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DDG2P v2.47 TMEM260 Sarah Leigh Gene: tmem260 has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.722 TMEM260 Sarah Leigh Classified gene: TMEM260 as Amber List (moderate evidence)
Fetal anomalies v1.722 TMEM260 Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Fetal anomalies v1.722 TMEM260 Sarah Leigh Gene: tmem260 has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.721 TMEM260 Sarah Leigh Publications for gene: TMEM260 were set to 28318500
Primary ciliary disorders v1.33 CFAP221 Ivone Leong Entity copied from Respiratory ciliopathies including non-CF bronchiectasis v1.47
Primary ciliary disorders v1.33 CFAP221 Ivone Leong gene: CFAP221 was added
gene: CFAP221 was added to Primary ciliary disorders. Sources: Expert Review Red,Literature
Mode of inheritance for gene: CFAP221 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CFAP221 were set to 31636325
Phenotypes for gene: CFAP221 were set to Primary ciliary dyskinesia, MONDO:0016575
Respiratory ciliopathies including non-CF bronchiectasis v1.47 CFAP221 Ivone Leong Phenotypes for gene: CFAP221 were changed from Primary ciliary dyskinesia to Primary ciliary dyskinesia, MONDO:0016575
Respiratory ciliopathies including non-CF bronchiectasis v1.46 CFAP221 Ivone Leong Classified gene: CFAP221 as Red List (low evidence)
Respiratory ciliopathies including non-CF bronchiectasis v1.46 CFAP221 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is currently not associated with a phenotype in OMIM and Gene2Phenotype. There is not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Respiratory ciliopathies including non-CF bronchiectasis v1.46 CFAP221 Ivone Leong Gene: cfap221 has been classified as Red List (Low Evidence).
CAKUT v1.164 DSTYK Zornitza Stark reviewed gene: DSTYK: Rating: RED; Mode of pathogenicity: None; Publications: 23862974; Phenotypes: Congenital anomalies of kidney and urinary tract 1, MIM# 610805; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Unexplained kidney failure in young people v1.96 DSTYK Zornitza Stark reviewed gene: DSTYK: Rating: RED; Mode of pathogenicity: None; Publications: 23862974; Phenotypes: Congenital anomalies of kidney and urinary tract 1, MIM# 610805; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Hypertrophic cardiomyopathy v2.27 ALPK3 Ivone Leong Tag Q3_21_NHS_review tag was added to gene: ALPK3.
Hypertrophic cardiomyopathy v2.27 ALPK3 Ivone Leong Phenotypes for gene: ALPK3 were changed from Cardiomyopathy, familial hypertrophic 27, 618052 to Cardiomyopathy, familial hypertrophic 27, OMIM:618052
Palmoplantar keratodermas v1.9 SPINK5 Ivone Leong reviewed gene: SPINK5: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Palmoplantar keratodermas v1.9 SPINK5 Ivone Leong Tag Q4_21_MOI tag was added to gene: SPINK5.
IUGR and IGF abnormalities v1.38 STAT5B Ivone Leong Publications for gene: STAT5B were set to
IUGR and IGF abnormalities v1.37 STAT5B Ivone Leong Added comment: Comment on mode of inheritance: MOI has been updated from Biallelic to Both monoallelic and biallelic. PMID: 29844444 reported 11 patients from 3 unrelated families with GH insensitivity. Most patients presented in the first or second decades of life with short stature (down to -5.3 SD), delayed bone age, and delayed puberty associated with decreased IGF1 levels.
IUGR and IGF abnormalities v1.37 STAT5B Ivone Leong Mode of inheritance for gene: STAT5B was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1349 KIRREL3 Ivone Leong Added comment: Comment on publications: New publication added (PMID:33853164)
Intellectual disability v3.1349 KIRREL3 Ivone Leong Publications for gene: KIRREL3 were set to 22965935; 19012874
Severe microcephaly v2.258 WDR11 Ivone Leong changed review comment from: Comment on list classification: Promoted from Red to Amber. This gene is associated with a relevant phenotype in Gene2Phenotype (probable) but not in OMIM. There is enough evidence to support a gene-disease association; however, the severity of ID in the patients described in PMID:34413497 does not fit the criteria for this panel (panel is for moderate to severe ID, patients have mild ID). Therefore, this gene has been given an Amber rating.

The OFC of patients in PMID: 34413497 ranged from -3.09 SD to -4.93 SD); to: Comment on list classification: Promoted from Red to Amber. This gene is associated with a relevant phenotype in Gene2Phenotype (probable) but not in OMIM. The OFC of patients in PMID: 34413497 ranged from -3.09 SD to -4.93 SD). There is enough evidence to support a gene-disease association, this gene should be rated Green at the next review.
Severe microcephaly v2.258 WDR11 Ivone Leong Tag watchlist was removed from gene: WDR11.
Tag Q4_21_rating tag was added to gene: WDR11.
Severe microcephaly v2.258 WDR11 Ivone Leong Entity copied from Intellectual disability v3.1348
Severe microcephaly v2.258 WDR11 Ivone Leong gene: WDR11 was added
gene: WDR11 was added to Severe microcephaly. Sources: Expert Review Amber
watchlist tags were added to gene: WDR11.
Mode of inheritance for gene: WDR11 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WDR11 were set to 26350204; 34413497
Phenotypes for gene: WDR11 were set to Intellectual disability, MONDO:0001071; Microcephaly, MONDO:0001149; Short stature,HP:0004322
Penetrance for gene: WDR11 were set to Complete
Intellectual disability v3.1348 WDR11 Ivone Leong Classified gene: WDR11 as Amber List (moderate evidence)
Intellectual disability v3.1348 WDR11 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber. This gene is associated with a relevant phenotype in Gene2Phenotype (probable) but not in OMIM. There is enough evidence to support a gene-disease association; however, the severity of ID in the patients described in PMID:34413497 does not fit the criteria for this panel (panel is for moderate to severe ID, patients have mild ID). Therefore, this gene has been given an Amber rating.

The OFC of patients in PMID: 34413497 ranged from -3.09 SD to -4.93 SD)
Intellectual disability v3.1348 WDR11 Ivone Leong Gene: wdr11 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1347 WDR11 Ivone Leong Added comment: Comment on phenotypes: Previously associated with Kallmann syndrome.
Intellectual disability v3.1347 WDR11 Ivone Leong Phenotypes for gene: WDR11 were changed from KALLMANN SYNDROME to Intellectual disability, MONDO:0001071; Microcephaly, MONDO:0001149; Short stature,HP:0004322
Intellectual disability v3.1346 WDR11 Ivone Leong Publications for gene: WDR11 were set to 26350204
Intellectual disability v3.1345 WDR11 Ivone Leong Added comment: Comment on mode of inheritance: Changed MOI from "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown" to "BIALLELIC, autosomal or pseudoautosomal" as biallelic variants in this gene is associated with ID.
Intellectual disability v3.1345 WDR11 Ivone Leong Mode of inheritance for gene: WDR11 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1344 WDR11 Ivone Leong Tag watchlist tag was added to gene: WDR11.
Intellectual disability v3.1344 PRICKLE2 Ivone Leong Phenotypes for gene: PRICKLE2 were changed from Epilepsy, progressive myoclonic 5, 613832 to Neurodevelopmental disorder; global developmental delay
Intellectual disability v3.1344 PRICKLE2 Ivone Leong Publications for gene: PRICKLE2 were set to
Intellectual disability v3.1343 PRICKLE2 Ivone Leong Tag Q4_21_rating tag was added to gene: PRICKLE2.
Intellectual disability v3.1343 PRICKLE2 Ivone Leong Classified gene: PRICKLE2 as Amber List (moderate evidence)
Intellectual disability v3.1343 PRICKLE2 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber. This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is currently enough evidence to support a gene-disease association. Therefore this gene should be rated Green at the next review.
Intellectual disability v3.1343 PRICKLE2 Ivone Leong Gene: prickle2 has been classified as Amber List (Moderate Evidence).
Hypertrophic cardiomyopathy v2.26 ALPK3 Ivone Leong Tag Q3_21_expert_review tag was added to gene: ALPK3.
Hypertrophic cardiomyopathy v2.26 ALPK3 Ivone Leong Tag Q3_21_MOI tag was added to gene: ALPK3.
DDG2P v2.46 GRIK2 Ivone Leong reviewed gene: GRIK2: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1342 GRIK2 Ivone Leong Phenotypes for gene: GRIK2 were changed from Mental retardation, autosomal recessive, 6, OMIM:611092; on-syndromic neurodevelopmental disorder (NDD), autosomal dominant to Mental retardation, autosomal recessive, 6, OMIM:611092; non-syndromic neurodevelopmental disorder (NDD), autosomal dominant
Early onset or syndromic epilepsy v2.442 GRIK2 Ivone Leong Phenotypes for gene: GRIK2 were changed from Mental retardation, autosomal recessive, 6, OMIM:611092; on-syndromic neurodevelopmental disorder (NDD), autosomal dominant to Mental retardation, autosomal recessive, 6, OMIM:611092; non-syndromic neurodevelopmental disorder (NDD), autosomal dominant
Early onset or syndromic epilepsy v2.441 GRIK2 Ivone Leong Mode of inheritance for gene: GRIK2 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.440 GRIK2 Ivone Leong Classified gene: GRIK2 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.440 GRIK2 Ivone Leong Added comment: Comment on list classification: Demoted from Green to Amber as this gene has not been approved to be on this panel yet. It should be noted that not all patients with variants in this gene develop seizures.
Early onset or syndromic epilepsy v2.440 GRIK2 Ivone Leong Gene: grik2 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.439 GRIK2 Ivone Leong Tag Q4_21_MOI was removed from gene: GRIK2.
Tag Q4_21_rating tag was added to gene: GRIK2.
Early onset or syndromic epilepsy v2.439 GRIK2 Ivone Leong Entity copied from Intellectual disability v3.1341
Early onset or syndromic epilepsy v2.439 GRIK2 Ivone Leong gene: GRIK2 was added
gene: GRIK2 was added to Genetic epilepsy syndromes. Sources: Radboud University Medical Center, Nijmegen,Expert Review Green,Victorian Clinical Genetics Services
Q4_21_MOI tags were added to gene: GRIK2.
Mode of inheritance for gene: GRIK2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GRIK2 were set to 34375587; 17847003; 25039795
Phenotypes for gene: GRIK2 were set to Mental retardation, autosomal recessive, 6, OMIM:611092; on-syndromic neurodevelopmental disorder (NDD), autosomal dominant
Penetrance for gene: GRIK2 were set to Complete
Intellectual disability v3.1341 GRIK2 Ivone Leong Tag Q4_21_MOI tag was added to gene: GRIK2.
Intellectual disability v3.1341 GRIK2 Ivone Leong reviewed gene: GRIK2: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1341 GRIK2 Ivone Leong Publications for gene: GRIK2 were set to
Intellectual disability v3.1340 GRIK2 Ivone Leong Phenotypes for gene: GRIK2 were changed from Mental retardation, autosomal recessive, 6, 611092; MENTAL RETARDATION AUTOSOMAL RECESSIVE TYPE 6 (MRT6) to Mental retardation, autosomal recessive, 6, OMIM:611092; on-syndromic neurodevelopmental disorder (NDD), autosomal dominant
Early onset or syndromic epilepsy v2.438 CACNA1I Ivone Leong Entity copied from Intellectual disability v3.1339
Early onset or syndromic epilepsy v2.438 CACNA1I Ivone Leong gene: CACNA1I was added
gene: CACNA1I was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
Q4_21_rating tags were added to gene: CACNA1I.
Mode of inheritance for gene: CACNA1I was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CACNA1I were set to 33704440
Phenotypes for gene: CACNA1I were set to Neurodevelopmental disorder
Mode of pathogenicity for gene: CACNA1I was set to Other
Intellectual disability v3.1339 CACNA1I Ivone Leong Classified gene: CACNA1I as Amber List (moderate evidence)
Intellectual disability v3.1339 CACNA1I Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1339 CACNA1I Ivone Leong Gene: cacna1i has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1338 CACNA1I Ivone Leong Tag Q4_21_rating tag was added to gene: CACNA1I.
Cerebral vascular malformations v2.58 PIK3CA Zornitza Stark reviewed gene: PIK3CA: Rating: GREEN; Mode of pathogenicity: None; Publications: 34496175; Phenotypes: Cerebral cavernous malformations 4, MIM#619538; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.1338 SHANK1 Zornitza Stark reviewed gene: SHANK1: Rating: GREEN; Mode of pathogenicity: None; Publications: 34113010, 22503632, 25188300; Phenotypes: Neurodevelopmental disorder; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Clefting v2.51 GDF11 Zornitza Stark gene: GDF11 was added
gene: GDF11 was added to Clefting. Sources: Literature
Mode of inheritance for gene: GDF11 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: GDF11 were set to 31215115; 34113007
Phenotypes for gene: GDF11 were set to Vertebral hypersegmentation and orofacial anomalies (VHO), OMIM #619122
Review for gene: GDF11 was set to GREEN
Added comment: PMID 34113007: Ravenscroft et al. (2021) report 6 probands who presented with craniofacial (5/6), vertebral (5/6), neurological (6/6), visual (4/6), cardiac (3/6), auditory (3/6), and connective tissue abnormalities (3/6). They found de novo and inherited variants in GDF11. gdf11 mutant zebrafish showed craniofacial abnormalities and body segmentation defects that matched some patient phenotypes. Expression of the patients’ variants in the fly showed that one nonsense variant in GDF11 is a severe loss-of-function (LOF) allele whereas the missense variants are partial LOF variants.

PMID 31215115: In 5 affected members over 3 generations of a family segregating vertebral hypersegmentation and orofacial anomalies, Cox et al. (2019) identified heterozygosity for a missense mutation in the GDF11 gene (R298Q) that was not found in unaffected family members or in public variant databases. Functional analysis demonstrated that the R298Q substitution prevents cleavage to the active form of the protein, resulting in loss of function.
Sources: Literature
Early onset or syndromic epilepsy v2.437 CHRM1 Ivone Leong Classified gene: CHRM1 as Red List (low evidence)
Early onset or syndromic epilepsy v2.437 CHRM1 Ivone Leong Added comment: Comment on list classification: Demoted from Amber to Red to match my review.
Early onset or syndromic epilepsy v2.437 CHRM1 Ivone Leong Gene: chrm1 has been classified as Red List (Low Evidence).
Early onset or syndromic epilepsy v2.436 CHRM1 Ivone Leong Tag watchlist was removed from gene: CHRM1.
Early onset or syndromic epilepsy v2.436 CHRM1 Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there is currently not enough evidence to support a gene-disease association this gene has been given an Amber rating.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there is currently only 1 case with epilepsy this gene has been given a Red rating.
Early onset or syndromic epilepsy v2.436 CHRM1 Ivone Leong Entity copied from Intellectual disability v3.1338
Early onset or syndromic epilepsy v2.436 CHRM1 Ivone Leong gene: CHRM1 was added
gene: CHRM1 was added to Genetic epilepsy syndromes. Sources: Literature,Expert Review Amber
watchlist tags were added to gene: CHRM1.
Mode of inheritance for gene: CHRM1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CHRM1 were set to 34212451; 31981491; 12483218
Phenotypes for gene: CHRM1 were set to Neurodevelopmental delay; intellectual disability, MONDO:0001071; autism
Intellectual disability v3.1338 PLXNA1 Zornitza Stark gene: PLXNA1 was added
gene: PLXNA1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: PLXNA1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: PLXNA1 were set to 34054129
Phenotypes for gene: PLXNA1 were set to Neurodevelopmental disorder with cerebral and eye anomalies
Review for gene: PLXNA1 was set to GREEN
Added comment: Dworschak et al. (2021) via WES reported 10 patients from 7 families with biallelic (n=7) or de novo (n=3) PLXNA1 variants. Shared phenotypic features include global developmental delay (9/10), brain anomalies (6/10), and eye anomalies (7/10). Seizures were predominantly reported in patients with monoallelic variants. Zebrafish studies showed an embryonic role of plxna1a in the development of the central nervous system and the eye. Biallelic variants in the extracellular Plexin-A1 domains lead to impaired dimerization or lack of receptor molecules, whereas monoallelic variants in the intracellular Plexin-A1 domains might impair downstream signaling through a dominant-negative effect.
Sources: Literature
Intellectual disability v3.1338 CHRM1 Ivone Leong Tag watchlist tag was added to gene: CHRM1.
Intellectual disability v3.1338 CHRM1 Ivone Leong Deleted their comment
Intellectual disability v3.1338 HNRNPD Zornitza Stark edited their review of gene: HNRNPD: Added comment: More individuals reported in PMID 33874999; Changed rating: GREEN; Changed publications to: 33057194, 33874999; Changed phenotypes to: Developmental disorders, Intellectual disability
Intellectual disability v3.1338 CHRM1 Ivone Leong Classified gene: CHRM1 as Amber List (moderate evidence)
Intellectual disability v3.1338 CHRM1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there is currently not enough evidence to support a gene-disease association this gene has been given an Amber rating.
Intellectual disability v3.1338 CHRM1 Ivone Leong Gene: chrm1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1338 CHRM1 Ivone Leong Classified gene: CHRM1 as Amber List (moderate evidence)
Intellectual disability v3.1338 CHRM1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there is currently not enough evidence to support a gene-disease association this gene has been given an Amber rating.
Intellectual disability v3.1338 CHRM1 Ivone Leong Gene: chrm1 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.435 UNC13B Zornitza Stark gene: UNC13B was added
gene: UNC13B was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: UNC13B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: UNC13B were set to 33876820
Phenotypes for gene: UNC13B were set to Epilepsy
Review for gene: UNC13B was set to RED
Added comment: No OMIM human disease association. Gene encodes a presynaptic protein Munc13-2 highly expressed in the brain (predominantly cerebral cortex).

Variant interpretation data in human epilepsy cohort somewhat conflicting and restricted to a single study. Wang et al, Brain, 2021 - trio-based whole-exome sequencing identified UNC13B in 12 individuals affected by partial epilepsy and/or febrile seizures from 8 unrelated families. Identified:
x1 de novo nonsense variant, absent in gnomad, damaging in silicos
x1 de novo splice site, absent in gnomad, damaging in silicos
x1 splice site variant present in unaffected mother (low frequency in gnomad)
x2 compound het in one individual - more severe phenotype postulated (x1 variant present in contro cohortl, the other variant present in low frequency in gnomad)
x1 missense variant - in Han Chinese major depressive disorders study, not in gnomad
x1 missense variant - highly conserved residue, not in gnomad
x2 other missense variant - highly conserved residue, low frequency in gnomad
Latter 4 missense variants cosegregated with affected individuals in the families

In Drosophila, seizure rate and duration were increased by Unc13b knockdown compared to wild-type flies, but these effects were less pronounced than in sodium voltage-gated channel alpha subunit 1 (Scn1a) knockdown Drosophila

De novo UNC13B variants previously reported in bipolar disorder and autism spectrum disorder
Sources: Literature
Intellectual disability v3.1337 CHRM1 Ivone Leong Phenotypes for gene: CHRM1 were changed from Neurodevelopmental delay; intellectual disability; autism to Neurodevelopmental delay; intellectual disability, MONDO:0001071; autism
Early onset or syndromic epilepsy v2.435 CHD4 Zornitza Stark gene: CHD4 was added
gene: CHD4 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: CHD4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CHD4 were set to 27479907; 27616479; 34109749
Phenotypes for gene: CHD4 were set to Sifrim-Hitz-Weiss syndrome, MIM# 617159; Childhood idiopathic epilepsy and sinus arrhythmia
Review for gene: CHD4 was set to GREEN
Added comment: PMID 34109749: 8 individuals from 4 families with childhood idiopathic epilepsy and sinus arrhythmia. This may be a distinct gene-disease association as the variants were located outside of the typical domains associated with SHW syndrome (central regions from SNF2-like region to DUF1087 domain).

SHW syndrome: seizures are also reported, though not as a common feature.
Sources: Literature
Respiratory ciliopathies including non-CF bronchiectasis v1.45 CFAP221 Zornitza Stark gene: CFAP221 was added
gene: CFAP221 was added to Respiratory ciliopathies including non-CF bronchiectasis. Sources: Literature
Mode of inheritance for gene: CFAP221 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CFAP221 were set to 31636325
Phenotypes for gene: CFAP221 were set to Primary ciliary dyskinesia
Review for gene: CFAP221 was set to RED
Added comment: WES in 1 family with 3 siblings with clinical symptoms of PCD identified compound heterozygous loss-of-function variants in CFAP221, which segregated with disease. No functional studies. Nasal epithelial cells from 1 of the subjects demonstrated slightly reduced beat frequency, however, waveform analysis revealed that the CFAP221 defective cilia beat in an aberrant circular pattern. A candidate gene in cases where PCD is suspected but cilia structure and beat frequency appear normal.
Sources: Literature
Intellectual disability v3.1336 SARS Zornitza Stark gene: SARS was added
gene: SARS was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: SARS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SARS were set to 28236339; 34570399
Phenotypes for gene: SARS were set to Intellectual disability
Review for gene: SARS was set to AMBER
Added comment: Summary - 2 unrelated families with overlapping ID phenotype, and supporting in vitro and patient cell assays.

PMID: 28236339 - an Iranian family (distantly related) segregating a homozygous missense (c.514G>A, p.Asp172Asn) with moderate ID, microcephaly, ataxia, speech impairment, and aggressive behaviour. Also, supporting in vitro functional assays demonstrating altered protein function.
PMID: 34570399 - a consanguineous Turkish family segregating a homozygous missense (c.638G>T, p.(Arg213Leu)) with developmental delay, central deafness, cardiomyopathy, and metabolic decompensation during fever leading to death. Also, reduced protein level and enzymatic activity in patient cells.
Sources: Literature
Intellectual disability v3.1336 ZNF699 Ivone Leong Tag Q4_21_rating tag was added to gene: ZNF699.
Intellectual disability v3.1336 ZNF699 Ivone Leong Classified gene: ZNF699 as Amber List (moderate evidence)
Intellectual disability v3.1336 ZNF699 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM but not Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1336 ZNF699 Ivone Leong Gene: znf699 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1335 ZDHHC15 Zornitza Stark reviewed gene: ZDHHC15: Rating: RED; Mode of pathogenicity: None; Publications: 34345675; Phenotypes: Mental retardation, X-linked 91, 300577, cerebral palsy, intellectual disability, autism spectrum disorder, epilepsy; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Ataxia and cerebellar anomalies - narrow panel v2.236 RFXANK Zornitza Stark gene: RFXANK was added
gene: RFXANK was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature
Mode of inheritance for gene: RFXANK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RFXANK were set to 33855173; 23314770; 28676232
Phenotypes for gene: RFXANK were set to Progressive Ataxia and Neurologic Regression; MHC class II deficiency, complementation group B MIM#209920
Review for gene: RFXANK was set to AMBER
Added comment: PMID: 33855173 - 1 family (2 affecteds, 3rd not sequenced) with a homozygous c.271+1G>C splice variant, late-onset immunodeficiency and subacute progressive neurodegenerative disease, including cognition, motor, visual and cerebellar features. MRI demonstrated global cerebral and cerebellar atrophy.

PMID: 23314770 - 1/34 MHCII deficient patients with biallelic variants reported with ataxia. Majority of patients (including patient with ataxia) share a founder variant (c.338-25_338del26).

PMID: 28676232 - single 30 month old patient with ataxic gait and dysarthria and a homozygous PTC.

Summary: 3 patients but uncommon feature of an established immunological disorder, variable expressivity
Sources: Literature
Hereditary ataxia with onset in adulthood v2.85 PRPS1 Zornitza Stark gene: PRPS1 was added
gene: PRPS1 was added to Hereditary ataxia - adult onset. Sources: Literature
Mode of inheritance for gene: PRPS1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: PRPS1 were set to 33898739; 28967191; 25491489
Phenotypes for gene: PRPS1 were set to Ataxia; deafness; eye disease
Review for gene: PRPS1 was set to AMBER
Added comment: PMID: 25491489:
Heterozygous missense variant, loss of function - PRS enzyme deficiency showed.
Proband and her mother have various degrees of ataxia (examinations at 34yrs and 70yrs, respectively), peripheral neuropathy and hearing loss beyond the ophthalmological symptoms, whereas the phenotype of the affected older sister (36yo) is currently confined to the eye and milder.

PMID: 28967191
in one of the families, heterozygous variants in proband with hearing loss and ataxia developed in the proband in her forties, and ocular manifestations of retinal changes and disc pallor were first confirmed in the two affected daughters in their twenties.

PMID: 33898739:
Heterozygous de novo missense variant in a 30yo female individual, presented with a 5-year history of progressive ataxia. She also had congenital strabismus, infantile-onset hearing loss, and a retinal dystrophy with progressive visual loss for the past 10 years.
Sources: Literature
Ataxia and cerebellar anomalies - narrow panel v2.236 DAB1 Zornitza Stark reviewed gene: DAB1: Rating: RED; Mode of pathogenicity: None; Publications: 33928188; Phenotypes: Ataxia, Intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Ataxia and cerebellar anomalies - narrow panel v2.236 TRIP4 Zornitza Stark gene: TRIP4 was added
gene: TRIP4 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature
Mode of inheritance for gene: TRIP4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRIP4 were set to 34075209
Phenotypes for gene: TRIP4 were set to cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures.
Review for gene: TRIP4 was set to AMBER
Added comment: PMID: 34075209:
One patient with cerebellar hypoplasia and spinal muscular atrophy (PCH1) and congenital bone fractures, hom PTV. The same PTV had been previously reported in 3 patients from 2 families with prenatal spinal muscular atrophy and congenital bone fractures (PMID: 26924529).

Possible phenotype expansion.
Sources: Literature
Intellectual disability v3.1335 ATP11A Zornitza Stark gene: ATP11A was added
gene: ATP11A was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ATP11A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ATP11A were set to 34403372
Phenotypes for gene: ATP11A were set to Neurodevelopmental disorder
Review for gene: ATP11A was set to AMBER
Added comment: PMID: 34403372:
- Single de novo missense variant reported in a patient with developmental delay and neurological deterioration.
- Patient MRI showed severe cerebral atrophy, ventriculomegaly, hypomyelination leukodystrophy, thinned corpus callosum. Axonal neuropathy suggested.
- K/I heterozygous mice died perinatally.
- Functional studies on missense variant show plasma membrane lipid content impairment, reduced ATPase activity etc.

gnomAD: some NMD PTCs present, good quality variants found with 4-5 hets.
Sources: Literature
Hereditary neuropathy or pain disorder v1.63 COX20 Zornitza Stark gene: COX20 was added
gene: COX20 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Literature
Mode of inheritance for gene: COX20 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: COX20 were set to 33751098
Phenotypes for gene: COX20 were set to Neuropathy
Review for gene: COX20 was set to GREEN
gene: COX20 was marked as current diagnostic
Added comment: Well established association with mitochondrial disease, presentation with neuropathy reported PMID 33751098
Sources: Literature
Fetal anomalies v1.720 LONP1 Zornitza Stark reviewed gene: LONP1: Rating: RED; Mode of pathogenicity: None; Publications: 34547244; Phenotypes: Congenital diaphragmatic hernia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.1335 ZNF699 Ivone Leong Phenotypes for gene: ZNF699 were changed from DEGCAGS syndrome, MIM# 619488 to DEGCAGS syndrome, OMIM:619488
Early onset or syndromic epilepsy v2.435 JAKMIP1 Ivone Leong Entity copied from Intellectual disability v3.1334
Early onset or syndromic epilepsy v2.435 JAKMIP1 Ivone Leong gene: JAKMIP1 was added
gene: JAKMIP1 was added to Genetic epilepsy syndromes. Sources: Literature,Expert Review Amber
watchlist tags were added to gene: JAKMIP1.
Mode of inheritance for gene: JAKMIP1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: JAKMIP1 were set to 29158550; 26627310; 27799067
Phenotypes for gene: JAKMIP1 were set to Intellectual disability, MONDO:0001071; seizures
Intellectual disability v3.1334 ABHD16A Zornitza Stark gene: ABHD16A was added
gene: ABHD16A was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ABHD16A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ABHD16A were set to 34587489
Phenotypes for gene: ABHD16A were set to Spastic paraplegia; Intellectual disability
Review for gene: ABHD16A was set to GREEN
gene: ABHD16A was marked as current diagnostic
Added comment: 11 individuals from 6 families with a complicated form of hereditary spastic paraplegia who carry bi-allelic deleterious variants in ABHD16A. Affected individuals present with a similar phenotype consisting of global developmental delay/intellectual disability, progressive spasticity affecting the upper and lower limbs, and corpus callosum and white matter anomalies. Immunoblot analysis on extracts from fibroblasts from four affected individuals demonstrated little to no ABHD16A protein levels compared to controls.
In 5 of the families the affected members were homozygous, 3 of these families were consanguineous. 2 families have the same variant- both families are French-Canadian.
4 missense variants, 1 frameshift, 1 nonsense.
Sources: Literature
Intellectual disability v3.1334 JAKMIP1 Ivone Leong Tag watchlist tag was added to gene: JAKMIP1.
Intellectual disability v3.1334 JAKMIP1 Ivone Leong Classified gene: JAKMIP1 as Amber List (moderate evidence)
Intellectual disability v3.1334 JAKMIP1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. Currently there are only 2 cases; however, there is very little information about the two cases in the papers. Therefore, this gene has been given an Amber rating until more evidence is available.
Intellectual disability v3.1334 JAKMIP1 Ivone Leong Gene: jakmip1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1333 JAKMIP1 Ivone Leong Phenotypes for gene: JAKMIP1 were changed from Intellectual disability; seizures to Intellectual disability, MONDO:0001071; seizures
Fetal anomalies v1.720 WLS Zornitza Stark gene: WLS was added
gene: WLS was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: WLS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WLS were set to 34587386
Phenotypes for gene: WLS were set to structural congenital anomalies
Review for gene: WLS was set to GREEN
Added comment: - Homozygous variants in 10 affected persons from 5 unrelated families.
- Affected individuals had multiorgan defects, including microcephaly, facial dysmorphism, foot syndactyly, renal agenesis, alopecia, iris coloboma, and heart defects.
- The mutations affected WLS protein stability and Wnt signaling. Knock-in mice showed tissue and cell vulnerability consistent with Wnt-signaling intensity and individual and collective functions of Wnts in embryogenesis.
Sources: Literature
Intellectual disability v3.1332 ATP6V0C Zornitza Stark gene: ATP6V0C was added
gene: ATP6V0C was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ATP6V0C was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ATP6V0C were set to 33190975; 33090716
Phenotypes for gene: ATP6V0C were set to Epilepsy; Intellectual Disability; microcephaly
Review for gene: ATP6V0C was set to AMBER
Added comment: 9 individuals reported with deletions and ID/seizures/microcephaly, minimum overlapping region implicates ATP6V0C as the causative gene. Single case report of de novo SNV and ID/seizures.
Sources: Literature
Intellectual disability v3.1332 ARFGEF1 Zornitza Stark gene: ARFGEF1 was added
gene: ARFGEF1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ARFGEF1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ARFGEF1 were set to 34113008
Phenotypes for gene: ARFGEF1 were set to Intellectual disability; Epilepsy
Review for gene: ARFGEF1 was set to GREEN
Added comment: 13 individuals reported with variants in this gene and a neurodevelopmental disorder characterised by variable ID, seizures present in around half. Variants were inherited from mildly affected parents in 40% of families.
Sources: Literature
Congenital disorders of glycosylation v2.76 ALG10 Zornitza Stark gene: ALG10 was added
gene: ALG10 was added to Congenital disorders of glycosylation. Sources: Literature
Mode of inheritance for gene: ALG10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ALG10 were set to 33798445
Phenotypes for gene: ALG10 were set to Progressive myoclonus epilepsy; CDG
Review for gene: ALG10 was set to RED
Added comment: Single individual with homozygous variant identified in a progressive myoclonus epilepsy cohort.
Sources: Literature
Intellectual disability v3.1332 KIF4A Zornitza Stark reviewed gene: KIF4A: Rating: GREEN; Mode of pathogenicity: None; Publications: 24812067, 34346154; Phenotypes: Mental retardation, X-linked 100, MIM# 300923; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Childhood onset dystonia, chorea or related movement disorder v1.157 SHQ1 Zornitza Stark gene: SHQ1 was added
gene: SHQ1 was added to Childhood onset dystonia or chorea or related movement disorder. Sources: Literature
Mode of inheritance for gene: SHQ1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SHQ1 were set to 34542157; 29178645
Phenotypes for gene: SHQ1 were set to Dystonia; Neurodegeneration
Review for gene: SHQ1 was set to AMBER
Added comment: Three unrelated families reported. Family 1: isolated dystonia only; Family 2: dystonia, and neurodegeneration; Family 3: neurodegeneration.

Functional data in PMID 34542157

Rated Amber as phenotypes likely represent a continuum but currently unclear.
Sources: Literature
Rare anaemia v1.27 HSCB Zornitza Stark gene: HSCB was added
gene: HSCB was added to Rare anaemia. Sources: Literature
Mode of inheritance for gene: HSCB was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HSCB were set to 32634119
Phenotypes for gene: HSCB were set to Anaemia, sideroblastic, 5 619523
Review for gene: HSCB was set to AMBER
Added comment: Single individual reported with compound heterozygous variants in this gene. Good functional data including animal model.
Sources: Literature
Fetal anomalies v1.720 WNT9B Zornitza Stark gene: WNT9B was added
gene: WNT9B was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: WNT9B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: WNT9B were set to 34145744
Phenotypes for gene: WNT9B were set to Renal agenesis/hypoplasia/dysplasia
Review for gene: WNT9B was set to AMBER
Added comment: WNT9B plays a key role in the development of the mammalian urogenital system. It is essential for the induction of mesonephric and metanephric tubules, the regulation of renal tubule morphogenesis, and the regulation of renal progenitor cell expansion and differentiation. WNT9B−/− mice have renal agenesis/hypoplasia and reproductive tract abnormalities.

Lemire et al. (2021) report 4 individuals from 2 unrelated consanguineous families with bilateral renal agenesis/hypoplasia/dysplasia and homozygous variants in WNT9B. The proband from Family 1 had bilateral renal cystic dysplasia and chronic kidney disease, with 2 deceased siblings with bilateral renal hypoplasia/agenesis. The 3 affected family members were homozygous for a Gly317Arg missense variant in WNT9B. Proband from Family 2 had renal hypoplasia/dysplasia, chronic kidney disease, and was homozygous for a Pro5Alafs*52 nonsense variant in WNT9B. The proband's unaffected brother is also homozygous for the nonsense variant in WNT9B, suggesting nonpenetrance.

