebrafish models recapitulated the phenotypes observed in patients including the kidney cysts. PMID:36276950 reported two sisters with fibrocystic renal and hepatic disease harboring a homozygous missense mutation in TULP3 (p.Arg382Trp). In addition, experiments with inner medullary collecting duct-3 cells expressing the TULP3 R382W patient variant showed that this variant had a severely reduced ability to localise membrane-associated proteins to the cilium, consistent with a loss of TULP3 function. PMID:36460032 reported two cases with biallelic variants in TULP3 (patient A: homozygous; patient B: compound heterozygous) and both had cystic kidney disease. Functional studies from mouse models also showed that knockout mice developed cystic kidney disease (PMIDs: 30799239 & 30799240).; to: PMID:35397207 reported individuals from eight unrelated families with biallelic variants in TULP3 gene, out of which individuals from six families had kidney abnormalities including presentation of kidney cysts in at least an individual from five families. In addition, experiments in TULP3 knockout zebrafish models recapitulated the phenotypes observed in patients including the kidney cysts. PMID:36276950 reported two sisters with fibrocystic renal and hepatic disease harboring a homozygous missense mutation in TULP3 (p.Arg382Trp). In addition, experiments with inner medullary collecting duct-3 cells expressing the TULP3 R382W patient variant showed that this variant had a severely reduced ability to localise membrane-associated proteins to the cilium, consistent with a loss of TULP3 function. PMID:36460032 reported two cases with biallelic variants in TULP3 (patient A: homozygous; patient B: compound heterozygous) and both had cystic kidney disease. Functional studies from mouse models also showed that knockout mice developed cystic kidney disease (PMIDs: 30799239 & 30799240). This gene has been associated with relevant phenotypes in OMIM (MIM #619902), but not in Gene2Phenotype. |
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| Cystic kidney disease v4.4 | TULP3 |
Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TULP3. Tag Q2_23_NHS_review tag was added to gene: TULP3. |
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| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Classified gene: TULP3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (8 unrelated cases and supporting functional evidence from animal models) for this gene to be promoted to GREEN rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Gene: tulp3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Classified gene: TULP3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (8 unrelated cases and supporting functional evidence from animal models) for this gene to be promoted to GREEN rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Gene: tulp3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Classified gene: TULP3 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (8 unrelated cases and supporting functional evidence from animal models) for this gene to be promoted to GREEN rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.4 | TULP3 | Achchuthan Shanmugasundram Gene: tulp3 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.3 | TULP3 | Achchuthan Shanmugasundram Phenotypes for gene: TULP3 were changed from cystic kidney disease; ductal plate malformation; congentital hepatic fibrosis; cardiomyopathy to Hepatorenocardiac degenerative fibrosis, OMIM:619902 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.2 | TULP3 | Achchuthan Shanmugasundram Publications for gene: TULP3 were set to 36460032; 36276950; 35397207 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Cystic kidney disease v4.1 | TULP3 | Achchuthan Shanmugasundram reviewed gene: TULP3: Rating: GREEN; Mode of pathogenicity: None; Publications: 30799239, 30799240, 35397207, 36276950, 36460032; Phenotypes: Hepatorenocardiac degenerative fibrosis, OMIM:619902; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There is sufficient evidence available to promote this gene to GREEN at the next major update.; to: Comment on list classification: There is sufficient evidence available to promote this gene to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Classified gene: TAF4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available to promote this gene to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Gene: taf4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Classified gene: TAF4 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available to promote this gene to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.152 | TAF4 | Achchuthan Shanmugasundram Gene: taf4 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.11 | INTS11 | Arina Puzriakova Entity copied from Intellectual disability - microarray and sequencing v5.151 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Ataxia and cerebellar anomalies - narrow panel v4.11 | INTS11 |
Arina Puzriakova gene: INTS11 was added gene: INTS11 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review Amber,Literature Q2_23_promote_green tags were added to gene: INTS11. Mode of inheritance for gene: INTS11 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: INTS11 were set to 37054711 Phenotypes for gene: INTS11 were set to Complex neurodevelopmental disorder, MONDO:0100038 |