I wasn't sure which panel this is more pertinent to: we have added this gene to our CAKUT panel.
Sources: Literature
Familial Meniere Disease v1.1 ADD3 Eldar Dedic reviewed gene: ADD3: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: Unknown
Limb disorders v2.60 UBA2 Eleanor Williams Classified gene: UBA2 as Amber List (moderate evidence)
Limb disorders v2.60 UBA2 Eleanor Williams Added comment: Comment on list classification: Leaving rating as amber for now, but with a recommendation for green rating following GMS review. There are now 5 cases reported with split hand malformation and plausible disease causing variants in this gene.
Limb disorders v2.60 UBA2 Eleanor Williams Gene: uba2 has been classified as Amber List (Moderate Evidence).
Limb disorders v2.59 UBA2 Eleanor Williams Publications for gene: UBA2 were set to 31332306; 24243649; 29988626; 31587267
Limb disorders v2.58 UBA2 Eleanor Williams Tag Q4_21_rating tag was added to gene: UBA2.
Limb disorders v2.58 UBA2 Eleanor Williams edited their review of gene: UBA2: Added comment: As reviewer notes, in PMID: 34159400 (Elsner et al 2021) they report 3 unrelated cases where a variant in UBA2 are reported in individuals with split hand malformation.; Changed rating: GREEN; Changed publications to: 31332306, 24243649, 29988626, 31587267, 34159400
Limb disorders v2.58 HMGB1 Eleanor Williams Classified gene: HMGB1 as Red List (low evidence)
Limb disorders v2.58 HMGB1 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to red based on 1 case, plus some supportive animal model data.
Limb disorders v2.58 HMGB1 Eleanor Williams Gene: hmgb1 has been classified as Red List (Low Evidence).
Clefting v2.51 SF3B2 Eleanor Williams Classified gene: SF3B2 as Amber List (moderate evidence)
Clefting v2.51 SF3B2 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber but with a green recommendation following GMS review. 4 families reported in which lateral oral clefting is part of the phenotype. Supportive Xenopus data.
Clefting v2.51 SF3B2 Eleanor Williams Gene: sf3b2 has been classified as Amber List (Moderate Evidence).
Clefting v2.50 SF3B2 Eleanor Williams Tag Q4_21_rating tag was added to gene: SF3B2.
Clefting v2.50 SF3B2 Eleanor Williams commented on gene: SF3B2
Monogenic hearing loss v2.195 CLDN9 Eleanor Williams Classified gene: CLDN9 as Amber List (moderate evidence)
Monogenic hearing loss v2.195 CLDN9 Eleanor Williams Added comment: Comment on list classification: Promoting from red to amber but with a green rating recommendation following GMS review. 3 unrelated cases plus mouse model and some functional data.
Monogenic hearing loss v2.195 CLDN9 Eleanor Williams Gene: cldn9 has been classified as Amber List (Moderate Evidence).
Familial Meniere Disease v1.1 ADD2 Eldar Dedic reviewed gene: ADD2: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: Unknown
Monogenic hearing loss v2.194 CLDN9 Eleanor Williams Phenotypes for gene: CLDN9 were changed from to Deafness, autosomal recessive 116, OMIM:619093; deafness, autosomal recessive 116, MONDO:0033670
Monogenic hearing loss v2.193 CLDN9 Eleanor Williams Publications for gene: CLDN9 were set to
Monogenic hearing loss v2.192 CLDN9 Eleanor Williams Mode of inheritance for gene: CLDN9 was changed from to BIALLELIC, autosomal or pseudoautosomal
Monogenic hearing loss v2.191 CLDN9 Eleanor Williams Tag Q4_21_rating tag was added to gene: CLDN9.
Monogenic hearing loss v2.191 CLDN9 Eleanor Williams reviewed gene: CLDN9: Rating: GREEN; Mode of pathogenicity: None; Publications: 31175426, 34265170; Phenotypes: Deafness, autosomal recessive 116, OMIM:619093; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1332 TAF2 Zornitza Stark reviewed gene: TAF2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34474177, 21937992, 22633631, 26350204; Phenotypes: Mental retardation, autosomal recessive 40, OMIM # 615599; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1332 DDX23 Zornitza Stark edited their review of gene: DDX23: Added comment: PMID 34050707: 9 unrelated individuals (gathered through GeneMatcher) with de novo missense alterations in DDX23. Clinical features include: tone abnormalities, global developmental delay, facial dysmorphism, autism spectrum disorder, and seizures. Additionally, there were a variety of other findings in the skeletal, renal, ocular, and cardiac systems. The missense alterations all occurred within a highly conserved RecA-like domain of the protein, and are located within or proximal to the DEAD box sequence. The gene is ubiquitously expressed and functions in RNA splicing, maintenance of genome stability, and the sensing of double-stranded RNA.; Changed rating: GREEN; Changed publications to: 33057194, 34050707
Arthrogryposis v3.122 ERGIC1 Zornitza Stark gene: ERGIC1 was added
gene: ERGIC1 was added to Arthrogryposis. Sources: Literature
Mode of inheritance for gene: ERGIC1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ERGIC1 were set to 28317099; 34037256
Phenotypes for gene: ERGIC1 were set to Arthrogryposis multiplex congenita 2, neurogenic type; OMIM # 208100
Review for gene: ERGIC1 was set to AMBER
Added comment: Reinstein et al. (2018) used WES in a large consanguineous Israeli Arab kindred consisting of 16 patients affected with the neurogenic type of arthrogryposis multiplex congenita. They identified a homozygous missense (V98E) mutation in ERGIC1 gene, which segregated with the disorder in the kindred, and was not found in the ExAC database or in 212 ethnically matched controls. Functional studies of the variant and studies of patient cells were not performed. ERGIC1 encodes a cycling membrane protein which has a possible role in transport between endoplasmic reticulum and Golgi.

Marconi et al (2021) used genome sequencing in a consanguineous family with 2 affected siblings presenting congenital arthrogryposis and some facial dysmorphism. They identified a homozygous 22.6 Kb deletion encompassing the promoter and first exon of ERGIC1. mRNA quantification showed the complete absence of ERGIC1 expression in the two affected siblings and a decrease in heterozygous parents.
Sources: Literature
Intellectual disability v3.1332 HMGB1 Zornitza Stark gene: HMGB1 was added
gene: HMGB1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: HMGB1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: HMGB1 were set to 34164801
Phenotypes for gene: HMGB1 were set to Developmental delay and microcephaly
Review for gene: HMGB1 was set to GREEN
gene: HMGB1 was marked as current diagnostic
Added comment: 13q12.3 microdeletion syndrome is a rare cause of syndromic ID. Previous studies identified four genes within the ~300 Kb minimal critical region including two candidate protein coding genes: KATNAL1 and HMGB1.

Uguen et al. (2021) report 6 patients with LOF variants involving HMGB1 with features similar to 13q12.3 microdeletion syndrome (i.e. developmental delay, language delay, microcephaly, obesity and dysmorphic features). In silico analyses suggest that HMGB1 is likely to be intolerant to LOF, and previous in vitro data are in line with the role of HMGB1 in neurodevelopment. They suggest that haploinsufficiency of the HMGB1 gene may play a critical role in the pathogenesis of the 13q12.3 microdeletion syndrome.
Sources: Literature
Intellectual disability v3.1332 WIPI2 Zornitza Stark edited their review of gene: WIPI2: Added comment: PMID: 34557665 (2021)
- two novel homozygous variants were identified in four individuals of two consanguineous families.
- one family presented with microcephaly, profound global developmental delay/intellectual disability, refractory infantile/childhood-onset epilepsy, progressive tetraplegia with joint contractures and dyskinesia.
- second family (similar to initial publication) presented with a milder phenotype, encompassing moderate intellectual disability, speech and visual impairment, autistic features, and an ataxic gait.
- functional studies showed dysregulation of the early steps of the autophagy pathway.; Changed rating: GREEN; Changed publications to: 30968111, 34557665; Set current diagnostic: yes
Hypertrophic cardiomyopathy v2.26 ALPK3 Oliver Watkinson reviewed gene: ALPK3: Rating: GREEN; Mode of pathogenicity: None; Publications: 32480058; Phenotypes: Hypertrophic Cardiomyopathy; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Arthrogryposis v3.122 SLC29A3 Lucy Jackson gene: SLC29A3 was added
gene: SLC29A3 was added to Arthrogryposis. Sources: Literature
Mode of inheritance for gene: SLC29A3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: SLC29A3 were set to Histiocytosis-lymphadenopathy plus syndrome
Review for gene: SLC29A3 was set to GREEN
gene: SLC29A3 was marked as current diagnostic
Added comment: Sources: Literature
Familial Meniere Disease v1.1 ADD1 Eleanor Williams changed review comment from: As noted by the expert reviewer Eldar Dedic, PMID: 30828346 - Gallego-Martinez, et al. (2019) reports a family in which two members have a rare variant of unknown signficance in ADD1 (chr4:2900221 A>G). In addition, two other rare variants in candidate genes are reported in 2 family members (KCNQ4) and in all cases within the famile (DPT). See Table 5, family 2.

This adds some weight to ADD1 being associated with Familial Meniere disease, and so the watchlist tag has been added to this gene.; to: As noted by the expert reviewer Eldar Dedic, PMID: 30828346 - Gallego-Martinez, et al. (2019) reports a family in which two members have a rare missense variant of unknown signficance in ADD1 (chr4:2900221 A>G (grch37, rs372777117). In addition, two other rare variants in candidate genes are reported in 2 members of the same family (variant in KCNQ4) and in all cases within the family (variant in DPT). See Table 5, family 2.

This adds some weight to ADD1 being associated with Familial Meniere disease, and so the watchlist tag has been added to this gene.
Familial Meniere Disease v1.1 ADD1 Eleanor Williams reviewed gene: ADD1: Rating: ; Mode of pathogenicity: None; Publications: 30828346; Phenotypes: ; Mode of inheritance: None
Familial Meniere Disease v1.1 ADD1 Eleanor Williams Tag watchlist tag was added to gene: ADD1.
Proteinuric renal disease v2.58 LCAT Eleanor Williams Classified gene: LCAT as Amber List (moderate evidence)
Proteinuric renal disease v2.58 LCAT Eleanor Williams Added comment: Comment on list classification: Leaving rating as amber for now, but with a green rating recommendation following GMS review. There are several reported cases where proteinuria is a prominent feature, plus a green expert review reporting a case of a family presenting with proteinuric kidney disease
Proteinuric renal disease v2.58 LCAT Eleanor Williams Gene: lcat has been classified as Amber List (Moderate Evidence).
Proteinuric renal disease v2.57 LCAT Eleanor Williams Phenotypes for gene: LCAT were changed from Norum disease #245900 to Norum disease, OMIM:245900; Norum disease, MONDO:0009515; LCAT DEFICIENCY
Proteinuric renal disease v2.56 LCAT Eleanor Williams Publications for gene: LCAT were set to 6078131
Proteinuric renal disease v2.55 LCAT Eleanor Williams edited their review of gene: LCAT: Changed publications to: 21315357, 30201532, 29535099, 22108153, 28508023, 25657982, 9884427
Proteinuric renal disease v2.55 LCAT Eleanor Williams Tag Q4_21_rating tag was added to gene: LCAT.
Proteinuric renal disease v2.55 LCAT Eleanor Williams edited their review of gene: LCAT: Added comment: Several cases in which proteinuria was noted in patients with LCAT deficiency are reported, including:

PMID: 21315357 - Holleboom et al 2011 - report 3 siblings (age 17, 12 and 3 years) in a family with HDL deficency. The 17-year-old was referred for renal pathology compatible with a metabolic disorder, including FLD. Corneal opacification and proteinuria were observed in all three and they were found to be homozygous for a missense variant in LCAT which disrupted the second disulfide. LCAT protein and activity were undetectable in the patients' plasma. The parents and an unaffected brother were heterozygous for the variant.

PMID: 30201532 - Hanna et al 2018 - report a 29-year-old female who initially presented with discomfort, photophobia, and decreased vision in both eyes. Bilateral corneal clouding, severely reduced HDL cholesterol, and proteinuria were noted. Two heterozygous mutations of the LCAT gene were identified: c.321C>A (p.Tyr107 *) and c.1034C>T (p.Thr345Met)

PMID: 29535099 - Morales et al 2018 - report 44-year-old woman diagnosed with corneal dystrophy and anaemia. Analysis showed proteinuria between 1 and 2 g/day. A missense homozygous variant in the LCAT gene c.368G>C (p (R123p)) was identified.

PMID: 22108153 - Roshan et al 2011 - report a 50-year-old man with uncontrolled hypertension, hemolytic anemia, and renal insufficiency. He had a long history of proteinuria (3+ for at least 30 years). He was found to have diffuse marked corneal opacification. Sequencing the LCAT gene showed a homozygous missense mutation. His parents were first cousins.


Cases presenting with proteinuria with a LCAT deficiency diagnosis but no molecular analyses:

PMID: 28508023 - Balwani et al 2016 - a patient with nephrotic syndrome, which renal biopsy revealed classic features of LCAT deficiency. There was no obvious family history and the patient was without any corneal deposits and normal HDL-C levels. NOTE NO MOLECULAR DIAGNOSIS.

PMID: 25657982 - Mahdi Althaf et al 2015 - 30-year-old male was referred for persistent proteinuria. Bilateral corneal ring opacities were noted. Renal biopsy findings were consistent with LCAT deficiency.; Changed phenotypes to: Norum disease, OMIM:245900, Norum disease, MONDO:0009515, LCAT DEFICIENCY
Fetal anomalies v1.720 TMEM260 Alistair Pagnamenta reviewed gene: TMEM260: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 28318500, 34612517; Phenotypes: ventricular septal defects, truncus arteriosus, elevated creatinine levels; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Monogenic hearing loss v2.191 USP48 Eleanor Williams Tag watchlist was removed from gene: USP48.
Tag Q4_21_rating tag was added to gene: USP48.
Monogenic hearing loss v2.191 USP48 Eleanor Williams Classified gene: USP48 as Amber List (moderate evidence)
Monogenic hearing loss v2.191 USP48 Eleanor Williams Added comment: Comment on list classification: Promoting from red to amber, with a recommendation for green rating following GMS review. 3 cases, 1 with segregation data (incomplete penetrance), plus supportive zebrafish model.
Monogenic hearing loss v2.191 USP48 Eleanor Williams Gene: usp48 has been classified as Amber List (Moderate Evidence).
Monogenic hearing loss v2.190 USP48 Eleanor Williams Phenotypes for gene: USP48 were changed from non-syndromic hearing loss to non-syndromic hearing loss; nonsyndromic genetic deafness, MONDO:0019497
Monogenic hearing loss v2.189 USP48 Eleanor Williams Publications for gene: USP48 were set to
Monogenic hearing loss v2.188 USP48 Eleanor Williams Mode of inheritance for gene: USP48 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Monogenic hearing loss v2.187 USP48 Eleanor Williams edited their review of gene: USP48: Added comment: PMID: 34059922 - Bassani et al 2021 - 3 cases reported with variants in USP48 and non syndromic hearing loss. They first analysed 4-generation Italian family with 6 individuals with hearing loss. The only rare variant segregating with the disease was a missense variant in USP48 (NM_032234.7:c.1216G > A, NP_115612.4:p.(Gly406Arg)). The variant is present in GnomAD v2.1.1 with a minor allele frequency (MAF) of 6.7 × 10−5 (17 allele out of 251 304 with no homozygotes). They also observed one hearing individual in the family who was heterozygous for the variant, suggesting incomplete penetrance.
In a Dutch family the found by exome sequencing a missense variant in USP48 (NM_032236.7:c.2215_2216delinsTT, NP_115612.4:p.(Thr739Leu)). The probands mother and uncle were also affected by no sequence data was available for analysis.
In a French family a proband is reported with right profound sensorineural hearing impairment (at 12 months), but normal left hearing (at 6 years old). The patient is heterozygote for a de novo splice variant in USP48 (NM_032236.7:c.3058 + 2 T > C, NP_115612.4:p.?;) which is not found in GnomAD and is predicted to result in a frameshift resulting in either NMD or a truncated protein.
In functional experiments they showed that the two missense variants found in the Italian and Dutch families, and a shortened protein as predicted for the variant found in the French variant, showed an impaired ability to cleave tetra-ubiquitin into tri-, di- and mono-ubiquitin. Using immunohistology, they show that the human USP48 protein is present in fetal inner ear specimens.
In addition zebrafish lacking usp48 showed a significant decrease of auditory response in acoustic startle response assays at 600 and 800 Hz wavelengths.; Changed rating: GREEN; Changed publications to: 34059922; Changed phenotypes to: nonsyndromic genetic deafness, MONDO:0019497; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.18 MARS Eleanor Williams gene: MARS was added
gene: MARS was added to Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome. Sources: Literature
new-gene-name tags were added to gene: MARS.
Mode of inheritance for gene: MARS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MARS were set to 33909043
Phenotypes for gene: MARS were set to trichothiodystrophy, MONDO:0018053
Review for gene: MARS was set to RED
Added comment: PMID: 33909043 - Botta et al 2021 - using WES/WGS analysis of 34 unsolved cases with multi-system phenotypes, but with hair alterations that are typical of trichothiodystrophy but no reported photosensitivity, they identified a homozygous variant in one Italian patient (c.1201G > A (p.Val401Me) that is very rare (gnomAD frequency 0.00001414). Functional studies suggest that the variant affects gene product stability.
Sources: Literature
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.17 AARS Eleanor Williams Classified gene: AARS as Amber List (moderate evidence)
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.17 AARS Eleanor Williams Added comment: Comment on list classification: Promoting to amber as 2 cases with plausible disease causing variants in the AARS gene reported.
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.17 AARS Eleanor Williams Gene: aars has been classified as Amber List (Moderate Evidence).
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.16 AARS Eleanor Williams gene: AARS was added
gene: AARS was added to Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome. Sources: Literature
new-gene-name tags were added to gene: AARS.
Mode of inheritance for gene: AARS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: AARS were set to 33909043
Phenotypes for gene: AARS were set to trichothiodystrophy, MONDO:0018053
Review for gene: AARS was set to AMBER
Added comment: PMID: 33909043 - Botta et al 2021 - using WES or WGS analysis of 34 unsolved cases with multi-system phenotypes, but with hair alterations that are typical of trichothiodystrophy but no reported photosensitivity, they identified 2 unrelated cases carrying 4 potentially pathogenic variants in the AARS1 gene (previously known as AARSB. Both patients had very rare compound heterozygous missense variants. In one family there was an older affected sibling but segregation data was not available for either family.
Sources: Literature
Severe microcephaly v2.257 ZNF668 Ivone Leong Entity copied from Intellectual disability v3.1332
Severe microcephaly v2.257 ZNF668 Ivone Leong gene: ZNF668 was added
gene: ZNF668 was added to Severe microcephaly. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: ZNF668.
Mode of inheritance for gene: ZNF668 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ZNF668 were set to 34313816; 26633546
Phenotypes for gene: ZNF668 were set to DNA damage repair defect; microcephaly; growth deficiency; severe global developmental delay; brain malformation; facial dysmorphism
Intellectual disability v3.1332 ZNF668 Ivone Leong Tag watchlist tag was added to gene: ZNF668.
Intellectual disability v3.1332 ZNF668 Ivone Leong Classified gene: ZNF668 as Amber List (moderate evidence)
Intellectual disability v3.1332 ZNF668 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). There is currently no phenotypes associated with this gene in OMIM or Gene2Phenotype. As there are only 2 cases there is currently not enough evidence to support a gene-disease association. Therefore, this gene has been given an Amber rating.
Intellectual disability v3.1332 ZNF668 Ivone Leong Gene: znf668 has been classified as Amber List (Moderate Evidence).
Bilateral congenital or childhood onset cataracts v2.85 UBE2U Ivone Leong Entity copied from Intellectual disability v3.1331
Bilateral congenital or childhood onset cataracts v2.85 UBE2U Ivone Leong gene: UBE2U was added
gene: UBE2U was added to Cataracts. Sources: Expert Review Red,Literature
Mode of inheritance for gene: UBE2U was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: UBE2U were set to 33776059
Phenotypes for gene: UBE2U were set to Retinoschisis, MONDO:0004579; cataracts; learning disability, MONDO:0004681; developmental delay
Intellectual disability v3.1331 UBE2U Ivone Leong Classified gene: UBE2U as Red List (low evidence)
Intellectual disability v3.1331 UBE2U Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a disease in Gene2Phenotype (there is currently no entry for this gene in OMIM). As there is currently only 1 case this gene has been given a Red rating.
Intellectual disability v3.1331 UBE2U Ivone Leong Gene: ube2u has been classified as Red List (Low Evidence).
Intellectual disability v3.1330 UBE2U Ivone Leong Phenotypes for gene: UBE2U were changed from Retinoschisis; cataracts; learning disabilities; developmental delay to Retinoschisis, MONDO:0004579; cataracts; learning disability, MONDO:0004681; developmental delay
Paediatric or syndromic cardiomyopathy v1.56 RNF220 Ivone Leong Phenotypes for gene: RNF220 were changed from Intellectual disability, MONDO:0001071 to Dilated cardiomyopathy,MONDO:0005021
Monogenic hearing loss v2.187 RNF220 Ivone Leong Phenotypes for gene: RNF220 were changed from Intellectual disability, MONDO:0001071 to Sensorineural hearing impairment, HP:0000407
Ataxia and cerebellar anomalies - narrow panel v2.236 RNF220 Ivone Leong Phenotypes for gene: RNF220 were changed from Intellectual disability, MONDO:0001071 to Ataxia, HP:0001251
Paediatric or syndromic cardiomyopathy v1.55 RNF220 Ivone Leong Tag Q4_21_rating tag was added to gene: RNF220.
Paediatric or syndromic cardiomyopathy v1.55 RNF220 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association; however, the ID severity in these patients do not meet the criteria (moderate to severe) for this panel (patients show mild (mostly) to moderate severity). Therefore, this gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association. Therefore, this gene should be Green at the next review.
Monogenic hearing loss v2.186 RNF220 Ivone Leong Tag Q4_21_rating tag was added to gene: RNF220.
Monogenic hearing loss v2.186 RNF220 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association; however, the ID severity in these patients do not meet the criteria (moderate to severe) for this panel (patients show mild (mostly) to moderate severity). Therefore, this gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association. Therefore, this gene should be Green at the next review.
Ataxia and cerebellar anomalies - narrow panel v2.235 RNF220 Ivone Leong Tag Q4_21_rating tag was added to gene: RNF220.
Ataxia and cerebellar anomalies - narrow panel v2.235 RNF220 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association; however, the ID severity in these patients do not meet the criteria (moderate to severe) for this panel (patients show mild (mostly) to moderate severity). Therefore, this gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association. Therefore, this gene should be Green at the next review.
White matter disorders and cerebral calcification - narrow panel v1.203 RNF220 Ivone Leong Phenotypes for gene: RNF220 were changed from Leukodystrophy; CNS hypomyelination; Ataxia; Intellectual disability; Sensorineural hearing impairment; Elevated hepatic transaminases; Hepatic fibrosis; Dilated cardiomyopathy; Spastic paraplegia; Dysarthria; Abnormality of the corpus callosum to Leukodystrophy, MONDO:0019046; Abnormal corpus callosum morphology, HP:0001273
White matter disorders and cerebral calcification - narrow panel v1.202 RNF220 Ivone Leong Tag Q4_21_rating tag was added to gene: RNF220.
White matter disorders and cerebral calcification - narrow panel v1.202 RNF220 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association; however, the ID severity in these patients do not meet the criteria (moderate to severe) for this panel (patients show mild (mostly) to moderate severity). Therefore, this gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association. Therefore, this gene should be Green at the next review.
Paediatric or syndromic cardiomyopathy v1.55 RNF220 Ivone Leong Entity copied from Intellectual disability v3.1329
Paediatric or syndromic cardiomyopathy v1.55 RNF220 Ivone Leong gene: RNF220 was added
gene: RNF220 was added to Cardiomyopathies - including childhood onset. Sources: Literature,Expert Review Amber,Other
Mode of inheritance for gene: RNF220 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF220 were set to 33964137; 10881263
Phenotypes for gene: RNF220 were set to Intellectual disability, MONDO:0001071
Penetrance for gene: RNF220 were set to Complete
Monogenic hearing loss v2.186 RNF220 Ivone Leong Entity copied from Intellectual disability v3.1329
Monogenic hearing loss v2.186 RNF220 Ivone Leong gene: RNF220 was added
gene: RNF220 was added to Hearing loss. Sources: Literature,Expert Review Amber,Other
Mode of inheritance for gene: RNF220 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF220 were set to 33964137; 10881263
Phenotypes for gene: RNF220 were set to Intellectual disability, MONDO:0001071
Penetrance for gene: RNF220 were set to Complete
Ataxia and cerebellar anomalies - narrow panel v2.235 RNF220 Ivone Leong Entity copied from Intellectual disability v3.1329
Ataxia and cerebellar anomalies - narrow panel v2.235 RNF220 Ivone Leong gene: RNF220 was added
gene: RNF220 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature,Expert Review Amber,Other
Mode of inheritance for gene: RNF220 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF220 were set to 33964137; 10881263
Phenotypes for gene: RNF220 were set to Intellectual disability, MONDO:0001071
Penetrance for gene: RNF220 were set to Complete
Intellectual disability v3.1329 RNF220 Ivone Leong Phenotypes for gene: RNF220 were changed from Leukodystrophy; CNS hypomyelination; Ataxia; Intellectual disability; Sensorineural hearing impairment; Elevated hepatic transaminases; Hepatic fibrosis; Dilated cardiomyopathy; Spastic paraplegia; Dysarthria; Abnormality of the corpus callosum to Intellectual disability, MONDO:0001071
White matter disorders and cerebral calcification - narrow panel v1.202 RNF220 Ivone Leong Entity copied from Intellectual disability v3.1328
White matter disorders and cerebral calcification - narrow panel v1.202 RNF220 Ivone Leong gene: RNF220 was added
gene: RNF220 was added to White matter disorders and cerebral calcification - narrow panel. Sources: Other,Expert Review Amber,Literature
Mode of inheritance for gene: RNF220 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF220 were set to 33964137; 10881263
Phenotypes for gene: RNF220 were set to Leukodystrophy; CNS hypomyelination; Ataxia; Intellectual disability; Sensorineural hearing impairment; Elevated hepatic transaminases; Hepatic fibrosis; Dilated cardiomyopathy; Spastic paraplegia; Dysarthria; Abnormality of the corpus callosum
Penetrance for gene: RNF220 were set to Complete
Intellectual disability v3.1328 RNF220 Ivone Leong Classified gene: RNF220 as Amber List (moderate evidence)
Intellectual disability v3.1328 RNF220 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There are >3 cases for this gene; however, 3 of the cases described in PMID:33964137 are of Roma descent and haplotype analysis has shown that the variant found in these families are due to a founder effect (c.1094G>A, p.Arg365Gly). A separate Roma family also has the same variant (c.1094G>A, p.Arg365Gly). An Italian family with similar phenotypes has a different variant (c.1088G>A, p.Arg363Gly). The authors also report on in vitro and in vivo studies.

There is enough evidence to support a gene-disease association; however, the ID severity in these patients do not meet the criteria (moderate to severe) for this panel (patients show mild (mostly) to moderate severity). Therefore, this gene has been given an Amber rating.
Intellectual disability v3.1328 RNF220 Ivone Leong Gene: rnf220 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1327 TCF7L2 Ivone Leong Tag Q4_21_rating tag was added to gene: TCF7L2.
Intellectual disability v3.1327 TCF7L2 Ivone Leong edited their review of gene: TCF7L2: Added comment: This gene is now associated with a relevant phenotype in Gene2Phenotype (confirmed). There is now enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; Changed rating: GREEN
Intellectual disability v3.1327 TCF7L2 Ivone Leong Phenotypes for gene: TCF7L2 were changed from Developmental disorders to Developmental disorders; Global developmental delay; Intellectual disability; Autism; Attention deficit hyperactivity disorder; Myopia; Abnormality of skeletal system
Intellectual disability v3.1326 TCF7L2 Ivone Leong Publications for gene: TCF7L2 were set to 33057194
Intellectual disability v3.1325 PLXNA2 Ivone Leong Classified gene: PLXNA2 as Amber List (moderate evidence)
Intellectual disability v3.1325 PLXNA2 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there are currently only 2 cases there is not enough evidence to support a gene-disease association. Therefore, this gene has been given an Amber rating.
Intellectual disability v3.1325 PLXNA2 Ivone Leong Gene: plxna2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1324 PLXNA2 Ivone Leong Phenotypes for gene: PLXNA2 were changed from Intellectual disability; Abnormality of the face; Failure to thrive; Abnormal heart morphology to Intellectual disability, MONDO:0001071; Abnormality of the face; Failure to thrive; Abnormal heart morphology
Intellectual disability v3.1323 PLXNA2 Ivone Leong Tag watchlist tag was added to gene: PLXNA2.
Rhabdomyolysis and metabolic muscle disorders v1.57 CAV3 Ivone Leong Publications for gene: CAV3 were set to
Rhabdomyolysis and metabolic muscle disorders v1.56 CAV3 Ivone Leong Tag Q3_21_MOI tag was added to gene: CAV3.
Rhabdomyolysis and metabolic muscle disorders v1.56 CAV3 Ivone Leong edited their review of gene: CAV3: Added comment: MOI should be changed from "BOTH monoallelic and biallelic, autosomal or pseudoautosomal" to "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown".

PMID: 9536092, reported one patient with homozygous G56S. The patient was the only member of the family to be affected by disease (proximal muscle weakness in the first decade of life). The variant was not found in 200 controls. The patient's skeletal muscle biopsy looked normal and expression of dystrophin, sarcoglycans and caveolin-3 was normal. This variant was later reclassified as a VUS as PMID:11251997 identified 2 Brazilian patients with LGMD with heterozygous G55S. Both patients had onset in adulthood, calf hypertrophy, elevated creatine kinase, and difficulty walking. Muscle protein analyses from both patients were normal. Screening 200 normal controls showed 4 controls also had this variant.
In OMIM: "Hamosh (2018) found that the G55S variant was present in heterozygous state in 3,142 of 277,064 alleles and in 184 homozygotes in the gnomAD database (January 24, 2018), calling into question the pathogenicity of the variant."

PMID: 12666119, reported an Italian patient with severe rippling muscle disease (A92T) who was AR. Actually A93T.

PMID: 15668980, the same authors of PMID: 12666119 reported 1 family with 2 affected sibs who have AR rippling muscle disease (same variant as above A92T). Unaffected parents were both heterozygous for the variant. The authors note that the parents were not known to be consanguineous but they are from the same small village in Germany. The authors also did a haplotype analysis and showed that this variant arose separately from the Italian case, suggesting that A92 might be a mutation hot spot. According to ClinVar, this variant has conflicting interpretations of pathogenicity (https://www.ncbi.nlm.nih.gov/clinvar/variation/8285/).

PMID: 16730439, reports on 1 patient (AR) with mild proximal muscle weakness of the lower limbs. No other family members were available for further analysis. Patient is homozygous for a splice variant (IVS1+2T>C).

While there are cases of biallelic variants causing disease there are currently no new cases reporting of this (newest report was in 2006). There is currently not enough evidence to support biallelic cause of disease, I suggest changing the MOI to Monoallelic until more evidence is available.; Changed publications to: 15668980, 12666119, 9536092, 11251997, 16730439; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.29 CAV3 Ivone Leong commented on gene: CAV3
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.29 CAV3 Ivone Leong Deleted their review
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.29 CAV3 Ivone Leong Tag Q3_21_MOI was removed from gene: CAV3.
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.29 CAV3 Ivone Leong Deleted their comment
Hereditary neuropathy or pain disorder v1.63 AIFM1 Arina Puzriakova commented on gene: AIFM1
Intellectual disability v3.1323 AIFM1 Arina Puzriakova Phenotypes for gene: AIFM1 were changed from Combined oxidative phosphorylation deficiency 6, 300816Cowchock syndrome, 310490; COWCHOCK SYNDROME to Cowchock syndrome, OMIM:310490; Combined oxidative phosphorylation deficiency 6, OMIM:300816; Spondyloepimetaphyseal dysplasia, X-linked, with hypomyelinating leukodystrophy, OMIM:300232
Hereditary neuropathy v1.416 AIFM1 Arina Puzriakova Phenotypes for gene: AIFM1 were changed from Cowchock syndrome; Combined oxidative phosphorylation deficiency 6 to Cowchock syndrome, OMIM:310490; Combined oxidative phosphorylation deficiency 6, OMIM:300816
Hereditary neuropathy or pain disorder v1.63 AIFM1 Arina Puzriakova Phenotypes for gene: AIFM1 were changed from Combined oxidative phosphorylation deficiency 6; Cowchock syndrome to Cowchock syndrome, OMIM:310490; Combined oxidative phosphorylation deficiency 6, OMIM:300816
Hereditary neuropathy or pain disorder v1.62 ABCA1 Arina Puzriakova commented on gene: ABCA1
Adult onset dystonia, chorea or related movement disorder v1.123 GBA Arina Puzriakova changed review comment from: GBA included on this panel to capture association with Parkinson disease (PD). However, GBA is only a risk factor and variants do not cause highly penetrant forms of PD. For these reasons, GBA was given an Amber rating on the 'Neurodegenerative disorders - adult onset' (R58) panel (https://panelapp.genomicsengland.co.uk/panels/474/gene/GBA/). Furthermore, issues regarding interpretation a GBA variant in the context of PD have been highlighted in the 100K (see Alison Callaway review on 100K PD panel - https://panelapp.genomicsengland.co.uk/panels/39/gene/GBA/). Given the potential carrier implications, inclusion of this gene will be flagged for review at the next GMS panel update.; to: GBA included on this panel to capture association with Parkinson disease (PD). However, variants do not cause highly penetrant forms of PD and for these reasons, GBA was given an Amber rating on the 'Neurodegenerative disorders - adult onset' (R58) panel (https://panelapp.genomicsengland.co.uk/panels/474/gene/GBA/). Furthermore, issues regarding interpretation a GBA variant in the context of PD have been highlighted in the 100K (see Alison Callaway review on 100K PD panel - https://panelapp.genomicsengland.co.uk/panels/39/gene/GBA/). Given that GBA is only a PD risk factor and the potential carrier implications, inclusion of this gene will be flagged for review at the next GMS panel update.
Adult onset dystonia, chorea or related movement disorder v1.123 GBA Arina Puzriakova commented on gene: GBA
Adult onset dystonia, chorea or related movement disorder v1.123 GBA Arina Puzriakova Tag Q4_21_MOI was removed from gene: GBA.
Adult onset dystonia, chorea or related movement disorder v1.123 GBA Arina Puzriakova Tag Q4_21_expert_review tag was added to gene: GBA.
Tag Q4_21_MOI tag was added to gene: GBA.
Retinal disorders v2.216 MED12 Eleanor Williams Tag Q3_21_MOI tag was added to gene: MED12.
Early onset or syndromic epilepsy v2.434 MED12 Eleanor Williams Tag Q3_21_MOI tag was added to gene: MED12.
Tag Q3_21_expert_review tag was added to gene: MED12.
Early onset or syndromic epilepsy v2.434 MED12 Eleanor Williams changed review comment from: Review of mode of inheritance shows that although in some families only males were affected, in 5 cases females with seizures as part of the phenotype were reported who had MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.; to: Review of mode of inheritance shows that although in some families only males were affected, in 5 cases females with seizures as part of the phenotype were reported who had MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct although consideration should be given to the carrier implications for the predominantly male-only phenotypes associated with this gene.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.
Clefting v2.50 MED12 Eleanor Williams Tag Q3_21_MOI tag was added to gene: MED12.
Fetal anomalies v1.720 MED12 Eleanor Williams changed review comment from: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome (Li et al 2021, PMID: 33244166). The phenotype includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation.

In addition Polla et al 2021 (PMID: 33244165) and Riccardi et al 2021 (PMID: 34079076) report 22 females in total with de novo variants in MED12. Some physical features such as syndactyly (10/22) and anteriorly placed anus (4/22) are noted. 12/22 have severe intellectual disability.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the predominantly male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases. ; to: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome (Li et al 2021, PMID: 33244166). The phenotype includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation.

In addition Polla et al 2021 (PMID: 33244165) and Riccardi et al 2021 (PMID: 34079076) report 22 females in total with de novo variants in MED12. Some physical features such as syndactyly (10/22) and anteriorly placed anus (4/22) are noted. 12/22 have severe intellectual disability.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the predominantly male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases, therefore waiting for GMS review before considering changing the mode of inheritance.
Non-syndromic familial congenital anorectal malformations v1.7 MED12 Eleanor Williams Added comment: Comment on mode of inheritance: Leaving the mode of inheritance as biallelic in females just now but noting that a few female cases have been reported, mainly with skewed x-chromosome inactivation.
Non-syndromic familial congenital anorectal malformations v1.7 MED12 Eleanor Williams Mode of inheritance for gene: MED12 was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Non-syndromic familial congenital anorectal malformations v1.6 MED12 Eleanor Williams changed review comment from: De novo variants in this gene gene have also been linked to disease in females (many of who show skewed X inactivation):

PMID: 33244166 - Li et al 2021 - report 7 females with Hardikar syndrome each of whom have had a nonsense or frameshift MED12 variant identified by exome sequencing. All five tested patients showed evidence of skewed x chromosome inactivation. 1 patient had imperforate anus and constipation.

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 3/22 have anteriorly placed anus and 1 additionally presented with anal stenosis . Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. Two patients had chronic constipation, one of whom also presented an anteriorly placed anus.; to: De novo variants in this gene gene have also been linked to disease in females (many of who show skewed X inactivation):

PMID: 33244166 - Li et al 2021 - report 7 females with Hardikar syndrome each of whom have had a nonsense or frameshift MED12 variant identified by exome sequencing. All five tested patients showed evidence of skewed x chromosome inactivation. 1 patient had imperforate anus and constipation.

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 3/22 have anteriorly placed anus and one of the three additionally presented with anal stenosis . Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. Two patients had chronic constipation, one of whom also presented an anteriorly placed anus.
Familial chylomicronaemia syndrome (FCS) v1.19 APOB Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: APOB.
Tag Q3_21_expert_review tag was added to gene: APOB.
Likely inborn error of metabolism v2.187 EHHADH Arina Puzriakova Classified gene: EHHADH as Amber List (moderate evidence)
Likely inborn error of metabolism v2.187 EHHADH Arina Puzriakova Added comment: Comment on list classification: Single family reported with additional functional data which is sufficient evidence to rate as Amber, awaiting further evidence.
Likely inborn error of metabolism v2.187 EHHADH Arina Puzriakova Gene: ehhadh has been classified as Amber List (Moderate Evidence).
Likely inborn error of metabolism v2.186 EHHADH Arina Puzriakova Phenotypes for gene: EHHADH were changed from L-bifunctional protein deficiency; Metabolic acidosis; Increased amino acids in urine to ?Fanconi renotubular syndrome 3, OMIM:615605; L-bifunctional protein deficiency; Metabolic acidosis; Increased amino acids in urine
Renal tubulopathies v2.28 EHHADH Arina Puzriakova Phenotypes for gene: EHHADH were changed from metabolic acidosis, glucosuria, phosphaturia, aminoaciduria, and proteinuria; ?Fanconi renotubular syndrome 3, 605615 to ?Fanconi renotubular syndrome 3, OMIM:615605; L-bifunctional protein deficiency; Metabolic acidosis; Increased amino acids in urine
Likely inborn error of metabolism v2.185 EHHADH Arina Puzriakova Publications for gene: EHHADH were set to PMID: 33340416
Likely inborn error of metabolism v2.184 EHHADH Arina Puzriakova Mode of inheritance for gene: EHHADH was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Likely inborn error of metabolism v2.183 EHHADH Arina Puzriakova reviewed gene: EHHADH: Rating: ; Mode of pathogenicity: None; Publications: 24401050, 27160910; Phenotypes: ?Fanconi renotubular syndrome 3, OMIM:615605; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Non-syndromic familial congenital anorectal malformations v1.6 MED12 Eleanor Williams Tag Skewed X-inactivation tag was added to gene: MED12.
Non-syndromic familial congenital anorectal malformations v1.6 MED12 Eleanor Williams commented on gene: MED12: De novo variants in this gene gene have also been linked to disease in females (many of who show skewed X inactivation):

PMID: 33244166 - Li et al 2021 - report 7 females with Hardikar syndrome each of whom have had a nonsense or frameshift MED12 variant identified by exome sequencing. All five tested patients showed evidence of skewed x chromosome inactivation. 1 patient had imperforate anus and constipation.

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 3/22 have anteriorly placed anus and 1 additionally presented with anal stenosis . Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. Two patients had chronic constipation, one of whom also presented an anteriorly placed anus.
Fetal anomalies v1.720 MED12 Eleanor Williams Tag Skewed X-inactivation tag was added to gene: MED12.
Early onset or syndromic epilepsy v2.434 MED12 Eleanor Williams Tag Skewed X-inactivation tag was added to gene: MED12.
Fetal anomalies v1.720 MED12 Eleanor Williams changed review comment from: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome (the phenotype that includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation).

In addition Polla et al 2021 (PMID: 33244165) and Riccardi et al 2021 (PMID: 34079076) report 22 females in total with de novo variants in MED12. Some physical features such as syndactyly (10/22) and anteriorly placed anus (4/22) also noted. 12/22 have severe intellectual disability.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the predominantly male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases. ; to: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome (Li et al 2021, PMID: 33244166). The phenotype includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation.

In addition Polla et al 2021 (PMID: 33244165) and Riccardi et al 2021 (PMID: 34079076) report 22 females in total with de novo variants in MED12. Some physical features such as syndactyly (10/22) and anteriorly placed anus (4/22) are noted. 12/22 have severe intellectual disability.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the predominantly male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases.
Familial Meniere Disease v1.1 ADD1 Eldar Dedic reviewed gene: ADD1: Rating: RED; Mode of pathogenicity: None; Publications: PMID:30828346; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Malformations of cortical development v2.92 VPS50 Ivone Leong Entity copied from Intellectual disability v3.1322
Malformations of cortical development v2.92 VPS50 Ivone Leong gene: VPS50 was added
gene: VPS50 was added to Malformations of cortical development. Sources: Literature,Expert Review Amber
watchlist tags were added to gene: VPS50.
Mode of inheritance for gene: VPS50 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS50 were set to 34037727
Phenotypes for gene: VPS50 were set to Neonatal cholestatic liver disease; Failure to thrive; Profound global developmental delay; Postnatal microcephaly; Seizures; Abnormality of the corpus callosum
Penetrance for gene: VPS50 were set to Complete
Early onset or syndromic epilepsy v2.434 VPS50 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic coprus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic corpus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Severe microcephaly v2.256 VPS50 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic coprus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic corpus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Intellectual disability v3.1322 VPS50 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic coprus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic corpus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Cholestasis v1.88 VPS50 Ivone Leong Entity copied from Intellectual disability v3.1322
Cholestasis v1.88 VPS50 Ivone Leong gene: VPS50 was added
gene: VPS50 was added to Cholestasis. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: VPS50.
Mode of inheritance for gene: VPS50 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS50 were set to 34037727
Phenotypes for gene: VPS50 were set to Neonatal cholestatic liver disease; Failure to thrive; Profound global developmental delay; Postnatal microcephaly; Seizures; Abnormality of the corpus callosum
Penetrance for gene: VPS50 were set to Complete
Severe microcephaly v2.256 VPS50 Ivone Leong Entity copied from Intellectual disability v3.1322
Severe microcephaly v2.256 VPS50 Ivone Leong gene: VPS50 was added
gene: VPS50 was added to Severe microcephaly. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: VPS50.
Mode of inheritance for gene: VPS50 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS50 were set to 34037727
Phenotypes for gene: VPS50 were set to Neonatal cholestatic liver disease; Failure to thrive; Profound global developmental delay; Postnatal microcephaly; Seizures; Abnormality of the corpus callosum
Penetrance for gene: VPS50 were set to Complete
Early onset or syndromic epilepsy v2.434 VPS50 Ivone Leong Tag watchlist tag was added to gene: VPS50.
Intellectual disability v3.1322 VPS50 Ivone Leong Tag watchlist tag was added to gene: VPS50.
Intellectual disability v3.1322 VPS50 Ivone Leong Tag Q3_21_rating was removed from gene: VPS50.
Intellectual disability v3.1322 VPS50 Ivone Leong Tag Q3_21_rating tag was added to gene: VPS50.
Early onset or syndromic epilepsy v2.434 VPS50 Ivone Leong Classified gene: VPS50 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.434 VPS50 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic coprus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Early onset or syndromic epilepsy v2.434 VPS50 Ivone Leong Gene: vps50 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1322 VPS50 Ivone Leong Classified gene: VPS50 as Amber List (moderate evidence)
Intellectual disability v3.1322 VPS50 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID: 34037727. Both patients have severe microcephaly (-7.65 to -10.35 z-score), height at 2 years (-2.65 to -3.84 z-score), seizures, hypoplastic coprus callosum, neonatal cholestasis and feeding difficulties.

Based on the available evidence there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Intellectual disability v3.1322 VPS50 Ivone Leong Gene: vps50 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.255 ARF3 Ivone Leong Tag watchlist was removed from gene: ARF3.
Severe microcephaly v2.255 ARF3 Ivone Leong Classified gene: ARF3 as Red List (low evidence)
Severe microcephaly v2.255 ARF3 Ivone Leong Added comment: Comment on list classification: Demoted from Amber to Red as per my review.
Severe microcephaly v2.255 ARF3 Ivone Leong Gene: arf3 has been classified as Red List (Low Evidence).
Severe microcephaly v2.254 ARF3 Ivone Leong changed review comment from: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID:34346499, individual 1 also has severe microcephaly (-3.3SD), spasticity, cerebellum atrophy and brainstem atrophy. Individual 2 does not have microcephaly, but has cerebellar hypoplasia.

Based on the available evidence, there is currently not enough evidence to support a gene-disease association, therefore this gene has been given an Amber rating.; to: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID:34346499, individual 1 also has severe microcephaly (-3.3SD), spasticity, cerebellum atrophy and brainstem atrophy. Individual 2 does not have microcephaly, but has cerebellar hypoplasia.

As only 1 patient has severe microcephaly. This gene has been given a Red rating.
Severe microcephaly v2.254 ARF3 Ivone Leong Entity copied from Intellectual disability v3.1321
Severe microcephaly v2.254 ARF3 Ivone Leong gene: ARF3 was added
gene: ARF3 was added to Severe microcephaly. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: ARF3.
Mode of inheritance for gene: ARF3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ARF3 were set to 34346499
Phenotypes for gene: ARF3 were set to Global developmental delay; Intellectual disability, MONDO:0001071; Seizures; Morphological abnormality of the central nervous system; microcephaly, MONDO:0001149
Penetrance for gene: ARF3 were set to unknown
Early onset or syndromic epilepsy v2.433 ARF3 Ivone Leong Classified gene: ARF3 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.433 ARF3 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. PMID:34346499, individual 1 also has severe microcephaly (-3.3SD), spasticity, cerebellum atrophy and brainstem atrophy. Individual 2 does not have microcephaly, but has cerebellar hypoplasia. Based on the available evidence, there is currently not enough evidence to support a gene-disease association, therefore this gene has been given an Amber rating.
Early onset or syndromic epilepsy v2.433 ARF3 Ivone Leong Gene: arf3 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.432 ARF3 Ivone Leong Phenotypes for gene: ARF3 were changed from Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system to Global developmental delay; Intellectual disability, MONDO:0001071; Seizures; Morphological abnormality of the central nervous system; microcephaly, MONDO:0001149
Intellectual disability v3.1321 ARF3 Ivone Leong Tag watchlist tag was added to gene: ARF3.
Early onset or syndromic epilepsy v2.431 ARF3 Ivone Leong Tag watchlist tag was added to gene: ARF3.
Intellectual disability v3.1321 ARF3 Ivone Leong Classified gene: ARF3 as Amber List (moderate evidence)
Intellectual disability v3.1321 ARF3 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID:34346499, individual 1 also has severe microcephaly (-3.3SD), spasticity, cerebellum atrophy and brainstem atrophy. Individual 2 does not have microcephaly, but has cerebellar hypoplasia.

Based on the available evidence, there is currently not enough evidence to support a gene-disease association, therefore this gene has been given an Amber rating.
Intellectual disability v3.1321 ARF3 Ivone Leong Gene: arf3 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1320 ARF3 Ivone Leong Phenotypes for gene: ARF3 were changed from Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system to Global developmental delay; Intellectual disability, MONDO:0001071; Seizures; Morphological abnormality of the central nervous system; microcephaly, MONDO:0001149
Rare anaemia v1.27 RPS27 Arina Puzriakova commented on gene: RPS27
Rare anaemia v1.27 RPS27 Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: RPS27.
Haematological malignancies for rare disease v1.5 RPS27 Arina Puzriakova Phenotypes for gene: RPS27 were changed from Class: BM failure syndrome (typ AR); Diamond Blackfan Anemia; MDS, AML; Osteosarcoma, soft tissue sarcomas to ?Diamond-Blackfan anemia 17, OMIM:617409; Class: BM failure syndrome (typ AR); MDS, AML; Osteosarcoma, soft tissue sarcomas
Haematological malignancies cancer susceptibility v2.19 RPS27 Arina Puzriakova Phenotypes for gene: RPS27 were changed from Class: BM failure syndrome (typ AR); Diamond Blackfan Anemia; MDS, AML; Osteosarcoma, soft tissue sarcomas to ?Diamond-Blackfan anemia 17, OMIM:617409; Class: BM failure syndrome (typ AR); MDS, AML; Osteosarcoma, soft tissue sarcomas
Cytopenia - NOT Fanconi anaemia v1.43 RPS27 Arina Puzriakova Phenotypes for gene: RPS27 were changed from Diamond-Blackfan anemia; ?Diamond-Blackfan anemia 17, 617409 to ?Diamond-Blackfan anemia 17, OMIM:617409
Cytopenias and congenital anaemias v1.88 RPS27 Arina Puzriakova Phenotypes for gene: RPS27 were changed from Diamond-Blackfan anemia; ?Diamond-Blackfan anemia 17, 617409 to ?Diamond-Blackfan anemia 17, OMIM:617409
Rare anaemia v1.27 RPS27 Arina Puzriakova Phenotypes for gene: RPS27 were changed from Diamond-Blackfan anemia; ?Diamond-Blackfan anemia 17, 617409; 617409 ?Diamond-Blackfan anemia 17, to ?Diamond-Blackfan anemia 17, OMIM:617409
Arthrogryposis v3.122 MED12 Eleanor Williams reviewed gene: MED12: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Early onset or syndromic epilepsy v2.431 MED12 Eleanor Williams changed review comment from: Review of mode of inheritance shows that although in some families only males were affected, females were also reported in 5 cases seizures with MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.; to: Review of mode of inheritance shows that although in some families only males were affected, in 5 cases females with seizures as part of the phenotype were reported who had MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.
Early onset or syndromic epilepsy v2.431 MED12 Eleanor Williams changed review comment from: Review of mode of inheritance shows that although in some families only males were affected, females were also reported in 5 cases with MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.; to: Review of mode of inheritance shows that although in some families only males were affected, females were also reported in 5 cases seizures with MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.
Early onset or syndromic epilepsy v2.431 MED12 Eleanor Williams changed review comment from: Review of mode of inheritance shows that although in some families only males were affected, females were also reported in 5 cases with MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.; to: Review of mode of inheritance shows that although in some families only males were affected, females were also reported in 5 cases with MED12 variants therefore a mode of inheritance of X-LINKED: hemizygous mutation in males, monoallelic mutations in females appears correct.

Reports of males only affected:
PMID: 17369503 - Schwartz et al 2007 - report 2 kindreds with males (7 total) affected with Lujan-Fryns syndrome and variants in MED12. Seizures were noted in 1 individual from 1 kindred.

PMID: 23395478 - Vulto-van Silfhout et al 2013 - report 3 unrelated cases with males affected by Ohdo syndrome MKB type. In 2 families 2 males were affected, in the third 1 male. In all, missense changes in MED12 were detected. In family 2 a second segregating missense variant in the ATRX gene (linked to ATRX syndrome) but further investigation did not support a ATRX syndrome diagnosis. Intellectual disability was noted (1 mild, 1 moderate, 2 severe, 1 severity not noted) in all 5 individuals. Seizures were noted in 1.

PMID: 32715471 - Rubin et al 2020 - report 1 family with three male siblings of with intellectual disability and characteristic facial and distal extremity anomalies with a novel missense variant in MED12. The diagnosis most closely matched Ohdo syndrome. Seizures are not reported.

PMID: 17334363 - Risheg et al 2007 - report 6 families in with Opitz-Kaveggia syndrome (also known as FG syndrome) in with the same 2881C>T variant identified in MED12. Two of the families are stated to be from different ethnic groups. In all families only males were affected. Intellectual disability was present in all affected males (4 families) who survived long enough for developmental or cognitive assessment. Seizures were noted in 3 of the families (4/7 individuals). Marked skewed X inactivation was noted in female carriers in 3 families, moderate skewing in 1 family and absence of skewing in two families.

Reports with females affected:

PMID: 33244165 - Polla et al 2021 - report on assembled clinical and genetic data of 18 females with de novo variants in MED12. 11/18 have severe intellectual disability. Seizures were noted in 5.
Analysis of X-inactivation status showed extreme skewing (>95%) in 10 indivduals, skewing (85%) in 1 individual and it was random XCI in 6 (3 with protein truncating variants, 3 with missense). The androgen receptor alleles were non-informative for 1 person.

PMID: 34079076 - Riccardi et al 2021 - report an additional 4 female patients that carry de novo missense variants in MED12. All four patients had an intellectual disability, though it was severe only in one case. No seizures were noted.
Likely inborn error of metabolism v2.183 ACAT2 Arina Puzriakova Publications for gene: ACAT2 were set to PMID:33340416
Likely inborn error of metabolism v2.182 ACAT2 Arina Puzriakova Phenotypes for gene: ACAT2 were changed from Developmental delay to ?ACAT2 deficiency, OMIM:614055; Increased serum lactate and pyruvate; High levels of ketones; Low levels of cytosolic acetoacetyl-CoA thiolase; Hypotonia; Severe developmental delay
Mitochondrial disorders v2.54 ACAT2 Arina Puzriakova Phenotypes for gene: ACAT2 were changed from Increased serum lactate and pyruvate; high levels of ketones to ?ACAT2 deficiency, OMIM:614055; Increased serum lactate and pyruvate; High levels of ketones; Low levels of cytosolic acetoacetyl-CoA thiolase; Hypotonia; Severe developmental delay
Mitochondrial disorders v2.53 ACAT2 Arina Puzriakova Mode of inheritance for gene: ACAT2 was changed from Other to Unknown
Likely inborn error of metabolism v2.181 ACAT2 Arina Puzriakova Classified gene: ACAT2 as Red List (low evidence)
Likely inborn error of metabolism v2.181 ACAT2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Andžela Lazdāne. Currently associated with a provisional phenotype in OMIM (?ACAT2 deficiency, OMIM:614055) and not yet listed in G2P. In the 2 cases reported to date (PMIDs: 20597, 6150136), diagnoses were made based on molecular rather than genetic findings. Rating Red as at present there is no published evidence of deleterious variants in the ACAT2 gene leading to this phenotype.
Likely inborn error of metabolism v2.181 ACAT2 Arina Puzriakova Gene: acat2 has been classified as Red List (Low Evidence).
Mitochondrial disorders v2.52 ACAT2 Arina Puzriakova Classified gene: ACAT2 as Red List (low evidence)
Mitochondrial disorders v2.52 ACAT2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Andžela Lazdāne. Currently associated with a provisional phenotype in OMIM (?ACAT2 deficiency, OMIM:614055) and not yet listed in G2P. In the 2 cases reported to date (PMIDs: 20597, 6150136), diagnoses were made based on molecular rather than genetic findings. Rating Red as at present there is no published evidence of deleterious variants in the ACAT2 gene leading to this phenotype.
Mitochondrial disorders v2.52 ACAT2 Arina Puzriakova Gene: acat2 has been classified as Red List (Low Evidence).
Early onset or syndromic epilepsy v2.431 MED12 Eleanor Williams commented on gene: MED12
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.15 RNF113A Arina Puzriakova Classified gene: RNF113A as Amber List (moderate evidence)
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.15 RNF113A Arina Puzriakova Added comment: Comment on list classification: Associated with relevant phenotype in OMIM (MIM# 300953) and as possible Gen2Phen gene for X-linked trichothiodystrophy. At least 3 terminating variants reported in unrelated cases. Supportive functional studies also reported. Upgraded from Red to Amber but this gene should be promoted to Green at the next review.
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.15 RNF113A Arina Puzriakova Gene: rnf113a has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.431 RNF113A Arina Puzriakova Phenotypes for gene: RNF113A were changed from ?Trichothiodystrophy 5, nonphotosensitive, 300953 to Trichothiodystrophy 5, nonphotosensitive, OMIM:300953
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.14 RNF113A Arina Puzriakova Publications for gene: RNF113A were set to 25612912
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.13 RNF113A Arina Puzriakova Tag Q3_21_rating tag was added to gene: RNF113A.
White matter disorders and cerebral calcification - narrow panel v1.201 RNF113A Arina Puzriakova Phenotypes for gene: RNF113A were changed from ?Trichothiodystrophy 5, nonphotosensitive to Trichothiodystrophy 5, nonphotosensitive, OMIM:300953
Intellectual disability v3.1319 RNF113A Arina Puzriakova Phenotypes for gene: RNF113A were changed from X-linked trichothiodystrophy; Trichothiodystrophy 5, nonphotosensitive, 300953; Intellectual disability to Trichothiodystrophy 5, nonphotosensitive, OMIM:300953
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.13 RNF113A Arina Puzriakova Phenotypes for gene: RNF113A were changed from ?Trichothiodystrophy 5, nonphotosensitive to Trichothiodystrophy 5, nonphotosensitive, OMIM:300953
Severe microcephaly v2.253 GTF2E2 Arina Puzriakova Classified gene: GTF2E2 as Amber List (moderate evidence)
Severe microcephaly v2.253 GTF2E2 Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update - two distinct homozygous variants identified in 5 individuals from 4 families who all had microcephaly among other features. Supportive in vitro studies that demonstrate functional impairment.
Severe microcephaly v2.253 GTF2E2 Arina Puzriakova Gene: gtf2e2 has been classified as Amber List (Moderate Evidence).
Ichthyosis and erythrokeratoderma v1.68 GTF2E2 Arina Puzriakova Classified gene: GTF2E2 as Amber List (moderate evidence)
Ichthyosis and erythrokeratoderma v1.68 GTF2E2 Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update - two distinct homozygous variants identified in 5 individuals from 4 families who all had ichthyosis among other features. Supportive in vitro studies that demonstrate functional impairment.
Ichthyosis and erythrokeratoderma v1.68 GTF2E2 Arina Puzriakova Gene: gtf2e2 has been classified as Amber List (Moderate Evidence).
Ichthyosis and erythrokeratoderma v1.67 GTF2E2 Arina Puzriakova gene: GTF2E2 was added
gene: GTF2E2 was added to Ichthyosis and erythrokeratoderma. Sources: Literature
Q3_21_rating tags were added to gene: GTF2E2.
Mode of inheritance for gene: GTF2E2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GTF2E2 were set to 26996949; 28973399
Phenotypes for gene: GTF2E2 were set to Trichothiodystrophy 6, nonphotosensitive, OMIM:616943
Review for gene: GTF2E2 was set to GREEN
Added comment: Four individuals from 3 different Moroccan families with the same homozygous variant (c.C559T) in the GTF2E2 gene have been identified, as well as an additional patient from Asian origin with a distinct homozygous variant (c.448G>C). Predominant phenotype was that of trichothiodystrophy; however, all 5 individuals also had ID/DD, microcephaly and ichthyosis - and therefore adding GTF2E2 to these relevant panel.
Sources: Literature
Severe microcephaly v2.252 GTF2E2 Arina Puzriakova gene: GTF2E2 was added
gene: GTF2E2 was added to Severe microcephaly. Sources: Literature
Q3_21_rating tags were added to gene: GTF2E2.
Mode of inheritance for gene: GTF2E2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GTF2E2 were set to 26996949; 28973399
Phenotypes for gene: GTF2E2 were set to Trichothiodystrophy 6, nonphotosensitive, OMIM:616943
Review for gene: GTF2E2 was set to GREEN
Added comment: Four individuals from 3 different Moroccan families with the same homozygous variant (c.C559T) in the GTF2E2 gene have been identified, as well as an additional patient from Asian origin with a distinct homozygous variant (c.448G>C). Predominant phenotype was that of trichothiodystrophy; however, all 5 individuals also had ID/DD, microcephaly and ichthyosis - and therefore adding GTF2E2 to these relevant panel.
Sources: Literature
Intellectual disability v3.1318 GTF2E2 Arina Puzriakova changed review comment from: Comment on list classification: Two distinct homozygous variants identified in 5 individuals from 4 families who all presented with DD/ID. Despite indication that one of these represents a founder variants, discovery of a distinct homozygous variant in a patient with an overlapping phenotype corroborates pertinence of GTF2E2. Furthermore, there are some supportive functional studies.

Overall this is sufficient evidence to promote this gene to Green at the next GMS panel update.; to: Comment on list classification: Two distinct homozygous variants identified in 5 individuals from 4 families who all presented with DD/ID among other features. Despite indication that one of these represents a founder variant, discovery of a distinct homozygous variant in a patient with an overlapping phenotype corroborates pertinence of GTF2E2. Furthermore, there are some supportive in vitro studies that demonstrate functional impairment.

Overall this is sufficient evidence to promote this gene to Green at the next GMS panel update.
Intellectual disability v3.1318 GTF2E2 Arina Puzriakova Classified gene: GTF2E2 as Amber List (moderate evidence)
Intellectual disability v3.1318 GTF2E2 Arina Puzriakova Added comment: Comment on list classification: Two distinct homozygous variants identified in 5 individuals from 4 families who all presented with DD/ID. Despite indication that one of these represents a founder variants, discovery of a distinct homozygous variant in a patient with an overlapping phenotype corroborates pertinence of GTF2E2. Furthermore, there are some supportive functional studies.

Overall this is sufficient evidence to promote this gene to Green at the next GMS panel update.
Intellectual disability v3.1318 GTF2E2 Arina Puzriakova Gene: gtf2e2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1317 GTF2E2 Arina Puzriakova Tag watchlist was removed from gene: GTF2E2.
Tag Q3_21_rating tag was added to gene: GTF2E2.
Intellectual disability v3.1317 GTF2E2 Arina Puzriakova reviewed gene: GTF2E2: Rating: GREEN; Mode of pathogenicity: None; Publications: 26996949, 28973399; Phenotypes: Trichothiodystrophy 6, nonphotosensitive, OMIM:616943; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1317 GTF2E2 Arina Puzriakova Publications for gene: GTF2E2 were set to 30914295; 26996949
Fetal anomalies v1.720 MED12 Eleanor Williams changed review comment from: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome and phenotype that includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases; to: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome (the phenotype that includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation).

In addition Polla et al 2021 (PMID: 33244165) and Riccardi et al 2021 (PMID: 34079076) report 22 females in total with de novo variants in MED12. Some physical features such as syndactyly (10/22) and anteriorly placed anus (4/22) also noted. 12/22 have severe intellectual disability.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the predominantly male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases.
White matter disorders and cerebral calcification - narrow panel v1.200 GTF2E2 Arina Puzriakova Classified gene: GTF2E2 as Red List (low evidence)
White matter disorders and cerebral calcification - narrow panel v1.200 GTF2E2 Arina Puzriakova Added comment: Comment on list classification: Rating Red as only a single individual has been described to date with white matter alternations in the context of variants in this gene.
White matter disorders and cerebral calcification - narrow panel v1.200 GTF2E2 Arina Puzriakova Gene: gtf2e2 has been classified as Red List (Low Evidence).
White matter disorders and cerebral calcification - narrow panel v1.199 GTF2E2 Arina Puzriakova reviewed gene: GTF2E2: Rating: ; Mode of pathogenicity: None; Publications: 26996949, 28973399; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.1316 GTF2E2 Arina Puzriakova Phenotypes for gene: GTF2E2 were changed from Trichothiodystrophy 6, nonphotosensitive, 616943 to Trichothiodystrophy 6, nonphotosensitive, OMIM:616943
White matter disorders and cerebral calcification - narrow panel v1.199 GTF2E2 Arina Puzriakova Phenotypes for gene: GTF2E2 were changed from Trichothiodystrophy 6, nonphotosensitive; 616943 to Trichothiodystrophy 6, nonphotosensitive, OMIM:616943
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.12 GTF2E2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: GTF2E2.
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.12 GTF2E2 Arina Puzriakova Publications for gene: GTF2E2 were set to 26996949
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.11 GTF2E2 Arina Puzriakova Phenotypes for gene: GTF2E2 were changed from Trichothiodystrophy 6, nonphotosensitive; 616943 to Trichothiodystrophy 6, nonphotosensitive, OMIM:616943
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.10 GTF2E2 Arina Puzriakova Classified gene: GTF2E2 as Amber List (moderate evidence)
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.10 GTF2E2 Arina Puzriakova Added comment: Comment on list classification: Four individuals from 3 different Moroccan families with the same homozygous variant (c.C559T) in the GTF2E2 gene have been identified who all presented with non-photosensitive trichothiodystrophy. Even though this likely represents a founder effect in this population, an additional patient from Asian origin has been identified with a distinct homozygous variant (c.448G>C), corroborating pertinence of GTF2E2 variants in trichothiodystrophy. Furthermore, studies on primary fibroblasts of patients harbouring the founder variant demonstrated a reduction in the cellular levels of both subunits of the transcription initiation factor TFIIE.

Overall this is sufficient evidence to promote this gene to Green at the next GMS panel update.
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.10 GTF2E2 Arina Puzriakova Gene: gtf2e2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1315 MED12 Eleanor Williams Tag Skewed X-inactivation tag was added to gene: MED12.
Tag Q3_21_MOI tag was added to gene: MED12.
Tag Q3_21_expert_review tag was added to gene: MED12.
Intellectual disability v3.1315 MED12 Eleanor Williams changed review comment from: Comment on mode of inheritance: Leaving the mode of inheritance as XL hemizigous in males, biallelic in females for now, but there are several (10+ female cases reported now with de novo variants in MED12 and an intellectual disability phenotype) so consideration should be given to changing the mode of inheritance to monoallelic in females.; to: Comment on mode of inheritance: Leaving the mode of inheritance as XL hemizigous in males, biallelic in females for now, but there are several (10+) female cases reported now with de novo variants in MED12 and an intellectual disability phenotype so consideration should be given to changing the mode of inheritance to monoallelic in females.
Intellectual disability v3.1315 MED12 Eleanor Williams Added comment: Comment on mode of inheritance: Leaving the mode of inheritance as XL hemizigous in males, biallelic in females for now, but there are several (10+ female cases reported now with de novo variants in MED12 and an intellectual disability phenotype) so consideration should be given to changing the mode of inheritance to monoallelic in females.
Intellectual disability v3.1315 MED12 Eleanor Williams Mode of inheritance for gene: MED12 was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Intellectual disability v3.1314 MED12 Eleanor Williams Publications for gene: MED12 were set to 6711603
Intellectual disability v3.1313 MED12 Eleanor Williams edited their review of gene: MED12: Changed publications to: 33244165, 34079076, 33244166
Intellectual disability v3.1313 MED12 Eleanor Williams reviewed gene: MED12: Rating: ; 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)
Skeletal dysplasia v2.134 MYO18B Arina Puzriakova Classified gene: MYO18B as Amber List (moderate evidence)
Skeletal dysplasia v2.134 MYO18B Arina Puzriakova Added comment: Comment on list classification: There are sufficient unrelated cases presenting with a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Skeletal dysplasia v2.134 MYO18B Arina Puzriakova Gene: myo18b has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.133 MYO18B Arina Puzriakova Publications for gene: MYO18B were set to PMID: 32637634
Skeletal dysplasia v2.132 MYO18B Arina Puzriakova Tag Q3_21_rating tag was added to gene: MYO18B.
Skeletal dysplasia v2.132 MYO18B Arina Puzriakova reviewed gene: MYO18B: Rating: GREEN; Mode of pathogenicity: None; Publications: 25748484, 31195167, 32184166, 32637634, 33179433; Phenotypes: Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism, OMIM:616549; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Congenital myopathy v2.59 MYO18B Arina Puzriakova Publications for gene: MYO18B were set to 27879346; 27858739; 25748484; 32637634
Congenital myopathy v2.59 MYO18B Arina Puzriakova Publications for gene: MYO18B were set to 27879346; 27858739; 25748484
Intellectual disability v3.1313 CDH15 Zornitza Stark reviewed gene: CDH15: Rating: RED; Mode of pathogenicity: None; Publications: 19012874, 12052883, 28422132, 26506440; Phenotypes: Mental retardation, autosomal dominant 3, MIM#612580; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Skeletal dysplasia v2.132 MYO18B Arina Puzriakova Phenotypes for gene: MYO18B were changed from Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism to Klippel-Feil syndrome 4, autosomal recessive, with myopathy and facial dysmorphism, OMIM:616549
Skeletal dysplasia v2.131 ARCN1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: ARCN1.
Skeletal dysplasia v2.131 ARCN1 Arina Puzriakova Publications for gene: ARCN1 were set to PMID: 27476655
Skeletal dysplasia v2.130 ARCN1 Arina Puzriakova Classified gene: ARCN1 as Amber List (moderate evidence)
Skeletal dysplasia v2.130 ARCN1 Arina Puzriakova Added comment: Comment on list classification: New gene added to this panel by Andžela Lazdāne. ARCN1 is associated with a relevant phenotype in OMIM (MIM# 617164) which is characterised by rhizomelic short stature. At least 6 individuals from 5 unrelated families reported in literature (PMIDs: 27476655; 31075182; 33154040), which is sufficient to rate this gene as Green at the next GMS panel update.
Skeletal dysplasia v2.130 ARCN1 Arina Puzriakova Gene: arcn1 has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.129 ARCN1 Arina Puzriakova Phenotypes for gene: ARCN1 were changed from Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay to Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay, OMIM:617164
Brain cancer pertinent cancer susceptibility v1.1 Catherine Snow Panel types changed to Cancer Germline 100K; GMS Cancer Germline Virtual; GMS signed-off
Panel version 1.0 has been signed off on 2021-09-29
Breast cancer pertinent cancer susceptibility v1.2 Catherine Snow Panel types changed to Cancer Germline 100K; GMS Cancer Germline Virtual; GMS signed-off
Panel version 1.1 has been signed off on 2021-09-29
Breast cancer pertinent cancer susceptibility v1.1 PTEN Catherine Snow Classified gene: PTEN as Red List (low evidence)
Breast cancer pertinent cancer susceptibility v1.1 PTEN Catherine Snow Added comment: Comment on list classification: Rating red following review by C Turnball (ICR) of predisposition panels for GMS phase 2 indications.
Breast cancer pertinent cancer susceptibility v1.1 PTEN Catherine Snow Gene: pten has been classified as Red List (Low Evidence).
Ovarian cancer pertinent cancer susceptibility v1.4 Catherine Snow Panel types changed to Cancer Germline 100K; GMS Cancer Germline Virtual; GMS signed-off
Panel version 1.3 has been signed off on 2021-09-29
Ovarian cancer pertinent cancer susceptibility v1.3 BRIP1 Catherine Snow Classified gene: BRIP1 as Green List (high evidence)
Ovarian cancer pertinent cancer susceptibility v1.3 BRIP1 Catherine Snow Gene: brip1 has been classified as Green List (High Evidence).
Ovarian cancer pertinent cancer susceptibility v1.2 BRIP1 Catherine Snow gene: BRIP1 was added
gene: BRIP1 was added to Ovarian cancer pertinent cancer susceptibility. Sources: Expert list
Mode of inheritance for gene: BRIP1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Review for gene: BRIP1 was set to GREEN
Added comment: Rating Green, following review by C Turnball (ICR), of predisposition panels for GMS phase 2 indications.
Sources: Expert list
Ovarian cancer pertinent cancer susceptibility v1.1 PMS2 Catherine Snow Classified gene: PMS2 as Red List (low evidence)
Ovarian cancer pertinent cancer susceptibility v1.1 PMS2 Catherine Snow Added comment: Comment on list classification: Rating red, following review by C Turnball (ICR), of predisposition panels for GMS phase 2 indications.
Ovarian cancer pertinent cancer susceptibility v1.1 PMS2 Catherine Snow Gene: pms2 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.476 KDM6A Arina Puzriakova Publications for gene: KDM6A were set to 25142838; 15523604; 32048120; 25546742; 15887282; 32086639; 26411453; 22197486; 23076834; 31363182
Primary immunodeficiency or monogenic inflammatory bowel disease v2.475 KMT2A Arina Puzriakova Classified gene: KMT2A as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.475 KMT2A Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber but there is enough evidence to promote to Green at the next GMS panel update.