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| Severe microcephaly v4.13 | INTS11 | Arina Puzriakova Entity copied from Intellectual disability - microarray and sequencing v5.151 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Severe microcephaly v4.13 | INTS11 |
Arina Puzriakova gene: INTS11 was added gene: INTS11 was added to Severe microcephaly. Sources: Expert Review Amber,Literature Q2_23_promote_green tags were added to gene: INTS11. Mode of inheritance for gene: INTS11 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: INTS11 were set to 37054711 Phenotypes for gene: INTS11 were set to Complex neurodevelopmental disorder, MONDO:0100038 |
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| Intellectual disability v5.151 | INTS11 | Arina Puzriakova Phenotypes for gene: INTS11 were changed from intellectual disability, MONDO:0001071 to Complex neurodevelopmental disorder, MONDO:0100038 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.150 | INTS11 | Arina Puzriakova commented on gene: INTS11 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.150 | TAF4 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TAF4. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.86 | PRKACB | Arina Puzriakova Entity copied from Skeletal ciliopathies v3.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.86 | PRKACB |
Arina Puzriakova gene: PRKACB was added gene: PRKACB was added to Fetal anomalies. Sources: Expert Review Amber,Literature Q2_23_promote_green tags were added to gene: PRKACB. Mode of inheritance for gene: PRKACB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: PRKACB were set to 33058759 Phenotypes for gene: PRKACB were set to Cardioacrofacial dysplasia 2, OMIM:619143 Penetrance for gene: PRKACB were set to unknown Mode of pathogenicity for gene: PRKACB was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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| Fetal anomalies v3.85 | PRKACA | Arina Puzriakova Entity copied from Skeletal ciliopathies v3.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Fetal anomalies v3.85 | PRKACA |
Arina Puzriakova gene: PRKACA was added gene: PRKACA was added to Fetal anomalies. Sources: Expert Review Amber,Literature Q2_23_promote_green tags were added to gene: PRKACA. Mode of inheritance for gene: PRKACA was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PRKACA were set to 33058759; 31130284 Phenotypes for gene: PRKACA were set to Cardioacrofacial dysplasia 1, OMIM:619142 |
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| Limb disorders v4.5 | PRKACA | Arina Puzriakova Entity copied from Skeletal ciliopathies v3.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.5 | PRKACA |
Arina Puzriakova gene: PRKACA was added gene: PRKACA was added to Limb disorders. Sources: Expert Review Amber,Literature Q2_23_promote_green tags were added to gene: PRKACA. Mode of inheritance for gene: PRKACA was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PRKACA were set to 33058759; 31130284 Phenotypes for gene: PRKACA were set to Cardioacrofacial dysplasia 1, OMIM:619142 |
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| Skeletal ciliopathies v3.6 | PRKACA | Arina Puzriakova Tag Q2_23_promote_green tag was added to gene: PRKACA. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.6 | PRKACA | Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Zornitza Stark. There is sufficient evidence to promote this gene to Green at the next GMS panel update. At least 3 unrelated cases reported in literature (PMID: 33058759) and an additional case under the care of an NHS colleague with the same missense variant (p.Gly137Arg) and a limb phenotype.; to: Comment on list classification: New gene added by Zornitza Stark. There is sufficient evidence to promote this gene to Green at the next GMS panel update. At least 3 unrelated cases reported in literature (PMID: 33058759) and an additional case under the care of an NHS colleague with the same de novo missense variant (p.Gly137Arg) and a limb phenotype (reported features include micromelia, polydactyly and AVSD). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.6 | PRKACA | Arina Puzriakova Classified gene: PRKACA as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.6 | PRKACA | Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There is sufficient evidence to promote this gene to Green at the next GMS panel update. At least 3 unrelated cases reported in literature (PMID: 33058759) and an additional case under the care of an NHS colleague with the same missense variant (p.Gly137Arg) and a limb phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.6 | PRKACA | Arina Puzriakova Gene: prkaca has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.5 | PRKACB | Arina Puzriakova Tag Q2_23_promote_green tag was added to gene: PRKACB. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.5 | PRKACB | Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis. Rating Amber based on the evidence provided in one publication (PMID:33058759) reporting 2/4 unrelated individuals with ID among other features, although this presentation was mild in one of these cases.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis. There is sufficient evidence to promote this gene to Green at the next GMS panel update. At least 4 unrelated cases, displaying a ciliopathy-like phenotype. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.5 | PRKACB | Arina Puzriakova Entity copied from Intellectual disability - microarray and sequencing v5.150 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.5 | PRKACB |