Immune dysfunction, including early-onset CVID and recurrent infections, have been reported in multiple individuals with Wiedemann-Steiner syndrome. Immunopathology can be a presenting feature, and as there are sufficient unrelated cases with this phenotype, this gene should be promoted to Green.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.475 KMT2A Arina Puzriakova Gene: kmt2a has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.474 KMT2A Arina Puzriakova Publications for gene: KMT2A were set to 32048120; 27320412; 32086639
Primary immunodeficiency or monogenic inflammatory bowel disease v2.473 KMT2A Arina Puzriakova Tag Q3_21_rating tag was added to gene: KMT2A.
Intellectual disability v3.1313 KMT2A Arina Puzriakova Phenotypes for gene: KMT2A were changed from WSS to Wiedemann-Steiner syndrome, OMIM:605130
Fetal anomalies v1.720 KMT2A Arina Puzriakova Phenotypes for gene: KMT2A were changed from WIEDEMANN-STEINER SYNDROME to Wiedemann-Steiner syndrome, OMIM:605130
Primary immunodeficiency or monogenic inflammatory bowel disease v2.473 KMT2A Arina Puzriakova Phenotypes for gene: KMT2A were changed from Wiedemann-Steiner syndrome with Congenital immunodeficiency; Unclassified antibody deficiency; Respiratory infections, short stature, hypertelorism, hairy elbows, developmental delay, intellectual disability; Combined immunodeficiencies with associated or syndromic features to Wiedemann-Steiner syndrome, OMIM:605130
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.29 POPDC3 Arina Puzriakova Tag watchlist tag was added to gene: POPDC3.
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.29 POPDC3 Arina Puzriakova Mode of inheritance for gene: POPDC3 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BIALLELIC, autosomal or pseudoautosomal
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.28 POPDC3 Arina Puzriakova Classified gene: POPDC3 as Amber List (moderate evidence)
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.28 POPDC3 Arina Puzriakova Added comment: Comment on list classification: Since the initial report no further cohorts have been released validating POPDC3 variants in limb girdle muscular dystrophy. Given this and the lack of complete segregation studies, rating as Amber awaiting further evidence.
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.28 POPDC3 Arina Puzriakova Gene: popdc3 has been classified as Amber List (Moderate Evidence).
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.27 POPDC3 Arina Puzriakova reviewed gene: POPDC3: Rating: ; Mode of pathogenicity: None; Publications: 31610034; Phenotypes: Muscular dystrophy, limb-girdle, autosomal recessive 26, OMIM:618848; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.430 CERS1 Sarah Leigh changed review comment from: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.; to: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
However, the Q3_21_expert_review and Q3_21_phenotype tags have been added to this gene for an NHS review, because the phenotype associated with variants CERS1 includues progessive cognitive impairment and dementia.
Early onset or syndromic epilepsy v2.430 CERS1 Sarah Leigh Tag Q3_21_expert_review tag was added to gene: CERS1.
Tag Q3_21_phenotype tag was added to gene: CERS1.
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.27 POPDC3 Arina Puzriakova Publications for gene: POPDC3 were set to https://doi.org/10.1002/ana.25620
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.26 POPDC3 Arina Puzriakova Phenotypes for gene: POPDC3 were changed from Muscular dystrophy, limb-girdle, autosomal recessive 26 to Muscular dystrophy, limb-girdle, autosomal recessive 26, OMIM:618848
Hereditary ataxia with onset in adulthood v2.85 GLRB Sarah Leigh reviewed gene: GLRB: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Hereditary ataxia with onset in adulthood v2.85 GLRB Sarah Leigh Tag Q3_21_expert_review tag was added to gene: GLRB.
Tag Q3_21_phenotype tag was added to gene: GLRB.
Intellectual disability v3.1312 EIF2AK2 Arina Puzriakova Tag missense tag was added to gene: EIF2AK2.
Inherited white matter disorders v1.139 EIF2AK2 Arina Puzriakova Publications for gene: EIF2AK2 were set to 32197074
Inherited white matter disorders v1.138 EIF2AK2 Arina Puzriakova edited their review of gene: EIF2AK2: Added comment: A further 5 families reported (PMID: 33236446) harbouring 3 different variants in this gene (including the first homozygous case). Clinical presentation was prominent in all cases for dystonia with onset in infancy or childhood, with subsequent generalisation. 3 unrelated individuals additionally developed mild ID, spasticity, and brain MRI alterations (including white matter abnormalities); while 6 individuals from the remaining 2 families had only isolated dystonia.; Changed publications to: 32197074, 33236446
Intellectual disability v3.1312 EIF2AK2 Arina Puzriakova Publications for gene: EIF2AK2 were set to 32197074
Intellectual disability v3.1311 EIF2AK2 Arina Puzriakova edited their review of gene: EIF2AK2: Added comment: A further 5 families reported (PMID: 33236446) harbouring 3 different variants in this gene (including the first homozygous case). Clinical presentation was prominent in all cases for dystonia with onset in infancy or childhood, with subsequent generalisation. 3 unrelated individuals additionally developed mild ID, spasticity, and brain MRI alterations; while 6 individuals from the remaining 2 families had only isolated dystonia.; Changed publications to: 32197074, 33236446
Inherited white matter disorders v1.138 EIF2AK2 Arina Puzriakova Tag missense tag was added to gene: EIF2AK2.
Childhood onset dystonia, chorea or related movement disorder v1.157 EIF2AK2 Arina Puzriakova Tag missense tag was added to gene: EIF2AK2.
Childhood onset dystonia, chorea or related movement disorder v1.157 EIF2AK2 Arina Puzriakova edited their review of gene: EIF2AK2: Added comment: A further 6 families reported (PMID:33236446; 33866603) harbouring 3 different variants in this gene (including the first homozygous case). Clinical presentation was prominent in all cases for dystonia with onset in infancy or childhood, with subsequent generalisation. Additional clinical details are limited for the family described in PMID:33866603. However, in the remaining families detailed in PMID:33236446, 3 unrelated individuals additionally developed mild ID, spasticity, and brain MRI alterations; while the other 2 families (6 individuals) only had isolated dystonia.; Changed publications to: 32197074, 33236446, 33866603
Childhood onset dystonia, chorea or related movement disorder v1.157 EIF2AK2 Arina Puzriakova Publications for gene: EIF2AK2 were set to 32197074
Intellectual disability v3.1311 EIF2AK2 Arina Puzriakova Phenotypes for gene: EIF2AK2 were changed from Intellectual disability; white matter abnormalities; ataxia; regression with febrile illness to Leukoencephalopathy, developmental delay, and episodic neurologic regression syndrome, OMIM:618877
Severe early-onset obesity v2.43 CPE Arina Puzriakova Classified gene: CPE as Amber List (moderate evidence)
Severe early-onset obesity v2.43 CPE Arina Puzriakova Added comment: Comment on list classification: There are now sufficient unrelated families (5) reported in literature presenting a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Severe early-onset obesity v2.43 CPE Arina Puzriakova Gene: cpe has been classified as Amber List (Moderate Evidence).
Severe early-onset obesity v2.42 CPE Arina Puzriakova Publications for gene: CPE were set to 26120850; 15870393; 15358678
Severe early-onset obesity v2.41 CPE Arina Puzriakova Tag Q3_21_rating tag was added to gene: CPE.
Severe early-onset obesity v2.41 CPE Arina Puzriakova edited their review of gene: CPE: Added comment: Durmaz et al. 2021 (PMID: 32936766) identified the second family with 3 affected sibs with obesity, intellectual disability and hypogonadotropic hypogonadism, and a homozygous nonsense c.405C>A (p.Y135*) variant in CPE.

Bosch et al. 2021 (PMID: 34383079) reported on 4 individuals from 3 additional families harbouring 2 different homozygous truncating variants in this gene. Clinical presentation was prominent for obesity and intellectual disability. Hypogonadotropic hypogonadism was confirmed in one individual and was suspected but not tested for in another two subjects.; Changed rating: GREEN; Changed publications to: 26120850, 32936766, 34383079; Changed phenotypes to: Intellectual developmental disorder and hypogonadotropic hypogonadism, OMIM:619326; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Hypogonadotropic hypogonadism (GMS) v1.46 CPE Arina Puzriakova Publications for gene: CPE were set to 26120850; 32936766
Hypogonadotropic hypogonadism (GMS) v1.45 CPE Arina Puzriakova Classified gene: CPE as Amber List (moderate evidence)
Hypogonadotropic hypogonadism (GMS) v1.45 CPE Arina Puzriakova Added comment: Comment on list classification: There are now sufficient unrelated families (5) reported in literature presenting a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Hypogonadotropic hypogonadism (GMS) v1.45 CPE Arina Puzriakova Gene: cpe has been classified as Amber List (Moderate Evidence).
Hypogonadotropic hypogonadism (GMS) v1.44 CPE Arina Puzriakova edited their review of gene: CPE: Added comment: Bosch et al. 2021 (PMID: 34383079) reported on 4 individuals from 3 additional families harbouring 2 different homozygous truncating variants in this gene. Clinical presentation was prominent for obesity and intellectual disability. Hypogonadotropic hypogonadism was confirmed in one individual and was suspected but not tested for in another two subjects.; Changed rating: GREEN; Changed publications to: 26120850, 32936766, 34383079; Changed phenotypes to: Intellectual developmental disorder and hypogonadotropic hypogonadism, OMIM:619326; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1310 CPE Arina Puzriakova Publications for gene: CPE were set to 26120850; 32936766
Hypogonadotropic hypogonadism (GMS) v1.44 CPE Arina Puzriakova Tag watchlist was removed from gene: CPE.
Tag Q3_21_rating tag was added to gene: CPE.
Intellectual disability v3.1309 CPE Arina Puzriakova Classified gene: CPE as Amber List (moderate evidence)
Intellectual disability v3.1309 CPE Arina Puzriakova Added comment: Comment on list classification: There are now sufficient unrelated families (5) reported in literature presenting a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Intellectual disability v3.1309 CPE Arina Puzriakova Gene: cpe has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1308 CPE Arina Puzriakova Tag watchlist was removed from gene: CPE.
Tag Q3_21_rating tag was added to gene: CPE.
Intellectual disability v3.1308 CPE Arina Puzriakova edited their review of gene: CPE: Added comment: Bosch et al. 2021 (PMID: 34383079) reported on 4 individuals from 3 additional families harbouring 2 different homozygous truncating variants in this gene. Clinical presentation was prominent for obesity and intellectual disability. Hypogonadotropic hypogonadism was confirmed in one individual and was suspected but not tested for in another two subjects.; Changed rating: GREEN; Changed publications to: 26120850, 32936766, 34383079; Changed phenotypes to: Intellectual developmental disorder and hypogonadotropic hypogonadism, OMIM:619326; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder v1.62 PIGB Arina Puzriakova Classified gene: PIGB as Amber List (moderate evidence)
Hereditary neuropathy or pain disorder v1.62 PIGB Arina Puzriakova Added comment: Comment on list classification: Axonal degenerative polyneuropathy and demyelinating sensorimotor polyneuropathy are observed in the more severely affected individuals with biallelic variants in this gene. There are sufficient cases with a relevant phenotype (5 individuals from 3 families) to rate as Green at the next GMS panel update.
Hereditary neuropathy or pain disorder v1.62 PIGB Arina Puzriakova Gene: pigb has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy or pain disorder v1.61 PIGB Arina Puzriakova Tag Q3_21_rating tag was added to gene: PIGB.
Retinal disorders v2.216 MED12 Eleanor Williams Tag Skewed X-inactivation tag was added to gene: MED12.
Clefting v2.50 MED12 Eleanor Williams Tag Skewed X-inactivation tag was added to gene: MED12.
Fetal anomalies v1.719 GREB1L Ivone Leong Publications for gene: GREB1L were set to 29261186; 29100091; 31424080; 32378186
Retinal disorders v2.216 IRX6 Eleanor Williams Tag Q3_21_rating tag was added to gene: IRX6.
Tag Q3_21_expert_review tag was added to gene: IRX6.
Retinal disorders v2.216 IRX6 Eleanor Williams edited their review of gene: IRX6: Added comment: Ideally, a region representing the IRX5/IRX6 duplication should be added to PanelApp with a monallelic mode of inheritance. There is a lack of single nucleotide variants reported in this gene with relevance to retinal disorders and and therefore adding this gene as green risks reporting irrelevant SNVs.; Changed rating: AMBER
Retinal disorders v2.216 IRX5 Eleanor Williams changed review comment from: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition (PMID: 22581230;17230486)

Duplication of gene
-------------------
PMID: 33891002 - Kohl et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

Loss of function/gene
---------
PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa.

PMID: 32045705 - Apuzzo et al 2020 - report 2 cases of loss of a region in 16q12.1q21 which encompasses IRX5 and IRX6 and many other genes, which together with 3 other previous reports of deletions in this region help define a syndrome with features that include dysmorphic features, short stature, microcephaly, global developmental delay/intellectual disability, autism spectrum disorder (ASD) and ocular abnormalities (nystagmus and strabismus).
; to: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition (PMID: 22581230;17230486)

Duplication of gene
-------------------
PMID: 33891002 - Kohl et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

Loss of gene/small variants
---------
PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa.

PMID: 32045705 - Apuzzo et al 2020 - report 2 cases of loss of a region in 16q12.1q21 which encompasses IRX5 and IRX6 and many other genes, which together with 3 other previous reports of deletions in this region help define a syndrome with features that include dysmorphic features, short stature, microcephaly, global developmental delay/intellectual disability, autism spectrum disorder (ASD) and ocular abnormalities (nystagmus and strabismus).
Retinal disorders v2.216 IRX5 Eleanor Williams edited their review of gene: IRX5: Changed rating: AMBER
Retinal disorders v2.216 IRX5 Eleanor Williams commented on gene: IRX5: Ideally, a region representing the IRX5/IRX6 duplication should be added to PanelApp with a monallelic mode of inheritance. There is a lack of single nucleotide variants reported in this gene with relevance to retinal disorders and and therefore adding this gene as green risks reporting irrelevant SNVs alongside carrier status for Hamamy syndrome (biallelic)
Retinal disorders v2.216 IRX5 Eleanor Williams Tag Q3_21_expert_review tag was added to gene: IRX5.
Fetal anomalies v1.718 MED12 Eleanor Williams Tag Q3_21_MOI tag was added to gene: MED12.
Fetal anomalies v1.718 MED12 Eleanor Williams Added comment: Comment on mode of inheritance: Variants in this gene have also been reported in females with Hardikar syndrome and phenotype that includes facial clefting, pigmentary retinopathy, biliary anomalies, hydronephrosis, and intestinal malrotation.

X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases
Fetal anomalies v1.718 MED12 Eleanor Williams Mode of inheritance for gene: MED12 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 v1.717 MED12 Eleanor Williams Tag Q3_21_expert_review tag was added to gene: MED12.
Primary ovarian insufficiency v1.49 ZSWIM7 Ivone Leong Classified gene: ZSWIM7 as Red List (low evidence)
Primary ovarian insufficiency v1.49 ZSWIM7 Ivone Leong Added comment: Comment on list classification: New gene added by Andrey Gagunashvili (UCL Great Ormond Street Institute of Child Health). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. Currently there is only 1 case (2 affected sisters) with POI associated with this gene. There is currently not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Primary ovarian insufficiency v1.49 ZSWIM7 Ivone Leong Gene: zswim7 has been classified as Red List (Low Evidence).
Retinal disorders v2.216 MED12 Eleanor Williams Tag Q3_21_rating tag was added to gene: MED12.
Retinal disorders v2.216 MED12 Eleanor Williams Added comment: Comment on mode of inheritance: X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases.
Retinal disorders v2.216 MED12 Eleanor Williams Mode of inheritance for gene: MED12 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Retinal disorders v2.215 MED12 Eleanor Williams Classified gene: MED12 as Amber List (moderate evidence)
Retinal disorders v2.215 MED12 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. 5 cases reported with a retinal phenotype and likely disease causing variants in MED12.
Retinal disorders v2.215 MED12 Eleanor Williams Gene: med12 has been classified as Amber List (Moderate Evidence).
Retinal disorders v2.214 MED12 Eleanor Williams gene: MED12 was added
gene: MED12 was added to Retinal disorders. Sources: Literature
Q3_21_expert_review tags were added to gene: MED12.
Mode of inheritance for gene: MED12 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: MED12 were set to 33244166
Phenotypes for gene: MED12 were set to Hardikar syndrome, OMIM:612726; cholestasis-pigmentary retinopathy-cleft palate syndrome, MONDO:0012997
Review for gene: MED12 was set to GREEN
Added comment: Zorntiza Stark reviewed this gene on the Clefting panel. Li et al 2021 (PMID: 33244166) report 7 females with Hardikar syndrome each of whom have had a nonsense or frameshift MED12 variant identified by exome sequencing. All five tested patients showed evidence of skewed x chromosome inactivation. 5 of the patients are reported to have a retinal phenotype (retinal rarefaction, pigmentary retinopathy, cat’s paw retinal pigmentation).

Hardikar syndrome is noted for the preserved neurodevelopment in patients unlike the other disorders associated with this gene.
Sources: Literature
Severe microcephaly v2.251 PCDHGC4 Sarah Leigh Tag Q3_21_rating was removed from gene: PCDHGC4.
Severe microcephaly v2.251 PCDHGC4 Sarah Leigh reviewed gene: PCDHGC4: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Primary ovarian insufficiency v1.48 YTHDC2 Ivone Leong Classified gene: YTHDC2 as Red List (low evidence)
Primary ovarian insufficiency v1.48 YTHDC2 Ivone Leong Added comment: Comment on list classification: New gene added by Andrey Gagunashvili (UCL Great Ormond Street Institute of Child Health). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There currently does not appear to be any human cases associated with this gene therefore this gene has been given a Red rating.
Primary ovarian insufficiency v1.48 YTHDC2 Ivone Leong Gene: ythdc2 has been classified as Red List (Low Evidence).
Clefting v2.50 MED12 Eleanor Williams Added comment: Comment on mode of inheritance: X-linked hemizygous mutation in males, monoallelic mutations in females is the appropriate mode of inheritance for Hardikar syndrome but there are carrier implications for the male-only phenotypes associated with this gene (e.g. Lujan-Fryns syndrome, Ohdo syndrome, X-linked and Opitz-Kaveggia syndrome) in female cases.
Clefting v2.50 MED12 Eleanor Williams Mode of inheritance for gene: MED12 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Clefting v2.49 MED12 Eleanor Williams Tag Q3_21_expert_review tag was added to gene: MED12.
Retinal disorders v2.213 SPTLC2 Ivone Leong Classified gene: SPTLC2 as Red List (low evidence)
Retinal disorders v2.213 SPTLC2 Ivone Leong Added comment: Comment on list classification: New gene added by Dmitrijs Rots (RadboudUMC). This gene is associated with a phenotype in OMIM and Gene2Phenotype.

PMID: 31509666 reported on 2 unrelated families (family 1 and 2) and 3 unrelated individuals (patients 1, 2 and 3) who have HSAN1 and have variants in SPTLC1 (2 families and patient 1 have the same heterozygous variant C133Y, and patient 2 and 3 have C133W, also heterozygous). Those with the C133Y variant have HSAN1 and macular telangiectasia type 2 and those with C133W variant only have HSAN1 and no eye phenotype. The authors note that patients with C133W both patients were under the age of 50 and had been treated with serine supplementation.

Affected members of family 3 was diagnosed with HSAN1C and were heterozygous for S384F in SPTLC2 and macular telangiectasia type 2.

As there is only one case, there is not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Retinal disorders v2.213 SPTLC2 Ivone Leong Gene: sptlc2 has been classified as Red List (Low Evidence).
Retinal disorders v2.212 SPTLC2 Ivone Leong Publications for gene: SPTLC2 were set to PMID: 31509666
Retinal disorders v2.211 SPTLC1 Ivone Leong Tag watchlist tag was added to gene: SPTLC1.
Retinal disorders v2.211 SPTLC1 Ivone Leong Classified gene: SPTLC1 as Amber List (moderate evidence)
Retinal disorders v2.211 SPTLC1 Ivone Leong Added comment: Comment on list classification: New gene added by Dmitrijs Rots (RadboudUMC). This gene is associated with a phenotype in OMIM but not in Gene2Phenotype.

PMID: 31509666 reported on 2 unrelated families (family 1 and 2) and 3 unrelated individuals (patients 1, 2 and 3) who have HSAN1 and have variants in SPTLC1 (2 families and patient 1 have the same heterozygous variant C133Y, and patient 2 and 3 have C133W, also heterozygous). Those with the C133Y variant have HSAN1 and macular telangiectasia type 2 and those with C133W variant only have HSAN1 and no eye phenotype. The authors note that patients with C133W both patients were under the age of 50 and had been treated with serine supplementation.

Affected members of family 3 was diagnosed with HSAN1C and were heterozygous for S384F in SPTLC2 and macular telangiectasia type 2.

While there appears to be a link between this gene and macular telangiectasia type 2, all affected families/individuals have the same variant. Therefore, there is currently enough evidence to support a gene-disease association. This gene has been given an Amber rating until more information is available.
Retinal disorders v2.211 SPTLC1 Ivone Leong Gene: sptlc1 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.251 PCDHGC4 Sarah Leigh Deleted their review
Severe microcephaly v2.251 PCDHGC4 Sarah Leigh Deleted their comment
Intellectual disability v3.1308 PCDHGC4 Sarah Leigh Classified gene: PCDHGC4 as Amber List (moderate evidence)
Intellectual disability v3.1308 PCDHGC4 Sarah Leigh Added comment: Comment on list classification: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Intellectual disability v3.1308 PCDHGC4 Sarah Leigh Gene: pcdhgc4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1307 PCDHGC4 Sarah Leigh Deleted their comment
Severe microcephaly v2.251 PCDHGC4 Sarah Leigh Entity copied from Intellectual disability v3.1307
Severe microcephaly v2.251 PCDHGC4 Sarah Leigh gene: PCDHGC4 was added
gene: PCDHGC4 was added to Severe microcephaly. Sources: Literature,Expert Review Amber
Q3_21_rating tags were added to gene: PCDHGC4.
Mode of inheritance for gene: PCDHGC4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PCDHGC4 were set to 34244665
Phenotypes for gene: PCDHGC4 were set to Neurodevelopmental abnormality HP:0012759
Intellectual disability v3.1307 PCDHGC4 Sarah Leigh Phenotypes for gene: PCDHGC4 were changed from neurodevelopmental syndrome to Neurodevelopmental abnormality HP:0012759
Early onset or syndromic epilepsy v2.430 PCDHGC4 Sarah Leigh Phenotypes for gene: PCDHGC4 were changed from neurodevelopmental syndrome to Neurodevelopmental abnormality HP:0012759
Intellectual disability v3.1306 KIRREL3 Aleš Maver reviewed gene: KIRREL3: Rating: RED; Mode of pathogenicity: None; Publications: PMID: 33853164; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Retinal disorders v2.210 SPTLC1 Ivone Leong Publications for gene: SPTLC1 were set to PMID: 31509666
Catecholaminergic polymorphic VT v2.19 TECRL Ivone Leong Tag Q3_21_rating tag was added to gene: TECRL.
Catecholaminergic polymorphic VT v2.19 TECRL Ivone Leong edited their review of gene: TECRL: Added comment: This gene is associated with a phenotype in OMIM and not Gene2Phenotype. There is now sufficient evidence to support a gene-disease association. This gene should be rated Green at the next review.; Changed rating: GREEN
Skeletal dysplasia v2.128 LRRK1 Eleanor Williams Classified gene: LRRK1 as Amber List (moderate evidence)
Skeletal dysplasia v2.128 LRRK1 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from grey to amber, but with a recommendation for a green rating following GMS review. More than 3 reported cases.
Skeletal dysplasia v2.128 LRRK1 Eleanor Williams Gene: lrrk1 has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.127 LRRK1 Eleanor Williams Tag Q3_21_rating tag was added to gene: LRRK1.
Tag Q3_21_NHS_review tag was added to gene: LRRK1.
Catecholaminergic polymorphic VT v2.19 TECRL Ivone Leong Added comment: Comment on publications: PMID: 30790670. 1 case (13 yo) with compound het variants in TECRL (R196Q, which was previously reported and a novel splice variant) was diagnosed with CPVT3. The proband's older brother suddenly died at 12 yo but DNA was unavailable for testing. Both heterozygous parents were unaffected.

PMID: 32173957. 4 families with novel homozygous/compound het TECRL variants (6 affected individuals).

PMID: 33367594. 7 additional families (10 affected individuals) with compound het/homozygous variants in TECRL.
Catecholaminergic polymorphic VT v2.19 TECRL Ivone Leong Publications for gene: TECRL were set to 27861123
Skeletal dysplasia v2.127 LRRK1 Eleanor Williams commented on gene: LRRK1
Long QT syndrome v2.23 TECRL Ivone Leong Classified gene: TECRL as Amber List (moderate evidence)
Long QT syndrome v2.23 TECRL Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber to match the gene rating suggested in my previous review.
Long QT syndrome v2.23 TECRL Ivone Leong Gene: tecrl has been classified as Amber List (Moderate Evidence).
Hypertrophic cardiomyopathy v2.26 TRIM63 Ivone Leong Classified gene: TRIM63 as Amber List (moderate evidence)
Hypertrophic cardiomyopathy v2.26 TRIM63 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber. This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID:32451364 reported 16 index cases with homozygous/compound het TRIM63 variants. 15 have HCM and 1 with restrictive cardiomyopathy. Only those with homozygous/compound het variants had disease (heterozygous family members were healthy).

This gene should be promoted to Green status at the next review as there is enough evidence to support a gene-disease association.
Hypertrophic cardiomyopathy v2.26 TRIM63 Ivone Leong Gene: trim63 has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.127 LRRK1 Eleanor Williams Phenotypes for gene: LRRK1 were changed from Osteosclerotic metaphyseal dysplasia (OSMD) (OMIM: 615198) to Osteosclerotic metaphyseal dysplasia (OSMD), OMIM: 615198; Osteosclerotic metaphyseal dysplasia, MONDO:0014080
Hypertrophic cardiomyopathy v2.25 TRIM63 Ivone Leong Tag Q3_21_rating tag was added to gene: TRIM63.
Tag Q3_21_NHS_review tag was added to gene: TRIM63.
Hypertrophic cardiomyopathy v2.25 TRIM63 Ivone Leong Phenotypes for gene: TRIM63 were changed from Hypertrophic cardiomyopathy to Hypertrophic cardiomyopathy, MONDO:0005045; restrictive cardiomyopathy, MONDO:0005201
Hypertrophic cardiomyopathy v2.24 TRIM63 Ivone Leong Mode of inheritance for gene: TRIM63 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
Hypertrophic cardiomyopathy v2.23 TRIM63 Ivone Leong Publications for gene: TRIM63 were set to
Hypertrophic cardiomyopathy v2.22 TRIM63 Oliver Watkinson reviewed gene: TRIM63: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID 32451364; Phenotypes: hypertrophic cardiomyopathy, restrictive cardiomyopathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.472 PSMB9 Arina Puzriakova Publications for gene: PSMB9 were set to 26524591
Primary immunodeficiency or monogenic inflammatory bowel disease v2.471 PSMB4 Arina Puzriakova Publications for gene: PSMB4 were set to 26524591
Primary immunodeficiency or monogenic inflammatory bowel disease v2.470 PSMB9 Arina Puzriakova reviewed gene: PSMB9: Rating: ; Mode of pathogenicity: None; Publications: 33727065; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Primary immunodeficiency or monogenic inflammatory bowel disease v2.470 PSMB4 Arina Puzriakova reviewed gene: PSMB4: Rating: ; Mode of pathogenicity: None; Publications: 34416217; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.470 PSMB9 Arina Puzriakova Phenotypes for gene: PSMB9 were changed from Autoinflammation, lipodystrophy, and dermatosis syndrome; CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome) to Proteasome-associated autoinflammatory syndrome 3, digenic, OMIM:617591; CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.469 PSMB4 Arina Puzriakova Phenotypes for gene: PSMB4 were changed from CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome) to Proteasome-associated autoinflammatory syndrome 3 and digenic forms, OMIM:617591; CANDLE syndrome (Autoinflammation, lipodystrophy, and dermatosis syndrome)
Hereditary haemorrhagic telangiectasia v2.9 GDF2 Arina Puzriakova Penetrance for gene GDF2 was set from to Complete
Hereditary haemorrhagic telangiectasia v2.8 GDF2 Arina Puzriakova Publications for gene: GDF2 were set to 23972370 - 3 unrelated probands with no variants identified in ENG, ACVRL1, and SMAD4; 27081547 - a variant of unknown significance in GDF2 was detected in one of 93 unrelated individuals clinically suspected to have HHT who previously tested negative for mutations in ENG, ACVRL1 and SMAD4; 25674101 - review from the same authors as PMID:23972370
Hereditary haemorrhagic telangiectasia v2.7 GDF2 Arina Puzriakova reviewed gene: GDF2: Rating: ; Mode of pathogenicity: None; Publications: 27081547, 32573726, 32669404, 33834622, https://doi.org/10.1164/ajrccm-conference.2020.201.1_MeetingAbstracts.A6356; Phenotypes: Telangiectasia, hereditary hemorrhagic, type 5, OMIM:615506; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Retinal disorders v2.209 SPTLC2 Dmitrijs Rots gene: SPTLC2 was added
gene: SPTLC2 was added to Retinal disorders. Sources: Literature
Mode of inheritance for gene: SPTLC2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SPTLC2 were set to PMID: 31509666
Phenotypes for gene: SPTLC2 were set to macular telangiectasia type 2; vision loss; neuropathy
Penetrance for gene: SPTLC2 were set to unknown
Review for gene: SPTLC2 was set to GREEN
Added comment: Common feature of HSAN1 macular telangiectasia type 2 and identified in two families with primarily diagnosed macular telangiectasia type 2 in PMID: 31509666.
Sources: Literature
Retinal disorders v2.209 SPTLC1 Dmitrijs Rots gene: SPTLC1 was added
gene: SPTLC1 was added to Retinal disorders. Sources: Literature
Mode of inheritance for gene: SPTLC1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SPTLC1 were set to PMID: 31509666
Phenotypes for gene: SPTLC1 were set to macular telangiectasia type 2; vision loss
Penetrance for gene: SPTLC1 were set to unknown
Review for gene: SPTLC1 was set to GREEN
Added comment: Common feature of HSAN1 macular telangiectasia type 2 and identified in two families with primarily diagnosed macular telangiectasia type 2 in PMID: 31509666.
Sources: Literature
Primary ovarian insufficiency v1.47 YTHDC2 Andrey Gagunashvili gene: YTHDC2 was added
gene: YTHDC2 was added to Primary ovarian insufficiency. Sources: Literature,Research
Mode of inheritance for gene: YTHDC2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: YTHDC2 were set to 29033321; 29360036
Phenotypes for gene: YTHDC2 were set to Premature ovarian insufficiency; female infertility; absent puberty; primary amenorrhea
Penetrance for gene: YTHDC2 were set to Complete
Review for gene: YTHDC2 was set to RED
Added comment: Sources: Literature, Research
Primary ovarian insufficiency v1.47 ZSWIM7 Andrey Gagunashvili changed review comment from: Sources: Literature, Research; to: Sources: Literature
Primary ovarian insufficiency v1.47 ZSWIM7 Andrey Gagunashvili edited their review of gene: ZSWIM7: Changed rating: RED
Primary ovarian insufficiency v1.47 ZSWIM7 Andrey Gagunashvili gene: ZSWIM7 was added
gene: ZSWIM7 was added to Primary ovarian insufficiency. Sources: Literature,Research
Mode of inheritance for gene: ZSWIM7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ZSWIM7 were set to 34402903
Phenotypes for gene: ZSWIM7 were set to Primary ovarian insufficiency; absent puberty; primary amenorrhea
Penetrance for gene: ZSWIM7 were set to Complete
Mode of pathogenicity for gene: ZSWIM7 was set to Other
Review for gene: ZSWIM7 was set to AMBER
Added comment: Sources: Literature, Research
Osteogenesis imperfecta v2.37 MBTPS2 Eleanor Williams Tag Q3_21_NHS_review tag was added to gene: MBTPS2.
Skeletal dysplasia v2.126 UNC45A Eleanor Williams commented on gene: UNC45A: Copied this gene from the Osteogenesis imperfecta panel, as all green genes on that panel should also be green on the Skeletal dysplasia panel
Skeletal dysplasia v2.126 UNC45A Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37
Skeletal dysplasia v2.126 UNC45A Eleanor Williams gene: UNC45A was added
gene: UNC45A was added to Skeletal dysplasia. Sources: Expert list,Expert Review Amber
Q3_21_rating, Q3_21_NHS_review tags were added to gene: UNC45A.
Mode of inheritance for gene: UNC45A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: UNC45A were set to 29429573
Phenotypes for gene: UNC45A were set to Osteootohepatoenteric syndrome, OMIM:619377
Skeletal dysplasia v2.125 SGMS2 Eleanor Williams commented on gene: SGMS2: Copied from the Osteogenesis imperfecta panel to the Skeletal dysplasia panel.
Skeletal dysplasia v2.125 SGMS2 Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37
Skeletal dysplasia v2.125 SGMS2 Eleanor Williams gene: SGMS2 was added
gene: SGMS2 was added to Skeletal dysplasia. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: SGMS2.
Mode of inheritance for gene: SGMS2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SGMS2 were set to 30779713; 32028018
Phenotypes for gene: SGMS2 were set to Calvarial doughnut lesions with bone fragility with or without spondylometaphyseal dysplasia, OMIM:126550; calvarial doughnut lesions-bone fragility syndrome, MONDO:0007470
Skeletal dysplasia v2.124 DSPP Eleanor Williams Tag Q3_21_expert_review tag was added to gene: DSPP.
Skeletal dysplasia v2.124 DSPP Eleanor Williams commented on gene: DSPP: This gene has been reviewed as RED on the Osteogenesis imperfecta panel by Zorntiza Stark with comment "Specifically NOT associated with fractures/OI.", and therefore has been tagged for further GMS review on this panel also.
Skeletal dysplasia v2.124 MESD Eleanor Williams Tag for-review was removed from gene: MESD.
Tag Q3_21_rating tag was added to gene: MESD.
Skeletal dysplasia v2.124 MESD Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37
Skeletal dysplasia v2.124 MESD Eleanor Williams gene: MESD was added
gene: MESD was added to Skeletal dysplasia. Sources: Expert Review Amber,Literature
for-review tags were added to gene: MESD.
Mode of inheritance for gene: MESD was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MESD were set to 31564437
Phenotypes for gene: MESD were set to Osteogenesis imperfecta, type XX, OMIM:618644; Osteogenesis imperfecta, type 20, MONDO:0032846
Skeletal dysplasia v2.123 MBTPS2 Eleanor Williams commented on gene: MBTPS2: Copied from the Osteogenesis imperfecta panel
Skeletal dysplasia v2.123 MBTPS2 Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37
Skeletal dysplasia v2.123 MBTPS2 Eleanor Williams gene: MBTPS2 was added
gene: MBTPS2 was added to Skeletal dysplasia. Sources: Expert list,Expert Review Amber
Q3_21_rating, Q3_21_expert_review tags were added to gene: MBTPS2.
Mode of inheritance for gene: MBTPS2 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: MBTPS2 were set to 27380894
Phenotypes for gene: MBTPS2 were set to Osteogenesis imperfecta, type XIX, OMIM:301014; osteogenesis imperfecta, type 19, MONDO:0049223
Skeletal dysplasia v2.122 SUCO Eleanor Williams commented on gene: SUCO: Copied from the Osteogenesis imperfecta panel to the Skeletal Dysplasia panel. Amber rating.
Skeletal dysplasia v2.122 SUCO Eleanor Williams Entity copied from Osteogenesis imperfecta v2.37
Skeletal dysplasia v2.122 SUCO Eleanor Williams gene: SUCO was added
gene: SUCO was added to Skeletal dysplasia. Sources: Expert Review Amber,Literature
Mode of inheritance for gene: SUCO was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SUCO were set to 29620724; 20440000
Phenotypes for gene: SUCO were set to Osteogenesis imperfecta, MONDO:0019019; skeletal dysplasia, HP:0002652; osteopenia
Skeletal dysplasia v2.121 COPB2 Eleanor Williams Classified gene: COPB2 as Amber List (moderate evidence)
Skeletal dysplasia v2.121 COPB2 Eleanor Williams Added comment: Comment on list classification: Gene copied from the Osteogenesis imperfecta panel. Leaving as amber for now, but there are 2 cases with fractures and 4 with osteopaenia, plus a mouse model with low bone mass, so sufficient to rate green after then next GMS review.
Skeletal dysplasia v2.121 COPB2 Eleanor Williams Gene: copb2 has been classified as Amber List (Moderate Evidence).
Osteogenesis imperfecta v2.37 COPB2 Eleanor Williams Classified gene: COPB2 as Amber List (moderate evidence)
Osteogenesis imperfecta v2.37 COPB2 Eleanor Williams Added comment: Comment on list classification: Leaving as amber for now, but there are 2 cases with fractures and 4 with osteopaenia, plus a mouse model with low bone mass, so sufficient to rate green after then next GMS review.
Osteogenesis imperfecta v2.37 COPB2 Eleanor Williams Gene: copb2 has been classified as Amber List (Moderate Evidence).
Skeletal dysplasia v2.120 COPB2 Eleanor Williams Entity copied from Osteogenesis imperfecta v2.36
Skeletal dysplasia v2.120 COPB2 Eleanor Williams gene: COPB2 was added
gene: COPB2 was added to Skeletal dysplasia. Sources: NHS GMS,Expert list,Expert Review Amber
Q3_21_rating, watchlist_moi tags were added to gene: COPB2.
Mode of inheritance for gene: COPB2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: COPB2 were set to 34450031; 29036432
Phenotypes for gene: COPB2 were set to juvenile osteoporosis; Osteopenia; Osteoporosis; recurrent fractures
Intellectual disability v3.1306 PITRM1 Ivone Leong Phenotypes for gene: PITRM1 were changed from Ataxia; Intellectual disability to Spinocerebellar ataxia, autosomal recessive 30, OMIM:619405
Primary immunodeficiency or monogenic inflammatory bowel disease v2.468 KMT2A Dmitrijs Rots reviewed gene: KMT2A: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 33783954, 28623346, 27320412; Phenotypes: Hypogammaglobulinemia, intellectual disability, hypertrichosis; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Primary immunodeficiency or monogenic inflammatory bowel disease v2.468 KDM6A Dmitrijs Rots changed review comment from: Immunodeficiency is a well-known and common feature of KS. Recent study shows:
"Overall, 44.1% (78/177) and 58.2% (46/79) of KS individuals exhibited infection susceptibility and hypogammaglobulinemia, respectively"; to: Immunodeficiency is a well-known and common feature of KS. Recent study shows:
"Overall, 44.1% (78/177) and 58.2% (46/79) of KS individuals exhibited infection susceptibility and hypogammaglobulinemia, respectively"

The gene is also included in Inborn errors of immunity classification: PMID 31953710
Thyroid cancer pertinent cancer susceptibility v1.3 CDKN1B Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'biallelic to 'monoallelic'. Literature review did not indicate presence of biallelic variants pertaining to thyroid or parathyroid tumours. The MOI for this gene is also monoallelic in OMIM and other PanelApp panels.
Thyroid cancer pertinent cancer susceptibility v1.3 CDKN1B Arina Puzriakova Mode of inheritance for gene: CDKN1B was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.1305 ATP1A3 Zornitza Stark Deleted their comment
Osteogenesis imperfecta v2.36 COPB2 Eleanor Williams Tag watchlist_moi tag was added to gene: COPB2.
DDG2P v2.46 ALG8 Sarah Leigh Added comment: Comment on mode of inheritance: Monoallelic variants are associated with Polycystic liver disease 3 with or without kidney cysts OMIM:617874, which is not relevant to this panel. Therefore biallelic moi is relevant to this panel.
DDG2P v2.46 ALG8 Sarah Leigh Mode of inheritance for gene: ALG8 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
DDG2P v2.45 ALG8 Sarah Leigh Phenotypes for gene: ALG8 were changed from ALG8-CDG 237145 to Congenital disorder of glycosylation, type Ih OMIM:608104; ALG8-CDG MONDO:0011969
Primary immunodeficiency or monogenic inflammatory bowel disease v2.468 B2M Eleanor Williams Added comment: Comment on mode of inheritance: Biallelic mode of inheritance is correct for Immunodeficiency 43. OMIM also has an entry for ?Amyloidosis, familial visceral, OMIM:105200 - Autosomal dominant but this phenotype is not relevant to this panel.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.468 B2M Eleanor Williams Mode of inheritance for gene: B2M was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder v1.156 ATXN7 Dmitrijs Rots reviewed gene: ATXN7: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Childhood onset dystonia, chorea or related movement disorder v1.156 ATXN1 Dmitrijs Rots reviewed gene: ATXN1: Rating: RED; Mode of pathogenicity: Other; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Severe microcephaly v2.250 TNPO2 Arina Puzriakova Classified gene: TNPO2 as Amber List (moderate evidence)
Severe microcephaly v2.250 TNPO2 Arina Puzriakova Added comment: Comment on list classification: There are sufficient unrelated cases presenting were a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Severe microcephaly v2.250 TNPO2 Arina Puzriakova Gene: tnpo2 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.429 TNPO2 Arina Puzriakova Classified gene: TNPO2 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.429 TNPO2 Arina Puzriakova Added comment: Comment on list classification: There are sufficient unrelated cases presenting were a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Early onset or syndromic epilepsy v2.429 TNPO2 Arina Puzriakova Gene: tnpo2 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.249 TNPO2 Arina Puzriakova gene: TNPO2 was added
gene: TNPO2 was added to Severe microcephaly. Sources: Literature
Q3_21_rating tags were added to gene: TNPO2.
Mode of inheritance for gene: TNPO2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNPO2 were set to 34314705
Phenotypes for gene: TNPO2 were set to Intellectual disability; Dysmorphic features; Microcephaly; Seizures; Hypotonia
Review for gene: TNPO2 was set to GREEN
Added comment: Goodman et al., 2021 (PMID: 34314705) reported on 15 unrelated individuals with different variants in this gene (14 de novo, 1 mosaic in mother; 12 SNVs, 3 in-frame deletions, 1 deletion-insertion). All had GDD and all those who were assessed also had ID (9/9), ranging from mild to severe. ID also suspected but not investigated in another 3 cases. 6 had seizures starting between 1 and 2.5 years of age. 5 individuals had microcephaly (HC ranging -2.77 to -4.53 SD). Other less common features were also observed such as variable brain, gastrointestinal and ophthalmologic abnormalities.

Notably 6 individuals had additional SNVs/CNVs of uncertain significance, some of which include known ID genes (e.g. SETBP1, CUX2, ARMC9, PDE4D), but were discounted due to lack of explanation of the overall patient phenotype.

Some functional studies conducted in Drosophila demonstrated that patient-associated variants caused neurodevelopmental defects that were dosage and location (of variant within protein) dependent.
Sources: Literature
Early onset or syndromic epilepsy v2.428 TNPO2 Arina Puzriakova gene: TNPO2 was added
gene: TNPO2 was added to Genetic epilepsy syndromes. Sources: Literature
Q3_21_rating tags were added to gene: TNPO2.
Mode of inheritance for gene: TNPO2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TNPO2 were set to 34314705
Phenotypes for gene: TNPO2 were set to Intellectual disability; Dysmorphic features; Microcephaly; Seizures; Hypotonia
Review for gene: TNPO2 was set to GREEN
Added comment: Goodman et al., 2021 (PMID: 34314705) reported on 15 unrelated individuals with different variants in this gene (14 de novo, 1 mosaic in mother; 12 SNVs, 3 in-frame deletions, 1 deletion-insertion). All had GDD and all those who were assessed also had ID (9/9), ranging from mild to severe. ID also suspected but not investigated in another 3 cases. 6 had seizures starting between 1 and 2.5 years of age. 5 individuals had microcephaly (HC ranging -2.77 to -4.53 SD). Other less common features were also observed such as variable brain, gastrointestinal and ophthalmologic abnormalities.

Notably 6 individuals had additional SNVs/CNVs of uncertain significance, some of which include known ID genes (e.g. SETBP1, CUX2, ARMC9, PDE4D), but were discounted due to lack of explanation of the overall patient phenotype.

Some functional studies conducted in Drosophila demonstrated that patient-associated variants caused neurodevelopmental defects that were dosage and location (of variant within protein) dependent.
Sources: Literature
Intellectual disability v3.1305 TNPO2 Arina Puzriakova Classified gene: TNPO2 as Amber List (moderate evidence)
Intellectual disability v3.1305 TNPO2 Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber but there are now sufficient unrelated cases with a relevant phenotype associated with various variants in this gene to rate as Green at the next GMS panel update.
Intellectual disability v3.1305 TNPO2 Arina Puzriakova Gene: tnpo2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1304 TNPO2 Arina Puzriakova Mode of inheritance for gene: TNPO2 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability v3.1303 TNPO2 Arina Puzriakova Phenotypes for gene: TNPO2 were changed from to Intellectual disability; Dysmorphic features; Microcephaly; Seizures; Hypotonia
Intellectual disability v3.1302 TNPO2 Arina Puzriakova Publications for gene: TNPO2 were set to 26350204
Intellectual disability v3.1301 TNPO2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: TNPO2.
Intellectual disability v3.1301 TNPO2 Arina Puzriakova reviewed gene: TNPO2: Rating: ; Mode of pathogenicity: None; Publications: 34314705; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Skeletal dysplasia v2.119 LRRK1 Conor Pallatt gene: LRRK1 was added
gene: LRRK1 was added to Skeletal dysplasia. Sources: NHS GMS,Literature
Mode of inheritance for gene: LRRK1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LRRK1 were set to 27829680; 27055475; 31571209; 32119750
Phenotypes for gene: LRRK1 were set to Osteosclerotic metaphyseal dysplasia (OSMD) (OMIM: 615198)
Penetrance for gene: LRRK1 were set to Complete
Review for gene: LRRK1 was set to GREEN
Added comment: A detailed phenotypic picture of Osteosclerotic metaphyseal dysplasia (OSMD) in patients with LRRK1 variants can be seen in table 1 of Howaldt et al (2020).

Lida et al (2016) identified homozygous deletion that is predicted to result in elongation of protein (p.E1980Afs*66) in a child with OSMD. Child was born to consanguineous parents, both heterozygous for variant.

Guo et al (2017) identified a family with OSMD. Healthy, non-consanguineous parents have two children with OSMD that are homozygous for 1bp insertion in LRRK1 that is predicted to result in a frame-shift and produce an elongated protein (p.A1991Gfs*31) without nonsense-mediated mRNA decay. A similar effect seen in Lida et al (2016).

Howaldt et al (2020) shows a patient with a homozygous splice site mutation resulting in near complete skipping of exon 3 in cDNA leading to a frameshift (p.Ala34Profs*33). The variant segregated with disorder in the family with parents being heterozygous for the variant and clinically unaffected.

Miryounesi et al (2020) identified a patient with suspected OSMD from healthy, consanguineous parents. Patient is homozygous for stop gain mutation (c.2785G > T, p.E929X) in LRRK1. Parents are heterozygous for the variant.

Homozygous nonsense variant in LRRK1 also identified in an individual recruited to the 100,000 genomes project for skeletal dysplasia, Osteosclerotic metaphyseal dysplasia is considered a good fit for phenotype.

LRRK1 gene should be included in the skeletal dysplasia panel as a green gene at the next GMS panel update.
Sources: NHS GMS, Literature
Severe microcephaly v2.248 ARCN1 Ivone Leong Phenotypes for gene: ARCN1 were changed from Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay (MIM#617164) to Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay, OMIM:617164
Severe microcephaly v2.247 ARCN1 Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype (probable). Patients 1, 3 and 4 (patients 3 and 4 are from the same family) from PMID:27476655 have a head circumference <-3 SD. Patient 2 has head circumference of -1.53 SD, which is not severe enough for this panel. Therefore, there is currently not enough evidence for a gene-disease association. This gene has been given an Amber rating.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype (probable). Patients 1, 3 and 4 (patients 3 and 4 are from the same family) from PMID:27476655 have a head circumference <-3 SD. Patient 2 has head circumference of -1.53 SD, which is not severe enough for this panel.

The patients in the 2 additional papers (PMID: 31075182 and 33154040) do have microcephaly; however, it is not clear as to what the severity is of the patients currently (only their birth head circumferences was given, which were not severe enough for this panel, and no measurements were given at later time points).

Therefore, there is currently not enough evidence for a gene-disease association. This gene has been given an Amber rating.
Intellectual disability v3.1301 LINGO4 Arina Puzriakova Classified gene: LINGO4 as Amber List (moderate evidence)
Intellectual disability v3.1301 LINGO4 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There a sufficient unrelated cases with a relevant phenotype to rate as Green at the next GMS panel update.
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PMID: 33098801 - 4 individuals from 3 unrelated families harbouring private biallelic variants in this gene which co-segregated with disease. 4/4 cases presented with GDD and ID.
Intellectual disability v3.1301 LINGO4 Arina Puzriakova Gene: lingo4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1300 LINGO4 Arina Puzriakova Tag Q3_21_rating tag was added to gene: LINGO4.
Severe microcephaly v2.247 ARCN1 Ivone Leong changed review comment from: Comment on publications: PMID:27476655. OMIM description of the patients, "exhibited rhizomelic short stature (4/4) as well as microcephaly (3/4), micrognathia (4/4), laxity of the small joints (3/4), and developmental delay (4/4). Other variable features included posterior cataract (1/4), cleft palate (1/4), ventricular septal defect (1/4), cryptorchidism (1/2), seizures (1/4), and autism (1/4)."

Additional publications. PMID: 31075182 describes a 5th case with de novo loss-of-function variant in ARCN1. Head circumference at birth (prematurely after 33 + 3 weeks of pregnancy) was 27.3 cm (<3rd percentile). The publication says the patient presented with microcephaly; however, I cannot find any recent head circumference measurements (child is 23 months old). From the paper "we report a de novo loss-of-function mutation in the delta-COP subunit of COPI, associated with microcephaly, retrognathia, muscular hypotonia, short stature, rhizomelic shortening, and transiently hypoglycosylation during febrile infections."

PMID: 33154040; to: Comment on publications: PMID:27476655. OMIM description of the patients, "exhibited rhizomelic short stature (4/4) as well as microcephaly (3/4), micrognathia (4/4), laxity of the small joints (3/4), and developmental delay (4/4). Other variable features included posterior cataract (1/4), cleft palate (1/4), ventricular septal defect (1/4), cryptorchidism (1/2), seizures (1/4), and autism (1/4)."

Additional publications. PMID: 31075182 describes a 5th case with de novo loss-of-function variant in ARCN1. Head circumference at birth (prematurely after 33 + 3 weeks of pregnancy) was 27.3 cm (<3rd percentile). The publication says the patient presented with microcephaly; however, I cannot find any recent head circumference measurements (child is 23 months old). From the paper "we report a de novo loss-of-function mutation in the delta-COP subunit of COPI, associated with microcephaly, retrognathia, muscular hypotonia, short stature, rhizomelic shortening, and transiently hypoglycosylation during febrile infections."

PMID: 33154040 describes another case. "3.5-yr-old Caucasian/Peruvian/Native American boy with microcephaly, severe global developmental delay, and multiple congenital abnormalities. At birth he was documented to have a small ventricular septal defect (which was closed by 3 wk), a patent foramen ovale, rhizomelic shortening of extremities on clinical examination, pectus carinatum, and underdeveloped genitalia including severe penoscrotal hypospadias and cryptorchidism." OFC at birth was just above 10th centile, at 3.5 yr OFC is below 3rd centile but no actual measurements were given. Microarrays identified a 95-kb loss at 12q23.2 including exons 1–4 of the NUP37 gene and exons 1–9 of the PARPBP gene, which were deemed nondiagnostic (neither parents had this deletion). A heterozygous variant was also found in HSPG2 (c.9893 C > T, p. Pro3298Leu). Biallelic variants in this gene is associated with skeletal disorders that did not fit the patient's phenotype and as the patient is heterozygous for a variant in HSPG2 it was deemed that this variant was not causative. WGS identified a de novo splice variant in ARCN1. mRNA studies showed that the variant caused retention of part of an intron in the transcript. The authors deemed the ARCN1 variant as the causative variant in this patient.
Severe microcephaly v2.247 ARCN1 Ivone Leong Added comment: Comment on publications: PMID:27476655. OMIM description of the patients, "exhibited rhizomelic short stature (4/4) as well as microcephaly (3/4), micrognathia (4/4), laxity of the small joints (3/4), and developmental delay (4/4). Other variable features included posterior cataract (1/4), cleft palate (1/4), ventricular septal defect (1/4), cryptorchidism (1/2), seizures (1/4), and autism (1/4)."

Additional publications. PMID: 31075182 describes a 5th case with de novo loss-of-function variant in ARCN1. Head circumference at birth (prematurely after 33 + 3 weeks of pregnancy) was 27.3 cm (<3rd percentile). The publication says the patient presented with microcephaly; however, I cannot find any recent head circumference measurements (child is 23 months old). From the paper "we report a de novo loss-of-function mutation in the delta-COP subunit of COPI, associated with microcephaly, retrognathia, muscular hypotonia, short stature, rhizomelic shortening, and transiently hypoglycosylation during febrile infections."

PMID: 33154040
Severe microcephaly v2.247 ARCN1 Ivone Leong Publications for gene: ARCN1 were set to 27476655
Severe microcephaly v2.246 ARCN1 Ivone Leong Tag Q3_21_rating was removed from gene: ARCN1.
Tag watchlist tag was added to gene: ARCN1.
Severe microcephaly v2.246 ARCN1 Ivone Leong Classified gene: ARCN1 as Amber List (moderate evidence)
Severe microcephaly v2.246 ARCN1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype (probable). Patients 1, 3 and 4 (patients 3 and 4 are from the same family) from PMID:27476655 have a head circumference <-3 SD. Patient 2 has head circumference of -1.53 SD, which is not severe enough for this panel. Therefore, there is currently not enough evidence for a gene-disease association. This gene has been given an Amber rating.
Severe microcephaly v2.246 ARCN1 Ivone Leong Gene: arcn1 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.245 ARCN1 Ivone Leong Tag Q3_21_rating tag was added to gene: ARCN1.
Childhood onset dystonia, chorea or related movement disorder v1.156 IMPDH2 Arina Puzriakova Publications for gene: IMPDH2 were set to 33098801
Childhood onset dystonia, chorea or related movement disorder v1.155 IMPDH2 Arina Puzriakova Classified gene: IMPDH2 as Amber List (moderate evidence)
Childhood onset dystonia, chorea or related movement disorder v1.155 IMPDH2 Arina Puzriakova Added comment: Comment on list classification: This gene is not yet associated with a relevant phenotype in OMIM or G2P, but there are sufficient unrelated cases (3) presenting with signs of dystonia to rate as Green at the next GMS review. Other cases reported with motor dysfunction, and it is plausible that this may develop into dystonia later in life.
Childhood onset dystonia, chorea or related movement disorder v1.155 IMPDH2 Arina Puzriakova Gene: impdh2 has been classified as Amber List (Moderate Evidence).
Childhood onset dystonia, chorea or related movement disorder v1.154 IMPDH2 Arina Puzriakova Deleted their comment
Childhood onset dystonia, chorea or related movement disorder v1.154 IMPDH2 Arina Puzriakova edited their review of gene: IMPDH2: Added comment: Kuukasjärvi et al., 2021 (PMID: 34305140) report on an additional large Finnish family (6 affected members) with a heterozygous truncating variant co-segregating with a dominantly inherited dystonia-tremor phenotype. Patient fibroblasts showed reduced IMPDH2 expression. IMPDH2 is the rate-limiting enzyme in the biosynthesis of guanine nucleotides, a dopamine synthetic pathway previously linked to childhood or adolescence-onset dystonia disorders.; Changed publications to: 33098801, 34305140
Childhood onset dystonia, chorea or related movement disorder v1.154 IMPDH2 Arina Puzriakova Entity copied from Intellectual disability v3.1300
Childhood onset dystonia, chorea or related movement disorder v1.154 IMPDH2 Arina Puzriakova gene: IMPDH2 was added
gene: IMPDH2 was added to Childhood onset dystonia or chorea or related movement disorder. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: IMPDH2.
Mode of inheritance for gene: IMPDH2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: IMPDH2 were set to 33098801
Phenotypes for gene: IMPDH2 were set to Neurodevelopmental disorder with dystonia
Intellectual disability v3.1300 IMPDH2 Arina Puzriakova Classified gene: IMPDH2 as Amber List (moderate evidence)
Intellectual disability v3.1300 IMPDH2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. This gene is not yet associated with a relevant phenotype in OMIM or G2P, but sufficient unrelated cases with relevant phenotype to rate Green at the next GMS review. Neurodevelopmental delay is an early feature that may be evident prior to other manifestations (plausible that other cases may develop dystonic signs later in life) and so inclusion on this panel is warranted.
Intellectual disability v3.1300 IMPDH2 Arina Puzriakova Gene: impdh2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1299 IMPDH2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: IMPDH2.
Intellectual disability v3.1299 IMPDH2 Arina Puzriakova reviewed gene: IMPDH2: Rating: GREEN; Mode of pathogenicity: None; Publications: 33098801; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy v2.427 CLCN3 Arina Puzriakova Entity copied from Intellectual disability v3.1299
Early onset or syndromic epilepsy v2.427 CLCN3 Arina Puzriakova gene: CLCN3 was added
gene: CLCN3 was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: CLCN3.
Mode of inheritance for gene: CLCN3 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: CLCN3 were set to 34186028
Phenotypes for gene: CLCN3 were set to Neurodevelopmental disorder with hypotonia and brain abnormalities, OMIM:619512; Neurodevelopmental disorder with seizures and brain abnormalities, OMIM:619517
Mode of pathogenicity for gene: CLCN3 was set to Other
Intellectual disability v3.1299 CLCN3 Arina Puzriakova Tag Q3_21_rating tag was added to gene: CLCN3.
Intellectual disability v3.1299 CLCN3 Arina Puzriakova Classified gene: CLCN3 as Amber List (moderate evidence)
Intellectual disability v3.1299 CLCN3 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There is enough evidence to promote this gene to Green at the next GMS panel update. Sufficient number of unrelated cases with relevant phenotype to add to the ID and epilepsy panels. Functional studies and animal model support pathogenicity. CLCN3 is also associated with a relevant phenotype in OMIM (MIM# 619512 and 619517)
Intellectual disability v3.1299 CLCN3 Arina Puzriakova Gene: clcn3 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1298 CLCN3 Arina Puzriakova Mode of inheritance for gene: CLCN3 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Intellectual disability v3.1297 CLCN3 Arina Puzriakova Phenotypes for gene: CLCN3 were changed from Neurodevelopmental disorder to Neurodevelopmental disorder with hypotonia and brain abnormalities, OMIM:619512; Neurodevelopmental disorder with seizures and brain abnormalities, OMIM:619517
Fetal anomalies v1.717 GREB1L Rhiannon Mellis edited their review of gene: GREB1L: Added comment: A further prenatal case reported in PMID 31974414 (Vora et al 2020) - c.4881_4882del; [p.H1627fs] inherited from parent, 2 affected pregnancies with bilateral renal agenesis plus a living child with single kidney.; Changed rating: GREEN; Changed publications to: PMID: 31424080, 32378186, 31974414
Intellectual disability v3.1296 ANK2 Arina Puzriakova Classified gene: ANK2 as Amber List (moderate evidence)
Intellectual disability v3.1296 ANK2 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 review - sufficient unrelated cases with relevant phenotype and de novo PTVs in this gene. Definitive gene-disease association is supported by the ClinGen ID and Autism Expert Panel.
Intellectual disability v3.1296 ANK2 Arina Puzriakova Gene: ank2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1295 ANK2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: ANK2.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.467 KDM6A Arina Puzriakova Phenotypes for gene: KDM6A were changed from Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present; Kabuki Syndrome 2 due to KDM6A deficiency; Combined immunodeficiencies with associated or syndromic features to Kabuki syndrome 2, OMIM:300867; Recurrent infections (otitis media, pneumonia); Autoimmunity; Combined immunodeficiencies with associated or syndromic features
Primary immunodeficiency or monogenic inflammatory bowel disease v2.466 KDM6A Arina Puzriakova Publications for gene: KDM6A were set to 25142838; 15523604; 32048120; 25546742; 15887282; 32086639; 26411453; 22197486; 23076834
Primary immunodeficiency or monogenic inflammatory bowel disease v2.465 KDM6A Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: KDM6A.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.465 KDM6A Arina Puzriakova commented on gene: KDM6A
Malformations of cortical development v2.91 TP73 Arina Puzriakova Entity copied from Intellectual disability v3.1295
Malformations of cortical development v2.91 TP73 Arina Puzriakova gene: TP73 was added
gene: TP73 was added to Malformations of cortical development. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: TP73.
Mode of inheritance for gene: TP73 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TP73 were set to 31130284; 34077761
Phenotypes for gene: TP73 were set to Ciliary dyskinesia, primary, 47, and lissencephaly, OMIM:619466
Intellectual disability v3.1295 TP73 Arina Puzriakova Publications for gene: TP73 were set to 31130284
Intellectual disability v3.1295 TP73 Arina Puzriakova Classified gene: TP73 as Amber List (moderate evidence)
Intellectual disability v3.1295 TP73 Arina Puzriakova Added comment: Comment on list classification: There is now sufficient evidence to promote this gene to Green at the next GMS panel review - at least 7 unrelated families with distinct variants and relevant phenotypes. Supported by some functional data.

TP73 is also now associated with a relevant phenotype in OMIM (MIM# 619466) but is not yet listed in G2P.
Intellectual disability v3.1295 TP73 Arina Puzriakova Gene: tp73 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1294 TP73 Arina Puzriakova Tag Q3_21_rating tag was added to gene: TP73.
Intellectual disability v3.1294 TP73 Arina Puzriakova edited their review of gene: TP73: Changed rating: GREEN; Changed publications to: 31130284, 34077761; Changed phenotypes to: Ciliary dyskinesia, primary, 47, and lissencephaly, OMIM:619466
Intellectual disability v3.1294 TP73 Arina Puzriakova commented on gene: TP73: PMID: 34077761 (2021) - Further 7 individuals from 5 families identified with different homozygous variants in this gene. All affected individuals exhibited cortical malformations characterised by lissencephaly, central muscular hypotonia and moderate to severe cognitive dysfunction.
Intellectual disability v3.1294 TP73 Arina Puzriakova Phenotypes for gene: TP73 were changed from Intellectual disability; lissencephaly to Ciliary dyskinesia, primary, 47, and lissencephaly, OMIM:619466
Early onset or syndromic epilepsy v2.426 AP1G1 Arina Puzriakova Entity copied from Intellectual disability v3.1293
Early onset or syndromic epilepsy v2.426 AP1G1 Arina Puzriakova gene: AP1G1 was added
gene: AP1G1 was added to Genetic epilepsy syndromes. Sources: Literature,Expert Review Amber
Q3_21_rating tags were added to gene: AP1G1.
Mode of inheritance for gene: AP1G1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: AP1G1 were set to 34102099
Phenotypes for gene: AP1G1 were set to Neurodevelopmental disorder (NDD); Intellectual Disability; Epilepsy
Intellectual disability v3.1293 AP1G1 Arina Puzriakova Mode of inheritance for gene AP1G1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability v3.1292 AP1G1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: AP1G1.
Intellectual disability v3.1292 AP1G1 Arina Puzriakova Classified gene: AP1G1 as Amber List (moderate evidence)
Intellectual disability v3.1292 AP1G1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Usmani et al., 2021 (PMID: 34102099) identified 9 families with heterozygous and 2 families with homozygous variants in this gene. All individuals (12) had GDD and ID of various severity (mild to severe), except one patient who died at 22 days. Other features include hypotonia (9/10), seizures (6/10) and spasticity (4/10). Some supportive functional data included.

There is sufficient evidence to promote this gene to Green at the next GMS panel update, with 'monoallelic' MOI. Biallelic cases would still be picked up by the Genomics England pipeline - but this may be reviewed if additional cases are discovered.
Intellectual disability v3.1292 AP1G1 Arina Puzriakova Gene: ap1g1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1291 ATP9A Arina Puzriakova Publications for gene: ATP9A were set to
Severe microcephaly v2.245 ATP9A Arina Puzriakova Publications for gene: ATP9A were set to http://dx.doi.org/10.1136/jmedgenet-2021-107843
Intellectual disability v3.1290 ATP9A Arina Puzriakova Classified gene: ATP9A as Amber List (moderate evidence)
Intellectual disability v3.1290 ATP9A Arina Puzriakova Added comment: Comment on list classification: Rating Amber, awaiting further cases/clinical evidence.
Intellectual disability v3.1290 ATP9A Arina Puzriakova Gene: atp9a has been classified as Amber List (Moderate Evidence).
Childhood onset dystonia, chorea or related movement disorder v1.153 CAMK4 Arina Puzriakova Entity copied from Intellectual disability v3.1289
Childhood onset dystonia, chorea or related movement disorder v1.153 CAMK4 Arina Puzriakova gene: CAMK4 was added
gene: CAMK4 was added to Childhood onset dystonia or chorea or related movement disorder. Sources: Other,Expert Review Amber,Literature
Q3_21_rating tags were added to gene: CAMK4.
Mode of inheritance for gene: CAMK4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CAMK4 were set to 30262571; 33098801; 33211350
Phenotypes for gene: CAMK4 were set to Global developmental delay; Intellectual disability; Autism; Behavioral abnormality; Abnormality of movement; Dystonia; Ataxia; Chorea; Myoclonus
Penetrance for gene: CAMK4 were set to Complete
Mode of pathogenicity for gene: CAMK4 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Intellectual disability v3.1289 CAMK4 Arina Puzriakova Classified gene: CAMK4 as Amber List (moderate evidence)
Intellectual disability v3.1289 CAMK4 Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. There are sufficient unrelated cases (3) presenting with a relevant phenotype in association with different variants in the CAMK4 gene.
Intellectual disability v3.1289 CAMK4 Arina Puzriakova Gene: camk4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1288 CAMK4 Arina Puzriakova Tag Q3_21_rating tag was added to gene: CAMK4.
Intellectual disability v3.1288 CAMK4 Arina Puzriakova Mode of pathogenicity for gene: CAMK4 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 v2.425 SYNCRIP Arina Puzriakova Classified gene: SYNCRIP as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.425 SYNCRIP Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. Rating Amber as only two individuals with seizures have been reported to date (MAE type)
Early onset or syndromic epilepsy v2.425 SYNCRIP Arina Puzriakova Gene: syncrip has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1287 SYNCRIP Arina Puzriakova Phenotypes for gene: SYNCRIP were changed from to Global developmental delay; Intellectual disability; Autism; Myoclonic atonic seizures; Abnormality of nervous system morphology
Intellectual disability v3.1286 SYNCRIP Arina Puzriakova Publications for gene: SYNCRIP were set to 27479843; 26350204
Intellectual disability v3.1285 SYNCRIP Arina Puzriakova Tag watchlist was removed from gene: SYNCRIP.
Tag Q3_21_rating tag was added to gene: SYNCRIP.
Intellectual disability v3.1285 SYNCRIP Arina Puzriakova Classified gene: SYNCRIP as Amber List (moderate evidence)
Intellectual disability v3.1285 SYNCRIP Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber but there are sufficient unrelated cases to rate as Green at the next GMS review. All individuals reported to date have presented with ID of various severity as the predominant feature.
Intellectual disability v3.1285 SYNCRIP Arina Puzriakova Gene: syncrip has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1284 SYNCRIP Arina Puzriakova Mode of inheritance for gene: SYNCRIP was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Severe microcephaly v2.244 EIF2S3 Ivone Leong Tag Q3_21_rating tag was added to gene: EIF2S3.
Severe microcephaly v2.244 EIF2S3 Ivone Leong Classified gene: EIF2S3 as Amber List (moderate evidence)
Severe microcephaly v2.244 EIF2S3 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype (probable). There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.244 EIF2S3 Ivone Leong Gene: eif2s3 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.243 EIF2S3 Ivone Leong Phenotypes for gene: EIF2S3 were changed from MEHMO syndrome, MIM# 300148 to MEHMO syndrome, OMIM:300148
Intellectual disability v3.1283 HIST1H4C Ivone Leong Tag watchlist was removed from gene: HIST1H4C.
Tag Q3_21_rating tag was added to gene: HIST1H4C.
Intellectual disability v3.1283 HIST1H4C Ivone Leong reviewed gene: HIST1H4C: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Severe microcephaly v2.242 HIST1H4C Ivone Leong Tag Q3_21_rating tag was added to gene: HIST1H4C.
Severe microcephaly v2.242 HIST1H4C Ivone Leong Classified gene: HIST1H4C as Amber List (moderate evidence)
Severe microcephaly v2.242 HIST1H4C Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (possible) but not OMIM. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.242 HIST1H4C Ivone Leong Gene: hist1h4c has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.241 HIST1H4C Ivone Leong commented on gene: HIST1H4C
Severe microcephaly v2.241 HIST1H4C Ivone Leong Tag new-gene-name tag was added to gene: HIST1H4C.
Severe microcephaly v2.241 LAGE3 Ivone Leong Tag Q3_21_rating tag was added to gene: LAGE3.
Severe microcephaly v2.241 LAGE3 Ivone Leong Classified gene: LAGE3 as Amber List (moderate evidence)
Severe microcephaly v2.241 LAGE3 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype (possible). There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.241 LAGE3 Ivone Leong Gene: lage3 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.240 LAGE3 Ivone Leong Phenotypes for gene: LAGE3 were changed from Galloway-Mowat syndrome 2, X-linked, MIM# 301006 to Galloway-Mowat syndrome 2, X-linked, OMIM:301006
Intellectual disability v3.1283 ATP1A3 Arina Puzriakova Publications for gene: ATP1A3 were set to 22842232; 29396171; 29291920; 22842232; 28969699; 32802951
Intellectual disability v3.1282 ATP1A3 Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: ATP1A3.
Intellectual disability v3.1282 ATP1A3 Arina Puzriakova commented on gene: ATP1A3: Gene was reassessed following a further Green review by Zornitza Stark (8 Jul 2021). Vetro et al. (PMID: 33880529) identified several individuals with variants in this gene who presented with DD/ID as the predominant feature. Therefore, ATP1A3 will be flagged for GMS expert review as inclusion on this panel may be of value in some patients but previous comments regarding association with several phenotypes should be considered.
Early onset or syndromic epilepsy v2.424 MED17 Ivone Leong Tag watchlist tag was added to gene: MED17.
Early onset or syndromic epilepsy v2.424 MED17 Ivone Leong Phenotypes for gene: MED17 were changed from Microcephaly, postnatal progressive, with seizures and brain atrophy 613668 to Microcephaly, postnatal progressive, with seizures and brain atrophy, OMIM:613668
Early onset or syndromic epilepsy v2.423 MED17 Ivone Leong Publications for gene: MED17 were set to 26004231; 20950787
Early onset or syndromic epilepsy v2.422 MED17 Ivone Leong reviewed gene: MED17: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Severe microcephaly v2.239 MED17 Ivone Leong Classified gene: MED17 as Amber List (moderate evidence)
Severe microcephaly v2.239 MED17 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. This gene as been given an Amber rating as 2 out of 3 cases (PMID:20950787 is caused by founder effect) have severe microcephaly. Until further evidence is available this gene will remain as Amber.
Severe microcephaly v2.239 MED17 Ivone Leong Gene: med17 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.238 MED17 Ivone Leong Tag watchlist tag was added to gene: MED17.
Severe microcephaly v2.238 MED17 Ivone Leong Phenotypes for gene: MED17 were changed from Microcephaly, postnatal progressive, with seizures and brain atrophy, MIM# 613668 to Microcephaly, postnatal progressive, with seizures and brain atrophy, OMIM:613668
Severe microcephaly v2.237 MED17 Ivone Leong Publications for gene: MED17 were set to 20950787; 30345598; 26004231
Intellectual disability v3.1282 CPE Dmitrijs Rots reviewed gene: CPE: Rating: GREEN; Mode of pathogenicity: None; Publications: 34383079; Phenotypes: Obesity, intellectual disability; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1282 RFX3 Arina Puzriakova Phenotypes for gene: RFX3 were changed from ID, ASD, ADHD to Intellectual disability, MONDO:0001071; Autism spectrum disorder, MONDO:0005258; Attention deficit-hyperactivity disorder, MONDO:0007743
Intellectual disability v3.1282 RFX7 Arina Puzriakova Phenotypes for gene: RFX7 were changed from Intellectual disability, MONDO:0001071, autism spectrum disorder, MONDO:0005258, attention deficit-hyperactivity disorder, MONDO:0007743 to Intellectual disability, MONDO:0001071; Autism spectrum disorder, MONDO:0005258; Attention deficit-hyperactivity disorder, MONDO:0007743
Intellectual disability v3.1281 RFX4 Arina Puzriakova Phenotypes for gene: RFX4 were changed from ID, ASD, ADHD to Intellectual disability, MONDO:0001071; Autism spectrum disorder, MONDO:0005258
Intellectual disability v3.1280 RFX7 Arina Puzriakova Classified gene: RFX7 as Amber List (moderate evidence)
Intellectual disability v3.1280 RFX7 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). 14 unrelated individuals were identified with different variants in the RFX7 gene (13 de novo, 1 unknown). Presenting phenotypes were predominantly of ID/GDD (13/14) and dysmorphism (12/14).