Arina Puzriakova gene: PRKACB was added gene: PRKACB was added to Skeletal ciliopathies. Sources: Expert Review Amber,Literature Mode of inheritance for gene: PRKACB was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: PRKACB were set to 33058759 Phenotypes for gene: PRKACB were set to Cardioacrofacial dysplasia 2, OMIM:619143 Penetrance for gene: PRKACB were set to unknown Mode of pathogenicity for gene: PRKACB was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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| Intellectual disability v5.150 | PRKACB | Arina Puzriakova Phenotypes for gene: PRKACB were changed from Postaxial hand polydactyly; Postaxial foot polydactyly; Common atrium; Atrioventricular canal defect; Narrow chest; Abnormality of the teeth; Intellectual disability to Cardioacrofacial dysplasia 2, OMIM:619143 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Limb disorders v4.4 | PRKACB | Arina Puzriakova Phenotypes for gene: PRKACB were changed from Postaxial hand polydactyly; Postaxial foot polydactyly; Common atrium; Atrioventricular canal defect; Narrow chest; Abnormality of the teeth; Intellectual disability to Cardioacrofacial dysplasia 2, OMIM:619143 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal ciliopathies v3.4 | PRKACA | Arina Puzriakova Phenotypes for gene: PRKACA were changed from Postaxial hand polydactyly; Postaxial foot polydactyly; Common atrium; Atrioventricular canal defect; Narrow chest; Abnormality of the teeth to Cardioacrofacial dysplasia 1, OMIM:619142 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.149 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.149 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.149 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from intellectual disability, MONDO:0001071 to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.148 | TAF4 | Achchuthan Shanmugasundram Phenotypes for gene: TAF4 were changed from Developmental disorder to intellectual disability, MONDO:0001071 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 27026076; 28191890; 33875846; 35904126 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.147 | TAF4 | Achchuthan Shanmugasundram Publications for gene: TAF4 were set to 33875846; 28191890; 27026076 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.146 | TAF4 | Achchuthan Shanmugasundram Mode of inheritance for gene: TAF4 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.146 | TAF4 | Achchuthan Shanmugasundram Mode of inheritance for gene: TAF4 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.146 | TAF4 | Achchuthan Shanmugasundram Mode of inheritance for gene: TAF4 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.146 | TAF4 | Achchuthan Shanmugasundram Mode of inheritance for gene: TAF4 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.146 | TAF4 | Achchuthan Shanmugasundram Mode of inheritance for gene: TAF4 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.146 | TAF4 | Achchuthan Shanmugasundram Mode of inheritance for gene: TAF4 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | TAF4 | Achchuthan Shanmugasundram reviewed gene: TAF4: Rating: GREEN; Mode of pathogenicity: None; Publications: 28191890, 33875846, 35904126; Phenotypes: intellectual disability, MONDO:0001071; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Classified gene: ZMYND8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>3 unrelated cases) for this gene to be rated GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Gene: zmynd8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Classified gene: ZMYND8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>3 unrelated cases) for this gene to be rated GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Gene: zmynd8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Classified gene: ZMYND8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>3 unrelated cases) for this gene to be rated GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Gene: zmynd8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Classified gene: ZMYND8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>3 unrelated cases) for this gene to be rated GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Gene: zmynd8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Classified gene: ZMYND8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>3 unrelated cases) for this gene to be rated GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Gene: zmynd8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: ZMYND8. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Classified gene: ZMYND8 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence (>3 unrelated cases) for this gene to be rated GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.145 | ZMYND8 | Achchuthan Shanmugasundram Gene: zmynd8 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.144 | ZMYND8 | Achchuthan Shanmugasundram Mode of inheritance for gene: ZMYND8 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.143 | ZMYND8 |