There are sufficient unrelated cases with a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Intellectual disability v3.1280 RFX7 Arina Puzriakova Gene: rfx7 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1279 RFX4 Arina Puzriakova Classified gene: RFX4 as Amber List (moderate evidence)
Intellectual disability v3.1279 RFX4 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). 6 individuals from 4 unrelated families were identified with different variants in the RFX4 gene (3 de novo, 1 inherited). Presenting phenotypes include ID/GDD (6/6) and ASD (5/6).

There are sufficient unrelated cases with a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Intellectual disability v3.1279 RFX4 Arina Puzriakova Gene: rfx4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1278 RFX7 Arina Puzriakova Tag Q3_21_rating tag was added to gene: RFX7.
Intellectual disability v3.1278 RFX4 Arina Puzriakova Tag Q3_21_rating tag was added to gene: RFX4.
Intellectual disability v3.1278 RFX3 Arina Puzriakova Tag Q3_21_rating tag was added to gene: RFX3.
Intellectual disability v3.1278 RFX3 Arina Puzriakova Classified gene: RFX3 as Amber List (moderate evidence)
Intellectual disability v3.1278 RFX3 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). 18 individuals from 15 unrelated families were identified with different heterozygous variants in the RFX3 gene (14 de novo, 1 inherited). Presenting phenotypes include ID/GDD (14/18), ASD (13/18) and ADHD (10/18).

There are sufficient unrelated cases with a relevant phenotype associated with variants in this gene to rate as Green at the next GMS panel update.
Intellectual disability v3.1278 RFX3 Arina Puzriakova Gene: rfx3 has been classified as Amber List (Moderate Evidence).
Osteogenesis imperfecta v2.36 TAPT1 Eleanor Williams Classified gene: TAPT1 as Green List (high evidence)
Osteogenesis imperfecta v2.36 TAPT1 Eleanor Williams Added comment: Comment on list classification: Leaving rating as green; 2 cases reported, supportive zebrafish data and green review by NHS expert.
Osteogenesis imperfecta v2.36 TAPT1 Eleanor Williams Gene: tapt1 has been classified as Green List (High Evidence).
Osteogenesis imperfecta v2.35 TAPT1 Eleanor Williams commented on gene: TAPT1: Only 2 cases reported but PMID: 26365339 - Symoens et al 2015 - also report that knock-down of zebrafish tapt1b resulted in severe malformations of the craniofacial skeleton and delayed ossification.

PMID: 17151244 - Howell et al 2007 - also reports a skeletal phenotype in a mouse with a homozygous mutation in Tapt1, primarily posterior-to-anterior transformations of the vertebral column midsection.
Severe microcephaly v2.236 NSD2 Ivone Leong Classified gene: NSD2 as Amber List (moderate evidence)
Severe microcephaly v2.236 NSD2 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There are >3 unrelated cases associated with this gene; however, the severity of microcephaly in these cases do not satisfy our criteria for severe microcephaly. Therefore, this gene has been given an Amber rating.
Severe microcephaly v2.236 NSD2 Ivone Leong Gene: nsd2 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.235 NSD2 Ivone Leong Publications for gene: NSD2 were set to 30345613; 31171569
Severe microcephaly v2.234 NSD2 Ivone Leong Phenotypes for gene: NSD2 were changed from microcephaly; intellectual disability to microcephaly, MONDO:0001149
Osteogenesis imperfecta v2.35 DSPP Eleanor Williams Tag Q3_21_expert_review tag was added to gene: DSPP.
Osteogenesis imperfecta v2.35 DSPP Eleanor Williams commented on gene: DSPP: Conflicting reviews so tagging for GMS review.
Severe microcephaly v2.233 NUP107 Ivone Leong Phenotypes for gene: NUP107 were changed from Galloway-Mowat syndrome 7, MIM# 618348 to Galloway-Mowat syndrome 7, OMIM:618348
Severe microcephaly v2.232 NUP107 Ivone Leong Classified gene: NUP107 as Amber List (moderate evidence)
Severe microcephaly v2.232 NUP107 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype (possible). There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.232 NUP107 Ivone Leong Gene: nup107 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.231 NUP107 Ivone Leong Tag Q3_21_rating tag was added to gene: NUP107.
Osteogenesis imperfecta v2.35 SGMS2 Eleanor Williams Classified gene: SGMS2 as Amber List (moderate evidence)
Osteogenesis imperfecta v2.35 SGMS2 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber but with a recommendation for green rating following GMS review. 8 cases reported with 3 different variants.
Osteogenesis imperfecta v2.35 SGMS2 Eleanor Williams Gene: sgms2 has been classified as Amber List (Moderate Evidence).
Osteogenesis imperfecta v2.34 SGMS2 Eleanor Williams Tag Q3_21_rating tag was added to gene: SGMS2.
Osteogenesis imperfecta v2.34 SGMS2 Eleanor Williams Phenotypes for gene: SGMS2 were changed from Calvarial doughnut lesions with bone fragility with or without spondylometaphyseal dysplasia MIM#126550 to Calvarial doughnut lesions with bone fragility with or without spondylometaphyseal dysplasia, OMIM:126550; calvarial doughnut lesions-bone fragility syndrome, MONDO:0007470
Osteogenesis imperfecta v2.33 SGMS2 Eleanor Williams reviewed gene: SGMS2: Rating: GREEN; Mode of pathogenicity: None; Publications: 30779713, 32028018; Phenotypes: Calvarial doughnut lesions with bone fragility with or without spondylometaphyseal dysplasia, OMIM:126550, calvarial doughnut lesions-bone fragility syndrome, MONDO:0007470; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Severe microcephaly v2.231 PCDH12 Ivone Leong Classified gene: PCDH12 as Amber List (moderate evidence)
Severe microcephaly v2.231 PCDH12 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.231 PCDH12 Ivone Leong Gene: pcdh12 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.230 PCDH12 Ivone Leong Tag Q3_21_rating tag was added to gene: PCDH12.
Severe microcephaly v2.230 PCDH12 Ivone Leong Phenotypes for gene: PCDH12 were changed from Diencephalic-mesencephalic junction dysplasia syndrome 1, MIM# 251280 to Diencephalic-mesencephalic junction dysplasia syndrome 1, OMIM:251280
Osteogenesis imperfecta v2.33 COPB2 Eleanor Williams Added comment: Comment on mode of inheritance: Left as monoallelic for now as only 1 biallelic case reported.
Osteogenesis imperfecta v2.33 COPB2 Eleanor Williams Mode of inheritance for gene: COPB2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Osteogenesis imperfecta v2.32 SUCO Eleanor Williams Phenotypes for gene: SUCO were changed from Osteogenesis imperfecta; skeletal dysplasia; osteopenia to Osteogenesis imperfecta, MONDO:0019019; skeletal dysplasia, HP:0002652; osteopenia
Osteogenesis imperfecta v2.31 SUCO Eleanor Williams Phenotypes for gene: SUCO were changed from Osteogenesis imperfecta to Osteogenesis imperfecta; skeletal dysplasia; osteopenia
Osteogenesis imperfecta v2.30 SUCO Eleanor Williams Classified gene: SUCO as Amber List (moderate evidence)
Osteogenesis imperfecta v2.30 SUCO Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber. 1 case plus supportive mouse model.
Osteogenesis imperfecta v2.30 SUCO Eleanor Williams Gene: suco has been classified as Amber List (Moderate Evidence).
Osteogenesis imperfecta v2.29 SUCO Eleanor Williams reviewed gene: SUCO: Rating: AMBER; Mode of pathogenicity: None; Publications: 29620724, 20440000; Phenotypes: skeletal dysplasia, osteopenia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1277 EIF2AK2 Dmitrijs Rots reviewed gene: EIF2AK2: 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: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Rare anaemia v1.26 RPS27 Zornitza Stark reviewed gene: RPS27: Rating: RED; Mode of pathogenicity: None; Publications: 25424902; Phenotypes: Diamond-Blackfan anemia 17, MIM# 617409; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Severe microcephaly v2.229 COPB2 Eleanor Williams gene: COPB2 was added
gene: COPB2 was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: COPB2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: COPB2 were set to 29036432
Phenotypes for gene: COPB2 were set to Microcephaly, HP:0000252
Review for gene: COPB2 was set to RED
Added comment: PMID: 29036432 - DiStasio et al 2017 - report of severe microcephaly (developing to be below -4.0 SD) and severe intellectual disability in the two siblings with a COPB2 homozygous variant.

The siblings were later investigated for low bone mass in PMID: 34450031 - Marom et al 2021 (in which heterozygous variants in COPB2 in 4 other families with probands with osteoporosis and developmental delay were identified, but no microcephaly reported).
Sources: Literature
Intellectual disability v3.1277 COPB2 Eleanor Williams Classified gene: COPB2 as Amber List (moderate evidence)
Intellectual disability v3.1277 COPB2 Eleanor Williams Added comment: Comment on list classification: Promoting from red to amber with a recommendation for green rating following GMS review.
Intellectual disability v3.1277 COPB2 Eleanor Williams Gene: copb2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1276 COPB2 Eleanor Williams Tag Q3_21_rating tag was added to gene: COPB2.
Intellectual disability v3.1276 COPB2 Eleanor Williams changed review comment from: PMID: 34450031 - Marom et al 2021 describes 6 individuals from 5 families. In 4 families loss of function heterozygous variants in COPB2 were found. In the 5th family, two affected siblings were found to have a homozygous variant in COPB2. Osteopenia was noted in 4/5 families (5th unknown) and fractures in 2/5. Developmental delay was observed in all 6 individuals with variable severity. Severe intellectual disability, seizures and microcephaly was noted in the siblings with the homozygous variants. Copb2þ +/-mice exhibit low bone mass
Sources: Literature; to: PMID: 34450031 - Marom et al 2021 describes 6 individuals from 5 families. In 4 families loss of function heterozygous variants in COPB2 were found. In the 5th family, two affected siblings were found to have a homozygous variant in COPB2. Osteopenia was noted in 4/5 families (5th unknown) and fractures in 2/5. Developmental delay was observed in all 6 individuals with variable severity. Severe intellectual disability, seizures and microcephaly was noted in the siblings with the homozygous variants. Copb2þ +/-mice exhibit low bone mass

PMID: 29036432 - original report of microcephaly in the two siblings with the COPB2 homozygous variant.
Osteogenesis imperfecta v2.29 COPB2 Eleanor Williams changed review comment from: As Zornitza Stark reports, PMID: 34450031 - Marom et al 2021 describes 6 individuals from 5 families. In 4 families loss of function heterozygous variants in COPB2 were found. In the 5th family, two affected siblings were found to have a homozygous variant in COPB2. Osteopenia was noted in 4/5 families (5th unknown) and fractures in 2/5. Developmental delay was observed in all 6 individuals. Severe intellectual disability, seizures and microcephaly was noted in the siblings with the homozygous variants. Copb2þ +/-mice exhibit low bone mass; to: As Zornitza Stark reports, PMID: 34450031 - Marom et al 2021 describes 6 individuals from 5 families. In 4 families loss of function heterozygous variants in COPB2 were found. In the 5th family, two affected siblings were found to have a homozygous variant in COPB2. Osteopenia was noted in 4/5 families (5th unknown) and fractures in 2/5. Developmental delay was observed in all 6 individuals. Severe intellectual disability, seizures and microcephaly was noted in the siblings with the homozygous variants. Copb2 +/-mice exhibit low bone mass.

PMID: 29036432 - original report of microcephaly in the two siblings with the COPB2 homozygous variant.
Osteogenesis imperfecta v2.29 COPB2 Eleanor Williams Publications for gene: COPB2 were set to 34450031
Intellectual disability v3.1276 COPB2 Eleanor Williams Added comment: Comment on mode of inheritance: 4 families with heterozygous variants and 1 with biallelic (more severe phenotype)
Intellectual disability v3.1276 COPB2 Eleanor Williams Mode of inheritance for gene: COPB2 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.1275 COPB2 Eleanor Williams gene: COPB2 was added
gene: COPB2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: COPB2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: COPB2 were set to 34450031
Phenotypes for gene: COPB2 were set to osteoporosis; developmental delay
Review for gene: COPB2 was set to GREEN
Added comment: PMID: 34450031 - Marom et al 2021 describes 6 individuals from 5 families. In 4 families loss of function heterozygous variants in COPB2 were found. In the 5th family, two affected siblings were found to have a homozygous variant in COPB2. Osteopenia was noted in 4/5 families (5th unknown) and fractures in 2/5. Developmental delay was observed in all 6 individuals with variable severity. Severe intellectual disability, seizures and microcephaly was noted in the siblings with the homozygous variants. Copb2þ +/-mice exhibit low bone mass
Sources: Literature
Osteogenesis imperfecta v2.28 COPB2 Eleanor Williams Phenotypes for gene: COPB2 were changed from juvenile osteoporosis to juvenile osteoporosis; Osteopenia; Osteoporosis; recurrent fractures
Osteogenesis imperfecta v2.27 COPB2 Eleanor Williams Publications for gene: COPB2 were set to Marom et al 2018 ASBMR: COPB2 Loss of Function Leads to Disrupted Collagen Trafficking and Juvenile Osteoporosis
Osteogenesis imperfecta v2.26 COPB2 Eleanor Williams Tag Q3_21_rating tag was added to gene: COPB2.
Osteogenesis imperfecta v2.26 COPB2 Eleanor Williams edited their review of gene: COPB2: Added comment: As Zornitza Stark reports, PMID: 34450031 - Marom et al 2021 describes 6 individuals from 5 families. In 4 families loss of function heterozygous variants in COPB2 were found. In the 5th family, two affected siblings were found to have a homozygous variant in COPB2. Osteopenia was noted in 4/5 families (5th unknown) and fractures in 2/5. Developmental delay was observed in all 6 individuals. Severe intellectual disability, seizures and microcephaly was noted in the siblings with the homozygous variants. Copb2þ +/-mice exhibit low bone mass; Changed rating: GREEN; Changed publications to: 34450031; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Osteogenesis imperfecta v2.26 MESD Eleanor Williams commented on gene: MESD: Further green review from NHS clinician, but already tagged for green rating in next GMS review.
Osteogenesis imperfecta v2.26 FAM46A Eleanor Williams commented on gene: FAM46A: Further green review by Meena Balasubramanian, so keeping green rating.
Osteogenesis imperfecta v2.26 FAM46A Eleanor Williams Phenotypes for gene: FAM46A were changed from Osteogenesis imperfecta, type XVIII, OMIM:617952 to Osteogenesis imperfecta, type XVIII, OMIM:617952; osteogenesis imperfecta, type 18, MONDO:0044329
Osteogenesis imperfecta v2.25 MBTPS2 Eleanor Williams Classified gene: MBTPS2 as Amber List (moderate evidence)
Osteogenesis imperfecta v2.25 MBTPS2 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber. Only 2 cases reported in literature so waiting for further GMS feedback on the rating of this gene.
Osteogenesis imperfecta v2.25 MBTPS2 Eleanor Williams Gene: mbtps2 has been classified as Amber List (Moderate Evidence).
Osteogenesis imperfecta v2.24 MBTPS2 Eleanor Williams changed review comment from: Associated with Osteogenesis imperfecta, type XIX #301014 (AR) in OMIM.

PMID: 27380894 - Lindert et al 2016 - report two independent OI pedigrees (Thai and German) without symptoms of any dermatological condition previously associated with variants in this gene(ichthyosis follicularis, atrichia, and photophobia (IFAP); BRESEK/BRESHECK syndrome; and keratosis follicularis spinulosa decalvans (KFSD)). In both families missense mutations were identified which was in or near the S2P NPDG motif vital for metal ion coordination. All those affected were male. Mutant S2P protein was found to be stable but cleavage or activation of S2P substrates OASIS and ATF6, respectively, was impaired, consistent with reduced proband collagen secretion.

A search of PubMed find no further cases.; to: Associated with Osteogenesis imperfecta, type XIX #301014 (AR) in OMIM.

PMID: 27380894 - Lindert et al 2016 - report two independent OI pedigrees (Thai and German) without symptoms of any dermatological condition previously associated with variants in this gene(ichthyosis follicularis, atrichia, and photophobia (IFAP); BRESEK/BRESHECK syndrome; and keratosis follicularis spinulosa decalvans (KFSD)). In both families missense mutations were identified which was in or near the S2P NPDG motif vital for metal ion coordination. All those affected were male. Mutant S2P protein was found to be stable but cleavage or activation of S2P substrates OASIS and ATF6, respectively, was impaired, consistent with reduced proband collagen secretion.

A search of PubMed finds no further cases.
Osteogenesis imperfecta v2.24 MBTPS2 Eleanor Williams Phenotypes for gene: MBTPS2 were changed from Osteogenesis imperfecta, type XIX, MIM# 301014 to Osteogenesis imperfecta, type XIX, OMIM:301014; osteogenesis imperfecta, type 19, MONDO:0049223
Osteogenesis imperfecta v2.23 MBTPS2 Eleanor Williams Tag Q3_21_rating tag was added to gene: MBTPS2.
Tag Q3_21_expert_review tag was added to gene: MBTPS2.
Osteogenesis imperfecta v2.23 MBTPS2 Eleanor Williams reviewed gene: MBTPS2: Rating: AMBER; Mode of pathogenicity: None; Publications: 27380894; Phenotypes: Osteogenesis imperfecta, type XIX, OMIM:301014; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Pituitary hormone deficiency v2.7 HID1 Arina Puzriakova Entity copied from Intellectual disability v3.1274
Pituitary hormone deficiency v2.7 HID1 Arina Puzriakova gene: HID1 was added
gene: HID1 was added to Pituitary hormone deficiency. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: HID1.
Mode of inheritance for gene: HID1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HID1 were set to 33999436
Phenotypes for gene: HID1 were set to Syndromic infantile encephalopathy; Hypopituitarism
Early onset or syndromic epilepsy v2.422 HID1 Arina Puzriakova Entity copied from Intellectual disability v3.1274
Early onset or syndromic epilepsy v2.422 HID1 Arina Puzriakova gene: HID1 was added
gene: HID1 was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: HID1.
Mode of inheritance for gene: HID1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HID1 were set to 33999436
Phenotypes for gene: HID1 were set to Syndromic infantile encephalopathy; Hypopituitarism
Intellectual disability v3.1274 HID1 Arina Puzriakova Tag Q3_21_rating tag was added to HID1.
Intellectual disability v3.1273 HID1 Arina Puzriakova Classified gene: HID1 as Amber List (moderate evidence)
Intellectual disability v3.1273 HID1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There is enough evidence to promote this gene to Green at the next GMS panel update.
Intellectual disability v3.1273 HID1 Arina Puzriakova Gene: hid1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1272 HID1 Arina Puzriakova reviewed gene: HID1: Rating: GREEN; Mode of pathogenicity: None; Publications: 33999436; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies v1.717 GNB1 Sarah Leigh Added comment: Comment on mode of pathogenicity: Gen2Phen entry for GNB1 (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=2121) lists the mutation consequence summary as Activating
Fetal anomalies v1.717 GNB1 Sarah Leigh Mode of pathogenicity for gene: GNB1 was changed from to None
Childhood onset dystonia, chorea or related movement disorder v1.152 GNB1 Sarah Leigh Added comment: Comment on mode of pathogenicity: Gen2Phen entry for GNB1 (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=2121) lists the mutation consequence summary as Activating
Childhood onset dystonia, chorea or related movement disorder v1.152 GNB1 Sarah Leigh Mode of pathogenicity for gene: GNB1 was changed from None to Other
Intellectual disability v3.1272 GNB1 Sarah Leigh Added comment: Comment on mode of pathogenicity: Gen2Phen entry for GNB1 (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=2121) lists the mutation consequence summary as Activating
Intellectual disability v3.1272 GNB1 Sarah Leigh Mode of pathogenicity for gene: GNB1 was changed from to None
Early onset or syndromic epilepsy v2.421 GNB1 Sarah Leigh Added comment: Comment on mode of pathogenicity: Gen2Phen entry for GNB1 (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=2121) lists the mutation consequence summary as Activating
Early onset or syndromic epilepsy v2.421 GNB1 Sarah Leigh Mode of pathogenicity for gene: GNB1 was changed from None to Other
Clefting v2.49 GNB1 Sarah Leigh Added comment: Comment on mode of pathogenicity: Gen2Phen entry for GNB1 (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=2121) lists the mutation consequence summary as Activating
Clefting v2.49 GNB1 Sarah Leigh Mode of pathogenicity for gene: GNB1 was changed from to Other
Childhood onset dystonia, chorea or related movement disorder v1.151 GRIN1 Sarah Leigh edited their review of gene: GRIN1: Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen, although there is a confirmed association with epileptic encephalopathy in Gen2Phen. At least 20 variants have been associated with Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254 and three have been associated with Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive OMIM:617820.; Changed rating: GREEN
Intellectual disability v3.1271 GRIN1 Sarah Leigh Phenotypes for gene: GRIN1 were changed from Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive, 617820; NDHMSR; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant, 614254; NDHMSD; Mental retardation, autosomal dominant 8, 614254; EPILEPTIC ENCEPHALOPATHY to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254; intellectual disability, autosomal dominant 8 MONDO:0013655; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive OMIM:617820; neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive MONDO:0060629
Early onset or syndromic epilepsy v2.420 GRIN1 Sarah Leigh Phenotypes for gene: GRIN1 were changed from Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive, 617820; NDHMSR; Mental retardation, autosomal dominant 8; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant, 614254; NDHMSD; early onset epileptic encephalopathies; involuntary movements; severe developmental delay; intellectual disability; EPILEPTIC ENCEPHALOPATHY to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254; intellectual disability, autosomal dominant 8 MONDO:0013655; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive OMIM:617820; neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive MONDO:0060629
Fetal anomalies v1.716 GRIN1 Sarah Leigh edited their review of gene: GRIN1: Added comment: The MOI monoallelic is listed for this panel, as the phenotype was initially listed as epileptic encephalopathy and only one biallelic case has been reported with this phenotype. However, other fetal phenotypes are associated with both monoallelic and biallelic GRIN1 variants in Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254 and Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive OMIM:617820.; Changed rating: GREEN
Fetal anomalies v1.716 GRIN1 Sarah Leigh changed review comment from: Comment on mode of inheritance: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.; to: Comment on mode of inheritance: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.
Fetal anomalies v1.716 GRIN1 Sarah Leigh Phenotypes for gene: GRIN1 were changed from EPILEPTIC ENCEPHALOPATHY to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254; intellectual disability, autosomal dominant 8 MONDO:0013655; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive OMIM:617820; neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive MONDO:0060629
Malformations of cortical development v2.90 GRIN1 Sarah Leigh Added comment: Comment on mode of inheritance: Although the MOI could be listed as "both mono and biallelic" in order to agree with the MOI listed in OMIM:138249, this was not done on this panel, as the phenotypes of malformation of cortical development have not been reported with biallelic variants.
Malformations of cortical development v2.90 GRIN1 Sarah Leigh Mode of inheritance for gene: GRIN1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
DDG2P v2.44 GRIN1 Sarah Leigh changed review comment from: Comment on mode of inheritance: The MOI could be changed to "both mono and biallelic" in order to agree with the MOI listed in OMIM:138249, however, this was not done on this panel, as the phenotype that is confirmed on Gen2Phen is epileptic encephalopathy, and only one biallelic case has been reported with this phenotype.; to: Comment on mode of inheritance: The MOI could be changed to "both mono and biallelic" in order to agree with the MOI listed in OMIM:138249, however, this was not done on this panel, as the phenotype that is confirmed on Gen2Phen is epileptic encephalopathy (https://www.ebi.ac.uk/gene2phenotype/gfd?dbID=1357), and only one biallelic case has been reported with this phenotype.
DDG2P v2.44 GRIN1 Sarah Leigh Deleted their comment
DDG2P v2.44 GRIN1 Sarah Leigh Added comment: Comment on phenotypes: EPILEPTIC ENCEPHALOPATHY
DDG2P v2.44 GRIN1 Sarah Leigh Phenotypes for gene: GRIN1 were changed from EPILEPTIC ENCEPHALOPATHY to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254; intellectual disability, autosomal dominant 8 MONDO:0013655
DDG2P v2.43 GRIN1 Sarah Leigh Added comment: Comment on mode of inheritance: The MOI could be changed to "both mono and biallelic" in order to agree with the MOI listed in OMIM:138249, however, this was not done on this panel, as the phenotype that is confirmed on Gen2Phen is epileptic encephalopathy, and only one biallelic case has been reported with this phenotype.
DDG2P v2.43 GRIN1 Sarah Leigh Mode of inheritance for gene: GRIN1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Fetal anomalies v1.715 GRIN1 Sarah Leigh Added comment: Comment on mode of inheritance: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.
Fetal anomalies v1.715 GRIN1 Sarah Leigh Mode of inheritance for gene: GRIN1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Fetal anomalies v1.714 GRIN1 Sarah Leigh Tag Q3_21_MOI tag was added to gene: GRIN1.
Malformations of cortical development v2.89 GRIN1 Sarah Leigh edited their review of gene: GRIN1: Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen, although there is a confirmed association with epileptic encephalopathy in Gen2Phen. Nine de novo GRIN1 variants in eleven cases of bilateral polymicrogyria have been reported by Fry et al (PMID: 29365063), analysis of available samples from parents confirmed the de novo occurance of these GRIN1 variants.; Changed rating: GREEN; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Malformations of cortical development v2.89 GRIN1 Sarah Leigh Tag Q3_21_rating tag was added to gene: GRIN1.
Malformations of cortical development v2.89 GRIN1 Sarah Leigh Phenotypes for gene: GRIN1 were changed from Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant, OMIM:614254 to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254; intellectual disability, autosomal dominant 8 MONDO:0013655
Malformations of cortical development v2.88 GRIN1 Sarah Leigh Publications for gene: GRIN1 were set to 29365063
Childhood onset dystonia, chorea or related movement disorder v1.151 GRIN1 Sarah Leigh Publications for gene: GRIN1 were set to 29365063; 27164704; 27164704; 28051072
Childhood onset dystonia, chorea or related movement disorder v1.150 GRIN1 Sarah Leigh Tag Q3_21_rating tag was added to gene: GRIN1.
Holoprosencephaly - NOT chromosomal v2.23 RAD21 Arina Puzriakova Tag Q3_21_rating tag was added to gene: RAD21.
Holoprosencephaly - NOT chromosomal v2.23 RAD21 Arina Puzriakova Classified gene: RAD21 as Amber List (moderate evidence)
Holoprosencephaly - NOT chromosomal v2.23 RAD21 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). At least 3 unrelated individuals reported in literature with different heterozygous KMT2D variants and holoprosencephaly, which may be observed with or without overt features of CdLS. Sufficient to rate this gene as Green at the next GMS panel update.
Holoprosencephaly - NOT chromosomal v2.23 RAD21 Arina Puzriakova Gene: rad21 has been classified as Amber List (Moderate Evidence).
Holoprosencephaly - NOT chromosomal v2.22 RAD21 Arina Puzriakova Added comment: Comment on publications: PMID: 32696056 (2020) - fourth unrelated individual reported presenting holoprosencephaly associated with a heterozygous RAD21 LoF variant
Holoprosencephaly - NOT chromosomal v2.22 RAD21 Arina Puzriakova Publications for gene: RAD21 were set to 31334757
Holoprosencephaly - NOT chromosomal v2.21 RAD21 Arina Puzriakova Phenotypes for gene: RAD21 were changed from Holoprosencephaly; Septo-optic dysplasia to Cornelia de Lange syndrome 4, OMIM:614701; Holoprosencephaly with or without CdLS features; Septo-optic dysplasia
Fetal hydrops v1.35 KMT2D Arina Puzriakova Classified gene: KMT2D as Green List (high evidence)
Fetal hydrops v1.35 KMT2D Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There are sufficient unrelated cases with prenatal hydrops and variants in this gene to rate as Green on this panel. KMT2D is also already Green on the GMS Fetal anomalies (R21) panel.
Fetal hydrops v1.35 KMT2D Arina Puzriakova Gene: kmt2d has been classified as Green List (High Evidence).
Holoprosencephaly - NOT chromosomal v2.20 KMT2D Arina Puzriakova Tag Q3_21_rating tag was added to gene: KMT2D.
Holoprosencephaly - NOT chromosomal v2.20 KMT2D Arina Puzriakova Classified gene: KMT2D as Amber List (moderate evidence)
Holoprosencephaly - NOT chromosomal v2.20 KMT2D Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). At least 3 unrelated individuals reported in literature with different heterozygous KMT2D variants and holoprosencephaly, which may be observed in the absence of overtly obvious features of Kabuki syndrome. Sufficient to rate this gene as Green at the next GMS panel update.
Holoprosencephaly - NOT chromosomal v2.20 KMT2D Arina Puzriakova Gene: kmt2d has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.228 OSGEP Ivone Leong Tag Q3_21_rating tag was added to gene: OSGEP.
Severe microcephaly v2.228 OSGEP Ivone Leong Classified gene: OSGEP as Amber List (moderate evidence)
Severe microcephaly v2.228 OSGEP Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.228 OSGEP Ivone Leong Gene: osgep has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.227 OSGEP Ivone Leong Phenotypes for gene: OSGEP were changed from Galloway-Mowat syndrome 3, MIM# 617729 to Galloway-Mowat syndrome 3, OMIM:617729
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.53 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki syndrome 147920; 147920 to Kabuki syndrome 1, OMIM:147920
Intellectual disability v3.1270 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki syndrome to Kabuki syndrome 1, OMIM:147920
Severe microcephaly v2.226 VRK1 Ivone Leong Tag Q3_21_rating tag was added to gene: VRK1.
Severe microcephaly v2.226 VRK1 Ivone Leong Classified gene: VRK1 as Amber List (moderate evidence)
Severe microcephaly v2.226 VRK1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe microcephaly v2.226 VRK1 Ivone Leong Gene: vrk1 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.225 VRK1 Ivone Leong Phenotypes for gene: VRK1 were changed from Pontocerebellar hypoplasia type 1A MIM#607596 to Pontocerebellar hypoplasia type 1A, OMIM:607596
Malformations of cortical development v2.87 GRIN1 Sarah Leigh Classified gene: GRIN1 as Amber List (moderate evidence)
Malformations of cortical development v2.87 GRIN1 Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Malformations of cortical development v2.87 GRIN1 Sarah Leigh Gene: grin1 has been classified as Amber List (Moderate Evidence).
Holoprosencephaly - NOT chromosomal v2.19 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki syndrome 1, MIM# 147920 to Kabuki syndrome 1, OMIM:147920
Childhood onset dystonia, chorea or related movement disorder v1.150 GRIN1 Sarah Leigh Classified gene: GRIN1 as Amber List (moderate evidence)
Childhood onset dystonia, chorea or related movement disorder v1.150 GRIN1 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 v1.150 GRIN1 Sarah Leigh Gene: grin1 has been classified as Amber List (Moderate Evidence).
Childhood onset dystonia, chorea or related movement disorder v1.149 GRIN1 Sarah Leigh Phenotypes for gene: GRIN1 were changed from Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant, MIM# 614254; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive, MIM# 617820 to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant OMIM:614254; intellectual disability, autosomal dominant 8 MONDO:0013655; Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive OMIM:617820; neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive MONDO:0060629
Intellectual disability v3.1269 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855 to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
Intellectual disability v3.1269 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Mental retardation, autosomal dominant 42, OMIM:616973 to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
Early onset or syndromic epilepsy v2.419 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Mental retardation, autosomal dominant 42, 616973; seizures to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
Clefting v2.48 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Mental retardation, autosomal dominant 42, 616973 to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
DDG2P v2.42 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Severe Neurodevelopmental Disability, Hypotonia, and Seizures to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
Fetal anomalies v1.714 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Severe Neurodevelopmental Disability, Hypotonia, and Seizures to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
Childhood onset dystonia, chorea or related movement disorder v1.148 GNB1 Sarah Leigh Phenotypes for gene: GNB1 were changed from Mental retardation, autosomal dominant 42, MIM# 616973 to Mental retardation, autosomal dominant 42 OMIM:616973; intellectual disability, autosomal dominant 42 MONDO:0014855
Childhood onset dystonia, chorea or related movement disorder v1.147 GNB1 Sarah Leigh Tag Q3_21_rating tag was added to gene: GNB1.
Childhood onset dystonia, chorea or related movement disorder v1.147 GNB1 Sarah Leigh edited their review of gene: GNB1: Added comment: Hemati et al (2018)(PMID: 30194818) reviewed 46 pathognic GNB1 variants in cases with Mental retardation, autosomal dominant 42 (OMIM:616973). They reported early hypotonia leading to hypertonia and spasticity in >75% of cases.; Changed rating: GREEN
Primary immunodeficiency or monogenic inflammatory bowel disease v2.465 KMT2D Arina Puzriakova Tag Q3_21_rating tag was added to gene: KMT2D.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.465 KMT2D Arina Puzriakova Publications for gene: KMT2D were set to 25142838; 15523604; 21671394; 32048120; 15887282; 21607748; 32086639; 23913813; 26411453
Primary immunodeficiency or monogenic inflammatory bowel disease v2.464 KMT2D Arina Puzriakova Classified gene: KMT2D as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.464 KMT2D Arina Puzriakova Added comment: Comment on list classification: Immunopathological manifestations are seen in ~50% of cases with KMT2D-related Kabuki syndrome. There is sufficient evidence to support this gene-disease association and therefore this gene should be promoted to Green status at the next GMS panel update.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.464 KMT2D Arina Puzriakova Gene: kmt2d has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.463 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki syndrome 1, 147920; Typical facial abnormalities, cleft or high arched palate, skeletal abnormalities, short stature, intellectual disability, congenital heart defects, recurrent infections (otitis media, pneumonia) in 50% of patients. Autoimmunity may be present; Combined immunodeficiencies with associated or syndromic features to Kabuki syndrome 1, OMIM:147920; Hypogammaglobulinemia; Recurrent infections (otitis media, pneumonia); Autoimmunity
Structural eye disease v1.81 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki syndrome 1 (can include coloboma), 147920 to Kabuki syndrome 1, OMIM:147920; Coloboma; Microphthalmia
IUGR and IGF abnormalities v1.36 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki to Kabuki syndrome 1, OMIM:147920
Kabuki syndrome v1.5 KMT2D Arina Puzriakova Phenotypes for gene: KMT2D were changed from Kabuki Syndrome; Kabuki Syndrome Type 1 to Kabuki syndrome 1, OMIM:147920
Primary immunodeficiency or monogenic inflammatory bowel disease v2.462 DCLRE1B Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: DCLRE1B.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.462 DCLRE1B Arina Puzriakova reviewed gene: DCLRE1B: Rating: ; Mode of pathogenicity: None; Publications: 20479256; Phenotypes: ; Mode of inheritance: None
Childhood onset dystonia, chorea or related movement disorder v1.147 GNB1 Sarah Leigh Classified gene: GNB1 as Amber List (moderate evidence)
Childhood onset dystonia, chorea or related movement disorder v1.147 GNB1 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 v1.147 GNB1 Sarah Leigh Gene: gnb1 has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.86 GRIN1 Ivone Leong Phenotypes for gene: GRIN1 were changed from Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant, MIM# 614254 to Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant, OMIM:614254
Monogenic hearing loss v2.185 HARS2 Ivone Leong Phenotypes for gene: HARS2 were changed from #614926:?Perrault syndrome 2 to Perrault syndrome 2, OMIM:614926
Monogenic hearing loss v2.184 HARS2 Ivone Leong Publications for gene: HARS2 were set to 12056811; 15779907; 21464306; 517579; 7755634; 27650058
Primary ovarian insufficiency v1.47 HARS2 Ivone Leong Classified gene: HARS2 as Green List (high evidence)
Primary ovarian insufficiency v1.47 HARS2 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. This gene is associated with a relevant phenotype in OMIM but not Gene2Phenotype. There is now enough evidence to support a gene-disease association. Therefore this gene has been promoted to Green.
Primary ovarian insufficiency v1.47 HARS2 Ivone Leong Gene: hars2 has been classified as Green List (High Evidence).
Primary ovarian insufficiency v1.46 HARS2 Ivone Leong Phenotypes for gene: HARS2 were changed from Perrault syndrome 2, 614926 to Perrault syndrome 2, OMIM:614926
Skeletal dysplasia v2.119 MYO1H Sarah Leigh Entity copied from Familial dysautonomia v1.15
Skeletal dysplasia v2.119 MYO1H Sarah Leigh gene: MYO1H was added
gene: MYO1H was added to Skeletal dysplasia. Sources: Expert Review Red,Literature
Mode of inheritance for gene: MYO1H was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYO1H were set to 28779001
Phenotypes for gene: MYO1H were set to ?Central hypoventilation syndrome, congenital, 2, and autonomic dysfunction OMIM:619482
Early onset or syndromic epilepsy v2.418 MYO1H Sarah Leigh Entity copied from Familial dysautonomia v1.15
Early onset or syndromic epilepsy v2.418 MYO1H Sarah Leigh gene: MYO1H was added
gene: MYO1H was added to Genetic epilepsy syndromes. Sources: Expert Review Red,Literature
Mode of inheritance for gene: MYO1H was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYO1H were set to 28779001
Phenotypes for gene: MYO1H were set to ?Central hypoventilation syndrome, congenital, 2, and autonomic dysfunction OMIM:619482
Intellectual disability v3.1268 MYO1H Sarah Leigh Entity copied from Familial dysautonomia v1.15
Intellectual disability v3.1268 MYO1H Sarah Leigh gene: MYO1H was added
gene: MYO1H was added to Intellectual disability. Sources: Expert Review Red,Literature
Mode of inheritance for gene: MYO1H was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYO1H were set to 28779001
Phenotypes for gene: MYO1H were set to ?Central hypoventilation syndrome, congenital, 2, and autonomic dysfunction OMIM:619482
Familial dysautonomia v1.15 MYO1H Sarah Leigh reviewed gene: MYO1H: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Primary immunodeficiency or monogenic inflammatory bowel disease v2.462 ELF4 Arina Puzriakova Phenotypes for gene: ELF4 were changed from X-linked hypogammaglobulinemia with isolated growth hormone deficiency to Inflammatory bowel disease; Mucosal inflammation; Fever; Ulcers; Behcet-like disease; X-linked hypogammaglobulinemia with isolated growth hormone deficiency
Primary immunodeficiency or monogenic inflammatory bowel disease v2.461 ELF4 Arina Puzriakova Classified gene: ELF4 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.461 ELF4 Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber but there is enough evidence to rate this gene as Green at the next GMS panel update. At least two variants identified in three unrelated individuals with autoinflammatory disease characterised by fever, oral ulcers and mucosal inflammation. Supported by functional studies and mouse model.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.461 ELF4 Arina Puzriakova Gene: elf4 has been classified as Amber List (Moderate Evidence).
Congenital myopathy v2.58 CNTN1 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: CNTN1.
Arthrogryposis v3.122 CNTN1 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: CNTN1.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.460 ELF4 Arina Puzriakova Tag Q3_21_rating tag was added to gene: ELF4.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.460 ELF4 Arina Puzriakova Publications for gene: ELF4 were set to 16264330
Familial dysautonomia v1.15 MYO1H Sarah Leigh Phenotypes for gene: MYO1H were changed from Central hypoventilation syndrome, congenital, 2, and autonomic dysfunction, MIM#619482 to ?Central hypoventilation syndrome, congenital, 2, and autonomic dysfunction OMIM:619482
Familial dysautonomia v1.14 MYO1H Sarah Leigh Classified gene: MYO1H as Red List (low evidence)
Familial dysautonomia v1.14 MYO1H Sarah Leigh Gene: myo1h has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.459 ELF4 Arina Puzriakova Mode of inheritance for gene: ELF4 was changed from Unknown to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Primary ovarian insufficiency v1.45 HARS2 Ivone Leong Publications for gene: HARS2 were set to 21464306
Thoracic aortic aneurysm or dissection v1.123 ARIH1 Ivone Leong Classified gene: ARIH1 as Green List (high evidence)
Thoracic aortic aneurysm or dissection v1.123 ARIH1 Ivone Leong Added comment: Comment on list classification: Promoted this gene to Green based on reviews.
Thoracic aortic aneurysm or dissection v1.123 ARIH1 Ivone Leong Gene: arih1 has been classified as Green List (High Evidence).
Thoracic aortic aneurysm or dissection v1.122 ARIH1 Ivone Leong Tag Q3_21_rating was removed from gene: ARIH1.
Thoracic aortic aneurysm or dissection v1.122 ARIH1 Ivone Leong Entity copied from Thoracic aortic aneurysm and dissection v1.18
Thoracic aortic aneurysm or dissection v1.122 ARIH1 Ivone Leong gene: ARIH1 was added
gene: ARIH1 was added to Thoracic aortic aneurysm or dissection. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: ARIH1.
Mode of inheritance for gene: ARIH1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ARIH1 were set to 29689197; 32102558
Phenotypes for gene: ARIH1 were set to Thoracic aortic aneurysm, MONDO:0005396
Thoracic aortic aneurysm or dissection (GMS) v1.18 ARIH1 Ivone Leong Classified gene: ARIH1 as Amber List (moderate evidence)
Thoracic aortic aneurysm or dissection (GMS) v1.18 ARIH1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Thoracic aortic aneurysm or dissection (GMS) v1.18 ARIH1 Ivone Leong Gene: arih1 has been classified as Amber List (Moderate Evidence).
Thoracic aortic aneurysm or dissection (GMS) v1.17 ARIH1 Ivone Leong Tag Q3_21_rating tag was added to gene: ARIH1.
Rare anaemia v1.26 GSR Arina Puzriakova Phenotypes for gene: GSR were changed from NA Enzyme Disorder; Hemolytic anemia due to glutathione reductase deficiency; Enzyme Disorder to Hemolytic anemia due to glutathione reductase deficiency, OMIM:618660
Thoracic aortic aneurysm or dissection (GMS) v1.17 ARIH1 Ivone Leong Phenotypes for gene: ARIH1 were changed from Thoracic aortic aneurysm to Thoracic aortic aneurysm, MONDO:0005396
Rare anaemia v1.25 GSR Arina Puzriakova Publications for gene: GSR were set to 8533822
Rare anaemia v1.24 GSR Arina Puzriakova commented on gene: GSR
Fetal anomalies v1.713 CNTN1 Arina Puzriakova changed review comment from: Comment on list classification: Upgraded from Red to Amber as two families with homozygous variants and a relevant phenotype have now been reported in literature.; to: Comment on list classification: Rating Amber as two families with homozygous variants have now been reported in literature. Both display fetally-relevant phenotypes such as fetal akinesia, polyhydramnios, and contractures.
Fetal anomalies v1.713 CNTN1 Arina Puzriakova Entity copied from Arthrogryposis v3.122
Fetal anomalies v1.713 CNTN1 Arina Puzriakova gene: CNTN1 was added
gene: CNTN1 was added to Fetal anomalies. Sources: Expert list,Radboud University Medical Center, Nijmegen,Expert Review Amber
Mode of inheritance for gene: CNTN1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CNTN1 were set to 19026398; 32779773
Phenotypes for gene: CNTN1 were set to Myopathy, congenital, Compton-North, OMIM:612540
Penetrance for gene: CNTN1 were set to Complete
Congenital myopathy v2.58 CNTN1 Arina Puzriakova Publications for gene: CNTN1 were set to 19026398
Congenital myopathy v2.57 CNTN1 Arina Puzriakova Phenotypes for gene: CNTN1 were changed from ?Myopathy, congenital, Compton-North, 612540 to Myopathy, congenital, Compton-North, OMIM:612540
Arthrogryposis v3.122 CNTN1 Arina Puzriakova Phenotypes for gene: CNTN1 were changed from Myopathy, congenital, Compton-North, 612540 to Myopathy, congenital, Compton-North, OMIM:612540
Arthrogryposis v3.121 CNTN1 Arina Puzriakova Publications for gene: CNTN1 were set to
Arthrogryposis v3.120 CNTN1 Arina Puzriakova Classified gene: CNTN1 as Amber List (moderate evidence)
Arthrogryposis v3.120 CNTN1 Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber as two families with homozygous variants and a relevant phenotype have now been reported in literature.
Arthrogryposis v3.120 CNTN1 Arina Puzriakova Gene: cntn1 has been classified as Amber List (Moderate Evidence).
Cholestasis v1.87 SLC51A Ivone Leong Classified gene: SLC51A as Red List (low evidence)
Cholestasis v1.87 SLC51A Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM but not Gene2Phenotype. As there is only 1 case there is currently not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Cholestasis v1.87 SLC51A Ivone Leong Gene: slc51a has been classified as Red List (Low Evidence).
Cholestasis v1.86 SLC51A Ivone Leong Phenotypes for gene: SLC51A were changed from Cholestasis, progressive familial intrahepatic, 6, MIM# 619484 to ?Cholestasis, progressive familial intrahepatic, 6, OMIM:619484
Retinal disorders v2.209 LRP1 Ivone Leong Classified gene: LRP1 as Red List (low evidence)
Retinal disorders v2.209 LRP1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is currently not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Retinal disorders v2.209 LRP1 Ivone Leong Gene: lrp1 has been classified as Red List (Low Evidence).
Intellectual disability v3.1267 PGRMC1 Ivone Leong Publications for gene: PGRMC1 were set to
Intellectual disability v3.1266 PGRMC1 Ivone Leong reviewed gene: PGRMC1: Rating: ; Mode of pathogenicity: None; Publications: 33867527; Phenotypes: ; Mode of inheritance: None
Bilateral congenital or childhood onset cataracts v2.84 PGRMC1 Ivone Leong Tag watchlist tag was added to gene: PGRMC1.
Bilateral congenital or childhood onset cataracts v2.84 PGRMC1 Ivone Leong Phenotypes for gene: PGRMC1 were changed from Isolated paediatric cataract to Isolated paediatric cataract; cataract, MONDO:0005129
Bilateral congenital or childhood onset cataracts v2.83 PGRMC1 Ivone Leong Classified gene: PGRMC1 as Amber List (moderate evidence)
Bilateral congenital or childhood onset cataracts v2.83 PGRMC1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark. This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Bilateral congenital or childhood onset cataracts v2.83 PGRMC1 Ivone Leong Gene: pgrmc1 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.224 NUF2 Ivone Leong Classified gene: NUF2 as Red List (low evidence)
Severe microcephaly v2.224 NUF2 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. As there is only 1 case there is currently not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Severe microcephaly v2.224 NUF2 Ivone Leong Gene: nuf2 has been classified as Red List (Low Evidence).
Intellectual disability v3.1266 TRAPPC10 Ivone Leong Phenotypes for gene: TRAPPC10 were changed from microcephaly (disease), MONDO:0001149 to Intellectual disability, MONDO:0001071
Intellectual disability v3.1265 TRAPPC10 Ivone Leong Entity copied from Severe microcephaly v2.223
Intellectual disability v3.1265 TRAPPC10 Ivone Leong gene: TRAPPC10 was added
gene: TRAPPC10 was added to Intellectual disability. Sources: Expert Review Red,Other
Mode of inheritance for gene: TRAPPC10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAPPC10 were set to 30167849
Phenotypes for gene: TRAPPC10 were set to microcephaly (disease), MONDO:0001149
Penetrance for gene: TRAPPC10 were set to Complete
Severe microcephaly v2.223 TRAPPC10 Ivone Leong Classified gene: TRAPPC10 as Red List (low evidence)
Severe microcephaly v2.223 TRAPPC10 Ivone Leong Added comment: Comment on list classification: New gene added by Aleš Maver (Clinical Institute of Medical Genetics). This gene is not associated with a phenotype in OMIM, but is possibly associated with a disease in Gene2Phenotype. The affected individuals in PMID:30167849 (2 individuals from the same family) had severe ID. As I do not have access to the ESHG2021 talk, this gene has been given a Red rating until further evidence is available.
Severe microcephaly v2.223 TRAPPC10 Ivone Leong Gene: trappc10 has been classified as Red List (Low Evidence).
Severe microcephaly v2.222 TRAPPC10 Ivone Leong Phenotypes for gene: TRAPPC10 were changed from to microcephaly (disease), MONDO:0001149
Intellectual disability v3.1264 ATP1A2 Arina Puzriakova Publications for gene: ATP1A2 were set to 15159495; 29610157
Severe microcephaly v2.221 TRAPPC10 Ivone Leong Publications for gene: TRAPPC10 were set to PMID: 30167849
Early onset or syndromic epilepsy v2.417 PARP6 Arina Puzriakova Entity copied from Intellectual disability v3.1263
Early onset or syndromic epilepsy v2.417 PARP6 Arina Puzriakova gene: PARP6 was added
gene: PARP6 was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: PARP6.
Mode of inheritance for gene: PARP6 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: PARP6 were set to 34067418
Phenotypes for gene: PARP6 were set to Intellectual disability; Epilepsy; Microcephaly
Malformations of cortical development v2.85 FAT4 Ivone Leong Tag watchlist tag was added to gene: FAT4.
Malformations of cortical development v2.85 FAT4 Ivone Leong Classified gene: FAT4 as Amber List (moderate evidence)
Malformations of cortical development v2.85 FAT4 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Malformations of cortical development v2.85 FAT4 Ivone Leong Gene: fat4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1263 PARP6 Arina Puzriakova Classified gene: PARP6 as Amber List (moderate evidence)
Intellectual disability v3.1263 PARP6 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. At least 3 individuals with heterozygous PARP6 variants and a relevant phenotype have been reported (PMID: 34067418) - however, segregation analysis has only been complete for one of these cases. Furthermore, identification of two sibs with biallelic variants and unaffected parents who were heterozygous carriers arises possibility of incomplete penetrance or role of variants in other genes.

Overall there is not enough evidence to add this gene as diagnostic grade, so rating Amber with watchlist tag.
Intellectual disability v3.1263 PARP6 Arina Puzriakova Gene: parp6 has been classified as Amber List (Moderate Evidence).
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.9 GTF2E2 Michael Yau reviewed gene: GTF2E2: Rating: GREEN; Mode of pathogenicity: None; Publications: (PMID: 26996949): (PMID:28973399):; Phenotypes: Trichothiodystrophy 6, nonphotosensitive:; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Malformations of cortical development v2.84 FAT4 Ivone Leong Phenotypes for gene: FAT4 were changed from Van Maldergem syndrome 2, MIM# 615546 to Van Maldergem syndrome 2, OMIM:615546
Intellectual disability v3.1262 PARP6 Arina Puzriakova Tag watchlist tag was added to gene: PARP6.
Intellectual disability v3.1262 PARP6 Arina Puzriakova reviewed gene: PARP6: Rating: ; Mode of pathogenicity: None; Publications: 34067418; Phenotypes: ; Mode of inheritance: None
Xeroderma pigmentosum, Trichothiodystrophy or Cockayne syndrome v2.9 RNF113A Michael Yau reviewed gene: RNF113A: Rating: GREEN; Mode of pathogenicity: None; Publications: (PMID: 19377476): (PMID: 25612912): (PMID:31793730): (PMID 31880405): (PMID:32152280); Phenotypes: X-linked nonphotosensitive trichothiodystrophy, intellectual disability, partial corpus callosum agenesis, microcephaly, microphallus, hypergonadotropic hypogonadism; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Paroxysmal central nervous system disorders v1.17 RHOBTB2 Zornitza Stark gene: RHOBTB2 was added
gene: RHOBTB2 was added to Paroxysmal central nervous system disorders. Sources: Literature
Mode of inheritance for gene: RHOBTB2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: RHOBTB2 were set to 33504645
Phenotypes for gene: RHOBTB2 were set to Developmental and epileptic encephalopathy 64 618004; Alternating hemiplegia
Review for gene: RHOBTB2 was set to GREEN
Added comment: Eleven affected patients were identified. All had heterozygous missense variants involving exon 9 of RHOBTB2, confirmed as de novo in 9 cases. All had a complex motor phenotype, including at least 2 different kinds of movement disorder, e.g., ataxia and dystonia. Many patients demonstrated several features fulfilling the criteria for AHC: 10 patients had a movement disorder including paroxysmal elements, and 8 experienced hemiplegic episodes. In contrast to classic AHC, commonly caused by mutations in ATP1A3, these events were reported later only in RHOBTB2 mutation-positive patients from 20 months of age. All had ID, and many had seizures, so this represents an expansion of the phenotype rather than a distinct disorder.
Sources: Literature
Early onset or syndromic epilepsy v2.416 SLC32A1 Zornitza Stark gene: SLC32A1 was added
gene: SLC32A1 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: SLC32A1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SLC32A1 were set to 34038384
Phenotypes for gene: SLC32A1 were set to Genetic epilepsy with febrile seizures plus
Review for gene: SLC32A1 was set to GREEN
Added comment: 8 unrelated families reported, including segregation evidence in two large pedigrees. Variants are predicted to alter γ-aminobutyric acid (GABA) transport into synaptic vesicles, leading to altered neuronal inhibition.
Sources: Literature
Intellectual disability v3.1262 ZNF668 Zornitza Stark gene: ZNF668 was added
gene: ZNF668 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ZNF668 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ZNF668 were set to 34313816; 26633546
Phenotypes for gene: ZNF668 were set to DNA damage repair defect; microcephaly; growth deficiency; severe global developmental delay; brain malformation; facial dysmorphism
Review for gene: ZNF668 was set to AMBER
Added comment: 2 consanguineous families reported with different biallelic truncating (not NMD) variants in ZNF668. Phenotypes included microcephaly, growth deficiency, severe global developmental delay, brain malformation, and distinct facial dysmorphism.

Immunofluorescence indicated ZNF668 deficiency. An increased DNA damage phenotype was demonstrated in patient fibroblasts.
Sources: Literature
Infantile enterocolitis & monogenic inflammatory bowel disease v1.22 IFIH1 Zornitza Stark gene: IFIH1 was added
gene: IFIH1 was added to Infantile enterocolitis & monogenic inflammatory bowel disease. Sources: Literature
Mode of inheritance for gene: IFIH1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: IFIH1 were set to 34185153
Phenotypes for gene: IFIH1 were set to Inflammatory Bowel Disease
Review for gene: IFIH1 was set to GREEN
Added comment: IFIH1 encodes MDA5, a key cystolic sensor for viral nucleic acids. Rare, likely loss-of-functions IFIH1 variants identified in eight independent probands with Very Early Onset Inflammatory Bowel Disease (VEOIBD) from a combined cohort of 42 children. IFIH1 variants were significantly enriched in children with VEOIBD as compared to controls (p=0.007).
In one case of neonatal-onset IBD, a homozygous truncating variant was identified. There were seven carriers of LoF variants identified (range of onset 6 months to 6 years of age). In three of these cases, a second hypomorphic missense variant was identified.
Luciferase reporter assays were employed to assess MDA5 activity. In some cases, the second missense variant was either proven to not affect protein function or was in cis with the LoF variant.
Complete and partial MDA5 deficiency is associated with VEOIBD with variable penetrance and expressivity, suggesting a role for impaired intestinal viral sensing in IBD pathogenesis.
Sources: Literature
Intellectual disability v3.1262 PRICKLE2 Zornitza Stark reviewed gene: PRICKLE2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34092786; Phenotypes: Neurodevelopmental disorder, global developmental delay, behavioural difficulties ± epilepsy, autistic features, attention deficit hyperactive disorder, psychiatric symptoms; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Bilateral congenital or childhood onset cataracts v2.82 PGRMC1 Zornitza Stark gene: PGRMC1 was added
gene: PGRMC1 was added to Cataracts. Sources: Literature
Mode of inheritance for gene: PGRMC1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: PGRMC1 were set to 33867527; 23783460
Phenotypes for gene: PGRMC1 were set to Isolated paediatric cataract
Review for gene: PGRMC1 was set to AMBER
Added comment: A single large family with X-linked isolated paediatric cataract in males segregating a large 127 kb deletion truncating PGRMC1. A supporting knockout zebrafish model with cataract. Also, two unrelated male probands with non-syndromic ID and cataract with a large deletion encompassing PGRMC1 and SLC25A5.
Sources: Literature
Intellectual disability v3.1262 UBE2U Zornitza Stark gene: UBE2U was added
gene: UBE2U was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: UBE2U was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: UBE2U were set to 33776059
Phenotypes for gene: UBE2U were set to Retinoschisis; cataracts; learning disabilities; developmental delay
Review for gene: UBE2U was set to RED
Added comment: Single family with 5 individuals reported.
Sources: Literature
Retinal disorders v2.208 LRP1 Zornitza Stark gene: LRP1 was added
gene: LRP1 was added to Retinal disorders. Sources: Literature
Mode of inheritance for gene: LRP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LRP1 were set to 33776059
Phenotypes for gene: LRP1 were set to Macular drusen
Review for gene: LRP1 was set to RED
Added comment: PMID: 33776059 - 2x unrelated individuals with compound heterozygous missense variants and inherited retinal disorder/macular drusen. No functional data.
Sources: Literature
Intellectual disability v3.1262 CACNA1I Zornitza Stark gene: CACNA1I was added
gene: CACNA1I was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: CACNA1I was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CACNA1I were set to 33704440
Phenotypes for gene: CACNA1I were set to Neurodevelopmental disorder
Mode of pathogenicity for gene: CACNA1I was set to Other
Review for gene: CACNA1I was set to GREEN
gene: CACNA1I was marked as current diagnostic
Added comment: 4 different missense variants identified and shown to result in a gain of function.

2 individuals with de novo variants (a 3rd also suspected de novo but their father was unavailable for testing) - these patients all had severe neurodevelopmental disorders, involving severe global developmental delay, absence of speech, gross motor delay, muscular hypotonia, early-onset seizures, cortical visual impairment, and feeding difficulties. Variable clinical features include various brain malformations, startle response or seizures, postnatal growth retardation, gastroesophageal reflux, and gastrostomy.

1 family had three affected individuals - variable cognitive impairment in all, involving borderline intellectual functioning or mild or moderate intellectual disability as main clinical feature, with late-onset seizures in the mother and speech retardation in one of the children. This variant had a milder functional effect than the variants in sporadic cases.
Sources: Literature
Fetal anomalies v1.712 FGF8 Zornitza Stark reviewed gene: FGF8: Rating: AMBER; Mode of pathogenicity: None; Publications: 34433009; Phenotypes: Femoral hypoplasia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Osteogenesis imperfecta v2.23 COPB2 Zornitza Stark reviewed gene: COPB2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34450031; Phenotypes: Osteoporosis, recurrent fractures and developmental delay; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 ELF4 Dmitrijs Rots reviewed gene: ELF4: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 34326534; Phenotypes: Ulcers, fever, inflammatory bowel disease, autoinflammatory condition; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 KDM6A Dmitrijs Rots Deleted their comment
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 KDM6A Dmitrijs Rots edited their review of gene: KDM6A: Added comment: Immunodeficiency is a well-known and common feature of KS. Recent study shows:
"Overall, 44.1% (78/177) and 58.2% (46/79) of KS individuals exhibited infection susceptibility and hypogammaglobulinemia, respectively"; Changed publications to: PMID: 31363182; Changed phenotypes to: Hypogammaglobulinemia, intellectual disability, short stature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 KDM6A Dmitrijs Rots reviewed gene: KDM6A: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 34326534; Phenotypes: Autoinflammatory, inflammatory bowel disease, ulcers; Mode of inheritance: 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 v2.458 KMT2D Dmitrijs Rots reviewed gene: KMT2D: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 31363182; Phenotypes: Hypogammaglobulinemia, intellectual disability, short stature; Mode of inheritance: None
Intellectual disability v3.1262 GRIK2 Zornitza Stark reviewed gene: GRIK2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34375587, 17847003, 25039795; Phenotypes: Mental retardation, autosomal recessive, 6 MIM# 611092, Non-syndromic neurodevelopmental disorder (NDD), autosomal dominant; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Congenital muscular dystrophy v2.16 GOSR2 Zornitza Stark reviewed gene: GOSR2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34167170, 33639315, 33639315, 29855340, DOI:https://doi.org/10.1016/j.nmd.2013.06.404; Phenotypes: Epilepsy, progressive myoclonic 6 MIM#614018, congenital muscluar dystrophy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1262 CHRM1 Zornitza Stark gene: CHRM1 was added
gene: CHRM1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: CHRM1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CHRM1 were set to 34212451; 31981491; 12483218
Phenotypes for gene: CHRM1 were set to Neurodevelopmental delay; intellectual disability; autism
Review for gene: CHRM1 was set to AMBER
Added comment: PMID: 34212451 - 2 unrelated cases with de novo missense variants (p.Pro380Leu and p.Phe425Ser), one case with early-onset refractory epilepsy, severe disability, and progressive cerebral and cerebellar atrophy, and the second case with mild dysmorphism, global developmental delay, and moderate intellectual disability. In vitro biochemical analyses of p.Pro380Leu demonstrated a reduction in protein levels, impaired cellular trafficking, and defective activation of intracellular signaling pathways.
PMID: 31981491 - an autism spectrum disorder (no other information on phenotype, except ascertained to have severe neurodevelopmental delay) case with a de novo missense variant p.(Arg210Leu)
PMID: 12483218 - null mouse model assessing memory demonstrated selective cognitive dysfunction.
Sources: Literature
Osteogenesis imperfecta v2.23 SUCO Zornitza Stark gene: SUCO was added
gene: SUCO was added to Osteogenesis imperfecta. Sources: Literature
Mode of inheritance for gene: SUCO was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SUCO were set to 29620724; 20440000
Phenotypes for gene: SUCO were set to Osteogenesis imperfecta
Review for gene: SUCO was set to AMBER
Added comment: A single case with diffuse osteopenia, multiple fractures with limb deformities, and short long bones, with biallelic variants (a missense and a splice site variant). Also, a null mouse model with acute onset skeletal defects that include impaired bone formation and spontaneous fractures.
Sources: Literature
Familial dysautonomia v1.13 MYO1H Zornitza Stark gene: MYO1H was added
gene: MYO1H was added to Familial dysautonomia. Sources: Literature
Mode of inheritance for gene: MYO1H was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYO1H were set to 28779001
Phenotypes for gene: MYO1H were set to Central hypoventilation syndrome, congenital, 2, and autonomic dysfunction, MIM#619482
Review for gene: MYO1H was set to RED
Added comment: Single family reported with three affected children, homozygous LoF variant.
Sources: Literature
Intellectual disability v3.1262 ZNF699 Zornitza Stark gene: ZNF699 was added
gene: ZNF699 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ZNF699 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ZNF699 were set to 33875846
Phenotypes for gene: ZNF699 were set to DEGCAGS syndrome, MIM# 619488
Review for gene: ZNF699 was set to GREEN
Added comment: DEGCAGS syndrome is a neurodevelopmental disorder characterized by global developmental delay, coarse and dysmorphic facial features, and poor growth and feeding apparent from infancy. Affected individuals have variable systemic manifestations often with significant structural defects of the cardiovascular, genitourinary, gastrointestinal, and/or skeletal systems. Additional features may include sensorineural hearing loss, hypotonia, anaemia or pancytopaenia, and immunodeficiency with recurrent infections.

12 unrelated families reported, 5 different homozygous frameshift variants.
Sources: Literature
Cholestasis v1.85 SLC51A Zornitza Stark gene: SLC51A was added
gene: SLC51A was added to Cholestasis. Sources: Literature
Mode of inheritance for gene: SLC51A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC51A were set to 31863603
Phenotypes for gene: SLC51A were set to Cholestasis, progressive familial intrahepatic, 6, MIM# 619484
Review for gene: SLC51A was set to RED
Added comment: Single individual reported with homozygous LoF variant, who presented with chronic malabsorptive diarrhoea, easy bruising, episodes of prolonged bleeding that required blood transfusions, and failure to thrive. Laboratory testing at age 2.5 years showed elevated liver transaminases and alkaline phosphatase. Liver biopsy demonstrated portal and periportal fibrosis and hepatocytes with foci of hepatocytic cholestasis. Analysis of bile acids in a blood spot were normal. Treatment with ursodiol and cholestyramine was started at 5 years of age. The coagulopathy resolved and his growth was adequate, but his liver transaminases, direct bilirubin, and GGT levels remained elevated.
Sources: Literature
Arthrogryposis v3.119 CNTN1 Rhiannon Mellis reviewed gene: CNTN1: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 32779773; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Congenital myopathy v2.56 CNTN1 Rhiannon Mellis reviewed gene: CNTN1: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID: 32779773; Phenotypes: Fetal akinesia deformation sequence; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Structural eye disease v1.80 FOXE3 Eleanor Williams changed review comment from: Review of mode of inheritance:
There are many reported cases of biallelic variants in FOXE3 associated with an eye phenotype, particularly cataracts, aphakia, microphthalmia and sclerocornea (PMID: 27218149 Khan et al 2016, PMID: 16826526 Valleix et al 2006, PMID: 19708017 Iseri et al 2009, PMID: 20140963 Reis et al 2010, PMID: 20664696 Ali et al 2010, PMID: 20361012 Anjum et al 2010, PMID: 24019743 Pantoja-Melendez et al 2013, PMID: 27669367 Saboo et al 2017, PMID: 29878917 Quiroz-Casian et al 2018, PMID: 32436650 Taha Najim et al 2020, PMID: 34046667 Reis et al 2021). Glaucoma is also noted in some individuals. Heterozygous carriers are largely unaffected in these cases.

Patients with monoallelic variants in FOXE3 and an eye phenotype are also reported:

PMID: 11159941 - Semina et al 2001 - screened FOXE3 in a cohort of 161 unrelated individuals affected with anterior segment ocular disorders and identified a 1 bp insertion in FOXE3 in a proband and affected mother that was not found in controls. Both affected individuals had prominent anterior Schwalbe’s line (posterior embryotoxon) and cataracts.

PMID: 19708017 - Iseri et al 2009 - identified 2 pedigrees with dominant mutations in the FOXE3 gene by screening a large cohort of 236 anophthalmia-microphthalmia subjects; one with anterior segment anomalies, including Peters’ anomaly, early onset cataract, and coloboma, and another with microphthalmia,coloboma, and cerulean type (blue dot) cataracts.

PMID: 20806047 - Bremond-Ginac et al 2010 - a dominant mutation at the stop codon of FOXE3, c.959G>C (p.X320SerextX72), was identified in a patient with congenital cataract.

PMID: 21150893 - Doucette et al 2011 - sequenced 9 candidate genes in a large Newfoundland family with 11 relatives have a variable ocular phenotype ranging from microcornea to Peters anomaly and found a c.959G>T) substitution that replaces the stop codon for a leucine residue, predicting the addition of 72 amino acids to the C-terminus of FOXE3. Analysis of lympohocytes suggests the c.959T allele is absent rather than an extended protein being expressed.

PMID: 11980846 - Ormestad et al 2002 - one individual with Peters anomaly (with eccentric corneal opacities and glaucoma but not cataract) was found to be heterozygous for a nonconservative missense mutation in FOXE3. 40% of mice heterozygous for Foxe3(dyl) have corneal and lenticular defects.

PMID: 34046667 - Reis et al 2021 - 2 families reported with dominant pathogenic extension alleles which modify the stop codon but keep the amino acids in frame, adding a 72–amino acid nonsense peptide. Cataracts were found in all cases where the lens could be evaluated. Eye size was normal in all individuals, but mild anterior segment anomalies affecting the cornea and/or iris were noted in some individuals. Sclerocornea was observed in two family members (15C and 16B).; to: Review of mode of inheritance:

There are many reported cases of biallelic variants in FOXE3 associated with an eye phenotype, particularly cataracts, aphakia, microphthalmia and sclerocornea (PMID: 27218149 Khan et al 2016, PMID: 16826526 Valleix et al 2006, PMID: 19708017 Iseri et al 2009, PMID: 20140963 Reis et al 2010, PMID: 20664696 Ali et al 2010, PMID: 20361012 Anjum et al 2010, PMID: 24019743 Pantoja-Melendez et al 2013, PMID: 27669367 Saboo et al 2017, PMID: 29878917 Quiroz-Casian et al 2018, PMID: 32436650 Taha Najim et al 2020, PMID: 34046667 Reis et al 2021). Glaucoma is also noted in some individuals. Heterozygous carriers are largely unaffected in these cases.

Patients with monoallelic variants in FOXE3 and an eye phenotype are also reported:

PMID: 11159941 - Semina et al 2001 - screened FOXE3 in a cohort of 161 unrelated individuals affected with anterior segment ocular disorders and identified a 1 bp insertion in FOXE3 in a proband and affected mother that was not found in controls. Both affected individuals had prominent anterior Schwalbe’s line (posterior embryotoxon) and cataracts.

PMID: 19708017 - Iseri et al 2009 - identified 2 pedigrees with dominant mutations in the FOXE3 gene by screening a large cohort of 236 anophthalmia-microphthalmia subjects; one with anterior segment anomalies, including Peters’ anomaly, early onset cataract, and coloboma, and another with microphthalmia,coloboma, and cerulean type (blue dot) cataracts.

PMID: 20806047 - Bremond-Ginac et al 2010 - a dominant mutation at the stop codon of FOXE3, c.959G>C (p.X320SerextX72), was identified in a patient with congenital cataract.

PMID: 21150893 - Doucette et al 2011 - sequenced 9 candidate genes in a large Newfoundland family with 11 relatives have a variable ocular phenotype ranging from microcornea to Peters anomaly and found a c.959G>T) substitution that replaces the stop codon for a leucine residue, predicting the addition of 72 amino acids to the C-terminus of FOXE3. Analysis of lympohocytes suggests the c.959T allele is absent rather than an extended protein being expressed.

PMID: 11980846 - Ormestad et al 2002 - one individual with Peters anomaly (with eccentric corneal opacities and glaucoma but not cataract) was found to be heterozygous for a nonconservative missense mutation in FOXE3. 40% of mice heterozygous for Foxe3(dyl) have corneal and lenticular defects.