Achchuthan Shanmugasundram edited their review of gene: ZMYND8: Added comment: As reviewed by Konstantinos Varvagiannis, PMID:35916866 reported intellectual disability in10 out of 11 unrelated cases, of which one patient had profound ID and two had moderate ID. This gene has not yet been associated with phenotypes in OMIM, but has been reported in Gene2Phenotype (with 'moderate' rating in the DD panel).; Changed phenotypes to: intellectual disability, MONDO:0001071 |
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| Intellectual disability v5.143 | ZMYND8 | Achchuthan Shanmugasundram reviewed gene: ZMYND8: Rating: GREEN; Mode of pathogenicity: None; Publications: 32530565, 35916866; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.143 | ZMYND15 | Achchuthan Shanmugasundram Publications for gene: ZMYND15 were set to 35916866; 32530565 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.142 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.143 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.142 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.142 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.142 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.142 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14 OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.140 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14 OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14, OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.141 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14 OMIM:615842 to ?Spermatogenic failure 14, OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.140 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14 OMIM:615842 to ?Spermatogenic failure 14 OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.140 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14 OMIM:615842 to ?Spermatogenic failure 14 OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.140 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14 OMIM:615842 to ?Spermatogenic failure 14 OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.140 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from ?Spermatogenic failure 14 OMIM:615842 to ?Spermatogenic failure 14 OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.140 | ZMYND15 | Achchuthan Shanmugasundram Phenotypes for gene: ZMYND15 were changed from Delayed speech and language development; Motor delay; Intellectual disability; Abnormality of cardiovascular system morphology; Hearing abnormality; Abnormality of vision; Abnormality of the face; Seizures to ?Spermatogenic failure 14 OMIM:615842 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram commented on gene: ZMYND15 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.139 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.138 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.138 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.138 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.138 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.138 | ZMYND15 | Achchuthan Shanmugasundram Classified gene: ZMYND15 as No list | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.138 | ZMYND15 | Achchuthan Shanmugasundram Gene: zmynd15 has been removed from the panel. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | ZMYND15 | Achchuthan Shanmugasundram Tag curated_removed tag was added to gene: ZMYND15. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.31 | NTRK1 |
Achchuthan Shanmugasundram changed review comment from: I agree with Zornitza Stark that it is a complex phenotype. However, neuropathy has been associated with the phenotype in sufficient number of cases and been reviewed by several expert reviewers. Hence, the rating should remain as Green. This gene has been associated with relevant phenotypes in both OMIM (MIM #256800) and Gene2Phenotype (with 'definitive' rating in DD and skin panels.; to: I agree with Zornitza Stark that it is a complex phenotype. However, neuropathy has been associated with the phenotype in sufficient number of cases and been reviewed by several expert reviewers. Hence, the rating should remain as Green. This gene has been associated with relevant phenotypes in both OMIM (MIM #256800) and Gene2Phenotype (with 'definitive' rating in DD and skin panels). |
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| COVID-19 research v1.136 | ABCC1 | Jamal Nasir reviewed gene: ABCC1: Rating: RED; Mode of pathogenicity: Other; Publications: ; Phenotypes: COVID-19; Mode of inheritance: Unknown | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Arthrogryposis v5.9 | FILIP1 |
Simon Thomas gene: FILIP1 was added gene: FILIP1 was added to Arthrogryposis. Sources: Literature Mode of inheritance for gene: FILIP1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FILIP1 were set to PubMed: 36344539; PubMed: 36943452; PMID: 37163662 Phenotypes for gene: FILIP1 were set to neurodevelopmental delay; arthrogryposis; muscular hypotonia; mild learning difficulties Penetrance for gene: FILIP1 were set to unknown Review for gene: FILIP1 was set to GREEN Added comment: FILIP1 is not an OMIM Morbid gene. All variants submitted to ClinVar are missense variants of uncertain clinical significance and there are only 3 variants recorded in HDMDPro as?DM. However, two publications in 2023 have established a gene-disease association in 7 unrelated families. All were consanguineous and had a homozygous FILIP1 variant (5 x LoF and 2 x missense). There is also a mouse model (PMID: 29618024). Sources: Literature |
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| Hereditary neuropathy or pain disorder v3.31 | NTRK1 | Achchuthan Shanmugasundram Phenotypes for gene: NTRK1 were changed from Hereditary Neuropathies; Insensitivity to pain, congenital, with anhidrosis to Hereditary Neuropathies; Insensitivity to pain, congenital, with anhidrosis, OMIM:256800 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.30 | NTRK1 | Achchuthan Shanmugasundram reviewed gene: NTRK1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Insensitivity to pain, congenital, with anhidrosis, OMIM:256800; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.30 | MYH14 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: MYH14. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.30 | MYH14 | Achchuthan Shanmugasundram Classified gene: MYH14 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.30 | MYH14 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There are four families reported with the same variant (p.Arg941Leu) and with supporting functional studies characterising this variant. As the reported cases came from both Korean and North American families, it is not likely to be a founder variant. Hence, this gene can be promoted to GREEN rating at the next GMS update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.30 | MYH14 | Achchuthan Shanmugasundram Gene: myh14 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.29 | MYH14 | Achchuthan Shanmugasundram Phenotypes for gene: MYH14 were changed from ?Peripheral neuropathy, myopathy, hoarseness, and hearing loss, 614369 to ?Peripheral neuropathy, myopathy, hoarseness, and hearing loss, OMIM:614369 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.28 | MYH14 | Achchuthan Shanmugasundram Publications for gene: MYH14 were set to 30373780; 21480433; 27875632 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.27 | MYH14 | Achchuthan Shanmugasundram reviewed gene: MYH14: Rating: GREEN; Mode of pathogenicity: None; Publications: 21480433, 27875632, 31231018, 35274842; Phenotypes: ?Peripheral neuropathy, myopathy, hoarseness, and hearing loss, OMIM:614369; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.11 | RFC1 | Sarah Leigh commented on gene: RFC1: Five recent papers (PMID: 35883251; 36250766; 36289003; 36524104; 36478048) report nine RFC1 pathogenic variants in trans with the RFC1_AAGGG expansion variant in at least nine unrelated cases. To date such variants have not been detected in the absence of the RFC1_AAGGG, which is why this gene is rated as Red in PanelApp. Detection of the RFC1_AAGGG expansion variant must be validated within the Genomics England pipeline and will be added to PanelApp in due course. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.11 | RFC1 | Sarah Leigh reviewed gene: RFC1: Rating: RED; Mode of pathogenicity: None; Publications: 35883251, 36250766, 36289003, 36524104, 36478048; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary neuropathy or pain disorder v3.27 | RFC1 | Sarah Leigh Phenotypes for gene: RFC1 were changed from Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, OMIM:614575; cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, MONDO:0013809; chronic idiopathic axonal polyneuropathy; chronic polyneuropathy, MONDO:0003335 to Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, OMIM:614575; cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome, MONDO:0044720 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Hereditary ataxia with onset in adulthood v4.11 | RFC1 | Sarah Leigh Phenotypes for gene: RFC1 were changed from Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, OMIM:614575; cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, MONDO:0013809; chronic idiopathic axonal polyneuropathy; chronic polyneuropathy, MONDO:0003335 to Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, OMIM:614575; cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome, MONDO:0044720 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.1 | CDH1 |
Lauma Freimane gene: CDH1 was added gene: CDH1 was added to Breast cancer pertinent cancer susceptibility. Sources: Literature Mode of inheritance for gene: CDH1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: CDH1 were set to 36436516 Phenotypes for gene: CDH1 were set to Lobular breast cancer Review for gene: CDH1 was set to GREEN Added comment: Sources: Literature |
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| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | TLR7 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: TLR7. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.35 | LETM1 | Sarah Leigh Classified gene: LETM1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.35 | LETM1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.35 | LETM1 | Sarah Leigh Gene: letm1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Breast cancer pertinent cancer susceptibility v2.1 | ATRIP |
Lauma Freimane gene: ATRIP was added gene: ATRIP was added to Breast cancer pertinent cancer susceptibility. Sources: Literature Mode of inheritance for gene: ATRIP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ATRIP were set to 36977412 Phenotypes for gene: ATRIP were set to Hereditary breast cancer Review for gene: ATRIP was set to GREEN gene: ATRIP was marked as current diagnostic Added comment: Meta-analysis confirms ATRIP role in breast cancer development (https://doi.org/10.1101/2022.06.17.22276537). Variants in ATRIP are associated with breast cancer susceptibility in the Polish population and UK Biobank. Sources: Literature |
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| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | TLR7 | Achchuthan Shanmugasundram Added comment: Comment on mode of pathogenicity: As reviewed by Boaz Palterer, gain-of-function variants are associated with systemic lupus erythematosus. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.22 | TLR7 | Achchuthan Shanmugasundram Mode of pathogenicity for gene: TLR7 was changed from None to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.21 | TLR7 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: As reviewed by Boaz Palterer, there are three unrelated cases and functional evidence from mouse models in support of the association of X-linked dominant variants from TLR7 gene to Systemic lupus erythematosus. Hence, this gene can be promoted to GREEN rating at the next major update.; to: Comment on list classification: As reviewed by Boaz Palterer, there are three unrelated cases and functional evidence from mouse models in support of the association of X-linked dominant variants from TLR7 gene to systemic lupus erythematosus. Hence, this gene can be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.21 | TLR7 | Achchuthan Shanmugasundram Added comment: Comment on mode of inheritance: There are three cases and supporting functional evidence available for systemic lupus erythematosus caused by X-linked dominant variants. However, there are only two unrelated cases in support of COVID19-related immunodeficiency caused by X-linked recessive variants. Hence, the MOI should be updated from "X-LINKED: hemizygous mutation in males, biallelic mutations in females" to "X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)". | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.21 | TLR7 | Achchuthan Shanmugasundram Mode of inheritance for gene: TLR7 was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.39 | LETM1 | Sarah Leigh Classified gene: LETM1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.39 | LETM1 | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.39 | LETM1 | Sarah Leigh Gene: letm1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.20 | TLR7 | Achchuthan Shanmugasundram Classified gene: TLR7 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.20 | TLR7 | Achchuthan Shanmugasundram Added comment: Comment on list classification: As reviewed by Boaz Palterer, there are three unrelated cases and functional evidence from mouse models in support of the association of X-linked dominant variants from TLR7 gene to Systemic lupus erythematosus. Hence, this gene can be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.20 | TLR7 | Achchuthan Shanmugasundram Gene: tlr7 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Mitochondrial disorders v4.38 | LETM1 | Sarah Leigh reviewed gene: LETM1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Likely inborn error of metabolism v4.34 | LETM1 | Sarah Leigh reviewed gene: LETM1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.19 | TLR7 | Achchuthan Shanmugasundram Phenotypes for gene: TLR7 were changed from Immunodeficiency 74, COVID19-related, X-linked, MIM# 301051 to Systemic lupus erythematosus 17, OMIM:301080; Immunodeficiency 74, COVID19-related, X-linked, OMIM:301051 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.18 | TLR7 | Achchuthan Shanmugasundram Publications for gene: TLR7 were set to 32706371 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Primary immunodeficiency or monogenic inflammatory bowel disease v4.17 | TLR7 | Achchuthan Shanmugasundram reviewed gene: TLR7: Rating: GREEN; Mode of pathogenicity: None; Publications: 32706371, 35477763; Phenotypes: Systemic lupus erythematosus 17, OMIM:301080, Immunodeficiency 74, COVID19-related, X-linked, OMIM:301051; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | PRSS12 |
Achchuthan Shanmugasundram changed review comment from: Comment on gene classification - This gene should remain as Green rating as there are four unrelated cases and two different variants reported. PMID:12459588 - Two unrelated families with the same variant (4bp homozygous deletion) and with intellectual disability. Although the cases were thought to be unrelated, they had the same haplotype across the PRSS12 locus, suggesting either distant consanguinity or a founder effect in the Algerian population. PMID:25529582 - Two unrelated cases with homozygous c.2389C>T/ p.Arg797Cys variants and with severe intellectual disability reported in the Deciphering Developmental Disorders (DDD) study. In addition, this gene has been associated with intellectual disability in both OMIM (MIM #249500) and Gene2Phenotype (with 'Definitive' rating in the DD panel).; to: Comment on gene classification - This gene should remain as Green as there are four unrelated cases and two different variants reported. PMID:12459588 - Two unrelated families with the same variant (4bp homozygous deletion) and with intellectual disability. Although the cases were thought to be unrelated, they had the same haplotype across the PRSS12 locus, suggesting either distant consanguinity or a founder effect in the Algerian population. PMID:25529582 - Two unrelated cases with homozygous c.2389C>T/ p.Arg797Cys variants and with severe intellectual disability reported in the Deciphering Developmental Disorders (DDD) study. In addition, this gene has been associated with intellectual disability in both OMIM (MIM #249500) and Gene2Phenotype (with 'Definitive' rating in the DD panel). |
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| Intellectual disability v5.137 | PRSS12 |
Achchuthan Shanmugasundram changed review comment from: PMID:12459588 - Two unrelated families with the same variant (4bp homozygous deletion) and with intellectual disability. Although the cases were thought to be unrelated, they had the same haplotype across the PRSS12 locus, suggesting either distant consanguinity or a founder effect in the Algerian population. PMID:25529582 - Two unrelated cases with homozygous c.2389C>T/ p.Arg797Cys variants and with severe intellectual disability reported in the Deciphering Developmental Disorders (DDD) study. In addition, this gene has been associated with intellectual disability in both OMIM (MIM #249500) and Gene2Phenotype (with 'Definitive' rating in the DD panel).; to: Comment on gene classification - This gene should remain as Green rating as there are four unrelated cases and two different variants reported. PMID:12459588 - Two unrelated families with the same variant (4bp homozygous deletion) and with intellectual disability. Although the cases were thought to be unrelated, they had the same haplotype across the PRSS12 locus, suggesting either distant consanguinity or a founder effect in the Algerian population. PMID:25529582 - Two unrelated cases with homozygous c.2389C>T/ p.Arg797Cys variants and with severe intellectual disability reported in the Deciphering Developmental Disorders (DDD) study. In addition, this gene has been associated with intellectual disability in both OMIM (MIM #249500) and Gene2Phenotype (with 'Definitive' rating in the DD panel). |
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| Intellectual disability v5.137 | PRSS12 |
Achchuthan Shanmugasundram changed review comment from: PMID:12459588 - Two unrelated families with the same variant (4bp homozygous deletion) and with intellectual disability. Although the cases were thought to be unrelated, they had the same haplotype across the PRSS12 locus, suggesting either distant consanguinity or a founder effect in the Algerian population. PMID:25529582 - Two unrelated cases with homozygous c.2389C>T/ p.Arg797Cys variants and with severe intellectual disability reported in the Deciphering Developmental Disorders (DDD) study. In addition, this gene has been associated with intellectual disability in both OMIM (MIM #249500) and Gene2Phenotype (with 'Definitive' rating in the DD panel).; to: PMID:12459588 - Two unrelated families with the same variant (4bp homozygous deletion) and with intellectual disability. Although the cases were thought to be unrelated, they had the same haplotype across the PRSS12 locus, suggesting either distant consanguinity or a founder effect in the Algerian population. PMID:25529582 - Two unrelated cases with homozygous c.2389C>T/ p.Arg797Cys variants and with severe intellectual disability reported in the Deciphering Developmental Disorders (DDD) study. In addition, this gene has been associated with intellectual disability in both OMIM (MIM #249500) and Gene2Phenotype (with 'Definitive' rating in the DD panel). |
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| Intellectual disability v5.137 | PRSS12 | Achchuthan Shanmugasundram reviewed gene: PRSS12: Rating: GREEN; Mode of pathogenicity: None; Publications: 12459588, 25529582; Phenotypes: Intellectual developmental disorder, autosomal recessive 1, OMIM:249500; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Tag Q2_23_promote_green tag was added to gene: MAN2C1. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Gene: man2c1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Gene: man2c1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Gene: man2c1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram changed review comment from: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update.; to: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN rating at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Gene: man2c1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Gene: man2c1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence for this gene to be promoted to GREEN at the next major update. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Gene: man2c1 has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Intellectual disability v5.137 | MAN2C1 | Achchuthan Shanmugasundram Classified gene: MAN2C1 as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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