PMID: 34046667 - Reis et al 2021 - 2 families reported with dominant pathogenic extension alleles which modify the stop codon but keep the amino acids in frame, adding a 72–amino acid nonsense peptide. Cataracts were found in all cases where the lens could be evaluated. Eye size was normal in all individuals, but mild anterior segment anomalies affecting the cornea and/or iris were noted in some individuals. Sclerocornea was observed in two family members (15C and 16B).
Fetal anomalies v1.712 FOXE3 Eleanor Williams Phenotypes for gene: FOXE3 were changed from Anterior segment dysgenesis 2, multiple subtypes, OMIM:610256; Cataract 34, multiple types, OMIM:612968; {Aortic aneurysm, familial thoracic 11, susceptibility to}, OMIM:617349 CONGENITAL PRIMARY APHAKIA to Anterior segment dysgenesis 2, multiple subtypes, OMIM:610256; Cataract 34, multiple types, OMIM:612968; {Aortic aneurysm, familial thoracic 11, susceptibility to}, OMIM:617349 CONGENITAL PRIMARY APHAKIA; ANTERIOR SEGMENT MESENCHYMAL DYSGENESIS
Fetal anomalies v1.711 FOXE3 Eleanor Williams Added comment: Comment on mode of inheritance: Monoallleic cases related to Aortic aneurysm, familial thoracic 11, susceptibility to and to some cases with an eye phenotype. Biallelic cases associated with an eye phenotype.
Fetal anomalies v1.711 FOXE3 Eleanor Williams Mode of inheritance for gene: FOXE3 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Fetal anomalies v1.710 FOXE3 Eleanor Williams Phenotypes for gene: FOXE3 were changed from ANTERIOR SEGMENT MESENCHYMAL DYSGENESIS; CONGENITAL PRIMARY APHAKIA to Anterior segment dysgenesis 2, multiple subtypes, OMIM:610256; Cataract 34, multiple types, OMIM:612968; {Aortic aneurysm, familial thoracic 11, susceptibility to}, OMIM:617349 CONGENITAL PRIMARY APHAKIA
Anophthalmia or microphthalmia v1.42 FOXE3 Eleanor Williams Phenotypes for gene: FOXE3 were changed from to Anterior segment dysgenesis 2, multiple subtypes, OMIM:610256; Ocular anterior segment dysgenesis, HP:0007700
Anophthalmia or microphthalmia v1.41 FOXE3 Eleanor Williams Added comment: Comment on mode of inheritance: Only 1 monoallelic case reported with microphthalmia so leaving the mode of inheritance as biallelic for now (PMID: 19708017 - Iseri et al 2009 - identified 2 pedigrees with dominant mutations in the FOXE3 gene by screening a large cohort of 236 anophthalmia-microphthalmia subjects; one with anterior segment anomalies, including Peters’ anomaly, early onset cataract, and coloboma, and another with microphthalmia,coloboma, and cerulean type (blue dot) cataracts). See full review on on the Structural eye disease panel for all monoallelic cases https://panelapp.genomicsengland.co.uk/panels/509/gene/FOXE3/.
Anophthalmia or microphthalmia v1.41 FOXE3 Eleanor Williams Mode of inheritance for gene: FOXE3 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1262 TCF7L2 Zornitza Stark edited their review of gene: TCF7L2: Added comment: Additional 11 cases reported.; Changed rating: GREEN; Changed publications to: 33057194, 34003604
White matter disorders and cerebral calcification - narrow panel v1.198 COLGALT1 Zornitza Stark gene: COLGALT1 was added
gene: COLGALT1 was added to White matter disorders and cerebral calcification - narrow panel. Sources: Literature
Mode of inheritance for gene: COLGALT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: COLGALT1 were set to 30412317; 33709034; 31759980
Phenotypes for gene: COLGALT1 were set to Brain small vessel disease 3 MIM#618360
Review for gene: COLGALT1 was set to GREEN
Added comment: 3 unrelated cases with biallelic variants, and supporting functional assays. The main features of the cases were porencephalic cysts, leukoencephalopathy, lacunar infarcts, cerebral microbleeds/haemorrhages and calcifications. A null mouse model was embryonic lethal, but had defects in the vascular networks of the embryos.
Sources: Literature
Intellectual disability v3.1262 JAKMIP1 Zornitza Stark gene: JAKMIP1 was added
gene: JAKMIP1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: JAKMIP1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: JAKMIP1 were set to 29158550; 26627310; 27799067
Phenotypes for gene: JAKMIP1 were set to Intellectual disability; seizures
Review for gene: JAKMIP1 was set to AMBER
Added comment: Identified in two independent patients in the literature with a mouse model. Patient 1 (27799067) with developmental delay, speech delay, and cognitive impairment; self-injurious and aggressive behaviour, seizures, dysmorphic features. De-novo missense JAKMIP1 (p.D586H). Patient 2 (29158550) with feeding difficulties, hypotonia, epilepsy, severe ID, no active speech, kyphoscoliosis, constipation, autism, short stature. Splice variant c.1432-2A>G, no segregation or RNA data available. KO mouse model (27799067) displays social deficits, stereotyped activity, abnormal postnatal vocalizations, and other autistic-like behaviors.
Sources: Literature
Thoracic aortic aneurysm or dissection (GMS) v1.16 ARIH1 Zornitza Stark gene: ARIH1 was added
gene: ARIH1 was added to Thoracic aortic aneurysm and dissection. Sources: Literature
Mode of inheritance for gene: ARIH1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ARIH1 were set to 29689197; 32102558
Phenotypes for gene: ARIH1 were set to Thoracic aortic aneurysm
Review for gene: ARIH1 was set to GREEN
Added comment: 3 unrelated families: A de novo case (R171*) with thoracic aortic aneurysm (TAA), and 2 siblings with TAA and a missense (E15Q). Another proband with cerebrovascular aneurysm (family history of TAA) and a missense variant (E44G). Supporting functional assays of the variants and a Drosophila model.
Sources: Literature
Ocular coloboma v1.44 FOXE3 Eleanor Williams Added comment: Comment on mode of inheritance: Review of mode of inheritance - two reports of coloboma in monoallelic cases from one publication but leaving inheritance as biallelic for now until a 3rd case is reported (PMID: 19708017 - Iseri et al 2009 - identified 2 pedigrees with dominant mutations in the FOXE3 gene by screening a large cohort of 236 anophthalmia-microphthalmia subjects; one with anterior segment anomalies, including Peters’ anomaly, early onset cataract, and coloboma, and another with microphthalmia, coloboma, and cerulean type (blue dot) cataracts.).
Ocular coloboma v1.44 FOXE3 Eleanor Williams Mode of inheritance for gene: FOXE3 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Bilateral congenital or childhood onset cataracts v2.82 FOXE3 Eleanor Williams Publications for gene: FOXE3 were set to Iseri et al (2009) Hum Mutat 30:1378-1386; Semina et al (2001) Hum Mol Genet 10:231-236; Br mond-Gignac et al (2010) Mol Vis 16:1705-1711.
Bilateral congenital or childhood onset cataracts v2.81 FOXE3 Eleanor Williams Phenotypes for gene: FOXE3 were changed from Autosomal dominant cataracts; Peter's anomaly, microphthalmia. to Cataract 34, multiple types, OMIM:612968; cataract 34 multiple types, MONDO:0013067; Peter's anomaly; microphthalmia.
Glaucoma (developmental) v1.39 FOXE3 Eleanor Williams Added comment: Comment on mode of inheritance: Only one report on a monoallelic case where glaucoma specified as part of the phenotype (PMID: 11980846 - Ormestad et al 2002 - one individual with Peters anomaly (with eccentric corneal opacities and glaucoma but not cataract) was found to be heterozygous for a nonconservative missense mutation in FOXE3) and so leaving the mode of inheritance as biallelic only for now.
Glaucoma (developmental) v1.39 FOXE3 Eleanor Williams Mode of inheritance for gene: FOXE3 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Bilateral congenital or childhood onset cataracts v2.80 FOXE3 Eleanor Williams Added comment: Comment on mode of inheritance: Review of mode of inheritance confirms that there are both biallelic and monoallelic cases with FOXE3 variants where cataracts are reported. See full review of MOI on the Structural eye disease panel https://panelapp.genomicsengland.co.uk/panels/509/gene/FOXE3/
Bilateral congenital or childhood onset cataracts v2.80 FOXE3 Eleanor Williams Mode of inheritance for gene: FOXE3 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Structural eye disease v1.80 FOXE3 Eleanor Williams reviewed gene: FOXE3: Rating: ; Mode of pathogenicity: None; Publications: 27218149, 16826526, 19708017, 20140963, 20664696, 20361012, 24019743, 27669367, 29878917, 32436650, 34046667, 11159941, 19708017, 20806047, 21150893, 11980846, 34046667; Phenotypes: Anterior segment dysgenesis 2, multiple subtypes, OMIM:610256, Cataract 34, multiple types, OMIM:612968; Mode of inheritance: None
Hereditary neuropathy v1.415 C1orf194 Sarah Leigh Classified gene: C1orf194 as Green List (high evidence)
Hereditary neuropathy v1.415 C1orf194 Sarah Leigh Gene: c1orf194 has been classified as Green List (High Evidence).
Hereditary neuropathy v1.414 C1orf194 Sarah Leigh Entity copied from Hereditary neuropathy NOT PMP22 copy number v1.61
Hereditary neuropathy v1.414 C1orf194 Sarah Leigh gene: C1orf194 was added
gene: C1orf194 was added to Hereditary neuropathy. Sources: Expert Review Amber,Literature
Q3_21_NHS_review tags were added to gene: C1orf194.
Mode of inheritance for gene: C1orf194 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: C1orf194 were set to 31199454; 32592472
Phenotypes for gene: C1orf194 were set to Charcot-Marie-Tooth disease, intermediate or demyelinating
Hereditary neuropathy or pain disorder v1.61 C1orf194 Sarah Leigh Tag Q3_21_rating was removed from C1orf194.
Hereditary neuropathy or pain disorder v1.60 C1orf194 Sarah Leigh edited their review of gene: C1orf194: Added comment: This green review is based on the review of Alexander Rossor (UCL Institute of Neurology), 8 Mar 2021, which was entered in error on the entry for C1orf94. The review is as follows: Two unrelated families, knock in mouse with relevant phenotype. Functional evidence for one variant only. Sources: Expert list.; Changed rating: GREEN
Hereditary neuropathy or pain disorder v1.60 C1orf194 Sarah Leigh Tag Q3_21_rating tag was added to gene: C1orf194.
Tag Q3_21_NHS_review tag was added to gene: C1orf194.
Hereditary neuropathy or pain disorder v1.60 C1orf194 Sarah Leigh Classified gene: C1orf194 as Amber List (moderate evidence)
Hereditary neuropathy or pain disorder v1.60 C1orf194 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 v1.60 C1orf194 Sarah Leigh Gene: c1orf194 has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy v1.413 C1orf94 Sarah Leigh Tag curated_removed tag was added to gene: C1orf94.
Hereditary neuropathy or pain disorder v1.59 C1orf94 Sarah Leigh Tag Q3_21_NHS_review was removed from gene: C1orf94.
Tag curated_removed tag was added to gene: C1orf94.
Hereditary neuropathy or pain disorder v1.59 C1orf94 Sarah Leigh Tag Q3_21_rating was removed from gene: C1orf94.
Hereditary neuropathy or pain disorder v1.59 C1orf94 Sarah Leigh Classified gene: C1orf94 as No list
Hereditary neuropathy or pain disorder v1.59 C1orf94 Sarah Leigh Added comment: Comment on list classification: Curator deletion of this gene from this panel.
This gene has been added to this panel in error. The publications, phenotype and reviews are appropriate for C1orf194 and not for C1orf94.
Hereditary neuropathy or pain disorder v1.59 C1orf94 Sarah Leigh Gene: c1orf94 has been removed from the panel.
Hereditary neuropathy v1.413 C1orf94 Sarah Leigh Classified gene: C1orf94 as No list
Hereditary neuropathy v1.413 C1orf94 Sarah Leigh Added comment: Comment on list classification: Curator deletion of this gene from this panel.
This gene has been added to this panel in error. The publications, phenotype and reviews are appropriate for C1orf194 and not for C1orf94.
Hereditary neuropathy v1.413 C1orf94 Sarah Leigh Gene: c1orf94 has been removed from the panel.
Malformations of cortical development v2.83 EML1 Arina Puzriakova Publications for gene: EML1 were set to 31710781
Malformations of cortical development v2.82 EML1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: EML1.
Malformations of cortical development v2.82 EML1 Arina Puzriakova Classified gene: EML1 as Amber List (moderate evidence)
Malformations of cortical development v2.82 EML1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). EML1 is associated with a relevant phenotype in OMIM (MIM# 600348) but is not yet listed in G2P. Animal models and sufficient number of unrelated cases (>3) with relevant phenotype (periventricular and ribbon-like subcortical heterotopia with polymicrogyria) and variants in this gene to rate as Green at the next GMS panel update.
Malformations of cortical development v2.82 EML1 Arina Puzriakova Gene: eml1 has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.81 EML1 Arina Puzriakova Phenotypes for gene: EML1 were changed from Band heterotopia (MIM# 600348) to Band heterotopia, OMIM:600348
Fetal anomalies v1.709 EML1 Arina Puzriakova Phenotypes for gene: EML1 were changed from Band heterotopia, 600348 to Band heterotopia, OMIM:600348
Intellectual disability v3.1262 EML1 Arina Puzriakova Phenotypes for gene: EML1 were changed from congenital hydrocephalus, profound global developmental delay and intractable epilepsy; Band heterotopia, 600348 (includes severe intellectual disability) to Band heterotopia, OMIM:600348
Early onset or syndromic epilepsy v2.416 EML1 Arina Puzriakova Phenotypes for gene: EML1 were changed from Band heterotopia, 600348 to Band heterotopia, OMIM:600348
Malformations of cortical development v2.80 DEPDC5 Arina Puzriakova Publications for gene: DEPDC5 were set to 31444548
Malformations of cortical development v2.79 DEPDC5 Arina Puzriakova Phenotypes for gene: DEPDC5 were changed from Epilepsy, familial focal, with variable foci 1, OMIM:604364 to Epilepsy, familial focal, with variable foci 1, OMIM:604364; Focal cortical dysplasia
Malformations of cortical development v2.78 DEPDC5 Arina Puzriakova Tag Q3_21_rating tag was added to gene: DEPDC5.
Malformations of cortical development v2.78 DEPDC5 Arina Puzriakova Classified gene: DEPDC5 as Amber List (moderate evidence)
Malformations of cortical development v2.78 DEPDC5 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). DEPDC5 is associated with a relevant phenotype in OMIM (MIM# 604364) and G2P ('confirmed' disease confidence rating). Sufficient number of unrelated cases (>3) with relevant phenotype (focal cortical dysplasia of variable severity) and variants in this gene to rate as Green at the next GMS panel update.
Malformations of cortical development v2.78 DEPDC5 Arina Puzriakova Gene: depdc5 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1261 DEPDC5 Arina Puzriakova Phenotypes for gene: DEPDC5 were changed from FAMILIAL FOCAL EPILEPSY WITH VARIABLE FOCI (FFEVF) to Epilepsy, familial focal, with variable foci 1, OMIM:604364
Early onset or syndromic epilepsy v2.415 DEPDC5 Arina Puzriakova Phenotypes for gene: DEPDC5 were changed from Epilepsy, familial focal, with variable foci 1 604364 to Epilepsy, familial focal, with variable foci 1, OMIM:604364
Malformations of cortical development v2.77 DEPDC5 Arina Puzriakova Phenotypes for gene: DEPDC5 were changed from Epilepsy, familial focal, with variable foci 1 (MIM#604364) to Epilepsy, familial focal, with variable foci 1, OMIM:604364
Malformations of cortical development v2.76 DCHS1 Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). DCHS1 is associated with a relevant phenotype in OMIM (MIM# 601390) and G2P ('confirmed' disease confidence rating). Sufficient number of unrelated cases with relevant phenotype and variants in this gene to rate as Green.

Brain MRI typically shows periventricular nodular heterotopia, often with a dysmorphic corpus callosum or simplified gyral pattern, consistent with a neuronal migration defect.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). DCHS1 is associated with a relevant phenotype in OMIM (MIM# 601390) and G2P ('confirmed' disease confidence rating). Sufficient number of unrelated cases (4 patients from 3 families) with relevant phenotype and confirmed variants in this gene to rate as Green.

Brain MRI typically shows periventricular nodular heterotopia, often with a dysmorphic corpus callosum or simplified gyral pattern, consistent with a neuronal migration defect.
Malformations of cortical development v2.76 DCHS1 Arina Puzriakova Publications for gene: DCHS1 were set to 27262615; 22473091
Malformations of cortical development v2.75 DCHS1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: DCHS1.
Malformations of cortical development v2.75 DCHS1 Arina Puzriakova Classified gene: DCHS1 as Amber List (moderate evidence)
Malformations of cortical development v2.75 DCHS1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). DCHS1 is associated with a relevant phenotype in OMIM (MIM# 601390) and G2P ('confirmed' disease confidence rating). Sufficient number of unrelated cases with relevant phenotype and variants in this gene to rate as Green.

Brain MRI typically shows periventricular nodular heterotopia, often with a dysmorphic corpus callosum or simplified gyral pattern, consistent with a neuronal migration defect.
Malformations of cortical development v2.75 DCHS1 Arina Puzriakova Gene: dchs1 has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.74 DCHS1 Arina Puzriakova Phenotypes for gene: DCHS1 were changed from Van Maldergem syndrome 1, OMIM:601390 to Van Maldergem syndrome 1, OMIM:601390; Periventricular nodular heterotopia
Malformations of cortical development v2.73 DCHS1 Arina Puzriakova Phenotypes for gene: DCHS1 were changed from Van Maldergem syndrome 1 (MIM#601390) to Van Maldergem syndrome 1, OMIM:601390
Primary lymphoedema v2.18 DCHS1 Arina Puzriakova Phenotypes for gene: DCHS1 were changed from Van Maldergem syndrome 1, 601390 to Van Maldergem syndrome 1, OMIM:601390
Intellectual disability v3.1260 DCHS1 Arina Puzriakova Phenotypes for gene: DCHS1 were changed from PERIVENTRICULAR NEURONAL HETEROTOPIA; Van Maldergem syndrome 1, 601390 to Van Maldergem syndrome 1, OMIM:601390
Malformations of cortical development v2.72 CTNNA2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: CTNNA2.
Malformations of cortical development v2.72 CTNNA2 Arina Puzriakova Classified gene: CTNNA2 as Amber List (moderate evidence)
Malformations of cortical development v2.72 CTNNA2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). CTNNA2 is associated with a relevant phenotype in OMIM (MIM# 618174) and G2P ('probable' disease confidence rating). There is sufficient evidence to rate this gene as Green at the next GMS panel update - 13 patients from 3 unrelated families, pachygyria without posterior-anterior gradient or focal dysplasias was common to all.
Malformations of cortical development v2.72 CTNNA2 Arina Puzriakova Gene: ctnna2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1259 CTNNA2 Arina Puzriakova Phenotypes for gene: CTNNA2 were changed from Cortical dysplasia, complex, with other brain malformations 9, 618174; intellectual disability; global developmental delay to Cortical dysplasia, complex, with other brain malformations 9, OMIM:618174
Early onset or syndromic epilepsy v2.414 CTNNA2 Arina Puzriakova Phenotypes for gene: CTNNA2 were changed from Cortical dysplasia, complex, with other brain malformations 4, 618174, seizures to Cortical dysplasia, complex, with other brain malformations 9, OMIM:618174
Malformations of cortical development v2.71 CTNNA2 Arina Puzriakova Phenotypes for gene: CTNNA2 were changed from Cortical dysplasia, complex, with other brain malformations 9, MIM#618174 to Cortical dysplasia, complex, with other brain malformations 9, OMIM:618174
Malformations of cortical development v2.70 CSNK2A1 Arina Puzriakova Classified gene: CSNK2A1 as Green List (high evidence)
Malformations of cortical development v2.70 CSNK2A1 Arina Puzriakova Added comment: Comment on list classification: Three individuals reported by Okur et al., 2016 (PMID: 27048600) displayed cortical abnormalities which meets the threshold for a Green rating. However it should be noted that this is not a common finding and has not been described since the initial report.
Malformations of cortical development v2.70 CSNK2A1 Arina Puzriakova Gene: csnk2a1 has been classified as Green List (High Evidence).
Malformations of cortical development v2.69 CSNK2A1 Arina Puzriakova Publications for gene: CSNK2A1 were set to 27048600
Osteogenesis imperfecta v2.23 KDELR2 Meena Balasubramanian reviewed gene: KDELR2: Rating: GREEN; Mode of pathogenicity: None; Publications: 33964184, 33053334; Phenotypes: Ostoegenesis Imperfecta, Fractures; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Osteogenesis imperfecta v2.23 MESD Meena Balasubramanian reviewed gene: MESD: Rating: GREEN; Mode of pathogenicity: None; Publications: 33596325, 31564437; Phenotypes: Ostoegenesis Imperfecta, Fractures; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1258 CSNK2A1 Arina Puzriakova Phenotypes for gene: CSNK2A1 were changed from Okur-Chung neurodevelopmental syndrome to Okur-Chung neurodevelopmental syndrome, OMIM:617062
Early onset or syndromic epilepsy v2.413 CSNK2A1 Arina Puzriakova Phenotypes for gene: CSNK2A1 were changed from Neurodevelopmental abnormalities and dysmorphic features; seizures; Okur-Chung neurodevelopmental syndrome, 617062; CSNK2A1 syndrome to Okur-Chung neurodevelopmental syndrome, OMIM:617062
Osteogenesis imperfecta v2.23 FAM46A Meena Balasubramanian reviewed gene: FAM46A: Rating: GREEN; Mode of pathogenicity: None; Publications: 29358272; Phenotypes: Ostoegenesis Imperfecta, Fractures; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Malformations of cortical development v2.68 CSNK2A1 Arina Puzriakova Phenotypes for gene: CSNK2A1 were changed from 617062 to Okur-Chung neurodevelopmental syndrome, OMIM:617062
Osteogenesis imperfecta v2.23 MBTPS2 Meena Balasubramanian reviewed gene: MBTPS2: Rating: GREEN; Mode of pathogenicity: None; Publications: 27380894; Phenotypes: Ostoegenesis Imperfecta, Fractures; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Rare anaemia v1.24 GSR Zornitza Stark reviewed gene: GSR: Rating: AMBER; Mode of pathogenicity: None; Publications: 17185460, 31122244; Phenotypes: Haemolytic anaemia due to glutathione reductase deficiency, MIM# 618660; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Malformations of cortical development v2.67 PEX7 Arina Puzriakova Tag Q3_21_rating tag was added to gene: PEX7.
Tag Q3_21_expert_review tag was added to gene: PEX7.
Malformations of cortical development v2.67 PEX7 Arina Puzriakova commented on gene: PEX7
Bilateral congenital or childhood onset cataracts v2.79 PEX7 Arina Puzriakova Phenotypes for gene: PEX7 were changed from Rhizomelic chondrodysplasia punctata type 1; Confirmed DD gene for Rhizomelic chondrodysplasia punctata type 1; Refsum disease; Peroxisome biogenesis disorder to Peroxisome biogenesis disorder 9B, OMIM:614879; Rhizomelic chondrodysplasia punctata, type 1, OMIM:215100
Peroxisomal disorders v1.16 PEX7 Arina Puzriakova Phenotypes for gene: PEX7 were changed from Peroxisome biogenesis disorder 9B 614879; Rhizomelic chondrodysplasia punctata, type 1 215100 to Peroxisome biogenesis disorder 9B, OMIM:614879; Rhizomelic chondrodysplasia punctata, type 1, OMIM:215100
Chondrodysplasia punctata v1.5 PEX7 Arina Puzriakova Phenotypes for gene: PEX7 were changed from Rhizomelic chondrodysplasia punctata, type 1, 215100 to Peroxisome biogenesis disorder 9B, OMIM:614879; Rhizomelic chondrodysplasia punctata, type 1, OMIM:215100
Early onset or syndromic epilepsy v2.412 PIDD1 Arina Puzriakova Classified gene: PIDD1 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.412 PIDD1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. Overall there are sufficient unrelated cases (>3) with a relevant phenotype and biallelic variants in this gene to rate as Green at the next GMS panel update.
Early onset or syndromic epilepsy v2.412 PIDD1 Arina Puzriakova Gene: pidd1 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.411 PIDD1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: PIDD1.
Intellectual disability v3.1257 PIDD1 Arina Puzriakova Classified gene: PIDD1 as Amber List (moderate evidence)
Intellectual disability v3.1257 PIDD1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis. Overall there are sufficient unrelated cases (>3) with a relevant phenotype and biallelic variants in this gene to rate as Green at the next GMS panel update.
Intellectual disability v3.1257 PIDD1 Arina Puzriakova Gene: pidd1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1256 PIDD1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: PIDD1.
Malformations of cortical development v2.67 PIDD1 Arina Puzriakova Classified gene: PIDD1 as Amber List (moderate evidence)
Malformations of cortical development v2.67 PIDD1 Arina Puzriakova Gene: pidd1 has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.66 PIDD1 Arina Puzriakova gene: PIDD1 was added
gene: PIDD1 was added to Malformations of cortical development. Sources: Literature
Q3_21_rating tags were added to gene: PIDD1.
Mode of inheritance for gene: PIDD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIDD1 were set to 33414379; 34163010
Phenotypes for gene: PIDD1 were set to Intellectual disability; Pachygyria; Lissencephaly; Seizures
Review for gene: PIDD1 was set to GREEN
Added comment: At least 9 distinct biallelic variants have been identified in 26 individuals from 11 families. All affected individuals had DD and variable degree of ID (mild to severe) and all those that had brain imaging exhibited cortical abnormalities, particularly pachygyria/lissencephaly and corpus callosum anomalies. Seizures were recorded in 9 patients (6 families).

Overall there is are sufficient unrelated cases with relevant phenotype and biallelic variants in this gene to rate as Green on this panel.
Sources: Literature
Hereditary neuropathy v1.412 C1orf94 Sarah Leigh Classified gene: C1orf94 as Green List (high evidence)
Hereditary neuropathy v1.412 C1orf94 Sarah Leigh Added comment: Comment on list classification: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least 2 variants reported, together with a supportive mouse knock-out model (PMID: 31199454; 32592472).
Hereditary neuropathy v1.412 C1orf94 Sarah Leigh Gene: c1orf94 has been classified as Green List (High Evidence).
Hereditary neuropathy or pain disorder v1.58 C1orf94 Sarah Leigh Classified gene: C1orf94 as Amber List (moderate evidence)
Hereditary neuropathy or pain disorder v1.58 C1orf94 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 v1.58 C1orf94 Sarah Leigh Gene: c1orf94 has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy or pain disorder v1.57 C1orf94 Sarah Leigh Tag Q3_21_rating tag was added to gene: C1orf94.
Hereditary neuropathy or pain disorder v1.57 C1orf94 Sarah Leigh Tag Q3_21_NHS_review tag was added to gene: C1orf94.
Hereditary neuropathy or pain disorder v1.57 C1orf94 Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least 2 variants reported, together with a supportive mouse knock-out model.; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least 2 variants reported, together with a supportive mouse knock-out model (PMID: 31199454; 32592472).
Hereditary neuropathy or pain disorder v1.57 C1orf94 Sarah Leigh reviewed gene: C1orf94: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Hereditary neuropathy or pain disorder v1.57 C1orf94 Sarah Leigh Entity copied from Hereditary neuropathy v1.411
Hereditary neuropathy or pain disorder v1.57 C1orf94 Sarah Leigh gene: C1orf94 was added
gene: C1orf94 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Expert list
Mode of inheritance for gene: C1orf94 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: C1orf94 were set to 31199454; 32592472
Phenotypes for gene: C1orf94 were set to Intermediate Charcot-Marie-Tooth disease
Penetrance for gene: C1orf94 were set to Complete
Mode of pathogenicity for gene: C1orf94 was set to Other
Hereditary neuropathy v1.411 C1orf94 Sarah Leigh Phenotypes for gene: C1orf94 were changed from Intermediate CMT to Intermediate Charcot-Marie-Tooth disease
Hereditary neuropathy v1.410 C1orf94 Sarah Leigh Publications for gene: C1orf94 were set to 31199454
Hereditary neuropathy v1.409 C1orf94 Sarah Leigh Publications for gene: C1orf94 were set to PMID: 31199454
Intellectual disability v3.1256 CRADD Arina Puzriakova Phenotypes for gene: CRADD were changed from Mental retardation, autosomal recessive 34, with variant lissencephaly 614499 to Mental retardation, autosomal recessive 34, with variant lissencephaly, OMIM:614499
Malformations of cortical development v2.65 CRADD Arina Puzriakova Phenotypes for gene: CRADD were changed from Mental retardation, autosomal recessive 34, with variant lissencephaly, MIM# 614499 to Mental retardation, autosomal recessive 34, with variant lissencephaly, OMIM:614499
Intellectual disability v3.1255 CRADD Arina Puzriakova Publications for gene: CRADD were set to 22279524; 27773430
Malformations of cortical development v2.64 CRADD Arina Puzriakova Publications for gene: CRADD were set to 27773430
Malformations of cortical development v2.63 CRADD Arina Puzriakova Classified gene: CRADD as Amber List (moderate evidence)
Malformations of cortical development v2.63 CRADD Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). Brain phenotypes include megalencephaly with variable lissencephaly/pachygyria. Sufficient number of unrelated cases (>3) to rate as Green on this panel.
Malformations of cortical development v2.63 CRADD Arina Puzriakova Gene: cradd has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.62 CRADD Arina Puzriakova Tag Q3_21_rating tag was added to gene: CRADD.
Malformations of cortical development v2.62 CDK13 Arina Puzriakova reviewed gene: CDK13: Rating: GREEN; Mode of pathogenicity: None; Publications: 27479907, 29021403; Phenotypes: Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder, OMIM:617360; Mode of inheritance: None
Neurological ciliopathies v1.18 LAMA1 Arina Puzriakova Classified gene: LAMA1 as Amber List (moderate evidence)
Neurological ciliopathies v1.18 LAMA1 Arina Puzriakova Added comment: Comment on list classification: Clinical features of Poretti-Boltshauser syndrome resemble Joubert syndrome which can lead to misdiagnosis. Although not a ciliopathy per se, inclusion on ciliopathy panels may be warranted to enable differential diagnosis. The LAMA1 gene will be flagged for GMS specialist review to determine whether it is appropriate to include this gene on this panel.
Neurological ciliopathies v1.18 LAMA1 Arina Puzriakova Gene: lama1 has been classified as Amber List (Moderate Evidence).
Ophthalmological ciliopathies v1.19 LAMA1 Arina Puzriakova Classified gene: LAMA1 as Amber List (moderate evidence)
Ophthalmological ciliopathies v1.19 LAMA1 Arina Puzriakova Added comment: Comment on list classification: Clinical features of Poretti-Boltshauser syndrome resemble Joubert syndrome which can lead to misdiagnosis. Although not a ciliopathy per se, inclusion on ciliopathy panels may be warranted to enable differential diagnosis. The LAMA1 gene will be flagged for GMS specialist review to determine whether it is appropriate to include this gene on this panel.
Ophthalmological ciliopathies v1.19 LAMA1 Arina Puzriakova Gene: lama1 has been classified as Amber List (Moderate Evidence).
Neurological ciliopathies v1.17 LAMA1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: LAMA1.
Tag Q3_21_expert_review tag was added to gene: LAMA1.
Ophthalmological ciliopathies v1.18 LAMA1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: LAMA1.
Tag Q3_21_expert_review tag was added to gene: LAMA1.
Neurological ciliopathies v1.17 LAMA1 Arina Puzriakova Entity copied from Rare multisystem ciliopathy disorders v1.146
Neurological ciliopathies v1.17 LAMA1 Arina Puzriakova gene: LAMA1 was added
gene: LAMA1 was added to Neurological ciliopathies. Sources: Expert Review,Expert Review Green
Mode of inheritance for gene: LAMA1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LAMA1 were set to 25105227; 34423300
Phenotypes for gene: LAMA1 were set to Poretti-Boltshauser syndrome OMIM:615960; ataxia - intellectual disability - oculomotor apraxia - cerebellar cysts syndrome MONDO:0014419
Penetrance for gene: LAMA1 were set to Complete
Ophthalmological ciliopathies v1.18 LAMA1 Arina Puzriakova Entity copied from Rare multisystem ciliopathy disorders v1.146
Ophthalmological ciliopathies v1.18 LAMA1 Arina Puzriakova gene: LAMA1 was added
gene: LAMA1 was added to Ophthalmological ciliopathies. Sources: Expert Review,Expert Review Green
Mode of inheritance for gene: LAMA1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LAMA1 were set to 25105227; 34423300
Phenotypes for gene: LAMA1 were set to Poretti-Boltshauser syndrome OMIM:615960; ataxia - intellectual disability - oculomotor apraxia - cerebellar cysts syndrome MONDO:0014419
Penetrance for gene: LAMA1 were set to Complete
Rare multisystem ciliopathy disorders v1.146 LAMA1 Arina Puzriakova Publications for gene: LAMA1 were set to 25105227
Hereditary neuropathy v1.408 JAG1 Arina Puzriakova Tag watchlist tag was added to gene: JAG1.
Hereditary neuropathy or pain disorder v1.56 JAG1 Arina Puzriakova Tag watchlist tag was added to gene: JAG1.
Hereditary neuropathy v1.408 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Vocal cord palsy to Vocal cord palsy; Peripheral neuropathy
Hereditary neuropathy or pain disorder v1.56 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Peripheral neuropathy to Vocal cord palsy; Peripheral neuropathy
Hereditary neuropathy v1.407 JAG1 Arina Puzriakova Classified gene: JAG1 as Amber List (moderate evidence)
Hereditary neuropathy v1.407 JAG1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Alexander Rossor (UCL). Sullivan et al., 2020 (PMID:32065591) report two unrelated families with segregation, presenting vocal fold paresis. Knock in mouse model showed slight but nonsignificant reduction in compound muscle action potential and morphological assessments of the recurrent laryngeal nerve were normal. Mice did however display an increased frequency of axons with focally folded myelin. Notably, variants in JAG1 are associated with several phenotypes that have not included neuropathy and there was no history of cardiac, kidney, or liver disease in affected individuals in either of the two families discussed here (possibly different mechanisms of pathogenesis but further investigation may be warranted).

At this point there is not enough evidence to add this gene as diagnostic-grade; however, additional cases would corroborate this gene-disease association - rating Amber with 'watchlist' tag.
Hereditary neuropathy v1.407 JAG1 Arina Puzriakova Gene: jag1 has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy or pain disorder v1.55 JAG1 Arina Puzriakova Classified gene: JAG1 as Amber List (moderate evidence)
Hereditary neuropathy or pain disorder v1.55 JAG1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). Sullivan et al., 2020 (PMID:32065591) report two unrelated families with segregation, presenting vocal fold paresis. Knock in mouse model showed slight but nonsignificant reduction in compound muscle action potential and morphological assessments of the recurrent laryngeal nerve were normal. Mice did however display an increased frequency of axons with focally folded myelin. Notably, variants in JAG1 are associated with several phenotypes that have not included neuropathy and there was no history of cardiac, kidney, or liver disease in affected individuals in either of the two families discussed here (possibly different mechanisms of pathogenesis but further investigation may be warranted).

At this point there is not enough evidence to add this gene as diagnostic-grade; however, additional cases would corroborate this gene-disease association - rating Amber with 'watchlist' tag.
Hereditary neuropathy or pain disorder v1.55 JAG1 Arina Puzriakova Gene: jag1 has been classified as Amber List (Moderate Evidence).
Retinal disorders v2.208 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from to Alagille syndrome 1, OMIM:118450
Retinal disorders v2.207 JAG1 Arina Puzriakova Mode of inheritance for gene: JAG1 was changed from to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Monogenic hearing loss v2.183 JAG1 Arina Puzriakova Mode of inheritance for gene: JAG1 was changed from to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Monogenic hearing loss v2.182 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome, 118450Deafness, congenital heart defects and posterior embryotoxonTetralogy of Fallot, 187500; Alagillesyndrome,118450TetralogyofFallot,187500Deafness,congenitalheartdefects,andposteriorembryotoxon to ?Deafness, congenital heart defects, and posterior embryotoxon, OMIM:617992
Intellectual disability v3.1254 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome, 118450; Tetralogy of Fallot, 187500; Deafness, congenital heart defects, and posterior embryotoxon to Alagille syndrome 1, OMIM:118450
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.52 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome to Alagille syndrome 1, OMIM:118450
Familial non syndromic congenital heart disease v1.65 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Tetralogy of Fallot; Alagille syndrome to Alagille syndrome 1, OMIM:118450; Tetralogy of Fallot, OMIM:187500; Deafness, congenital heart defects, and posterior embryotoxon, OMIM:617992
CAKUT v1.164 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome 1 118450 to Alagille syndrome 1, OMIM:118450
Ductal plate malformation v1.18 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome 1 (118450) to Alagille syndrome 1, OMIM:118450
Cerebral vascular malformations v2.58 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Moyamoya disease; Alagille syndrome 1, 118450 to Alagille syndrome 1, OMIM:118450; Moyamoya disease
Intellectual disability v3.1253 JAG1 Arina Puzriakova Mode of inheritance for gene: JAG1 was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Cholestasis v1.85 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome; Neonatal and Adult Cholestasis; Alagille syndrome 1, 118450 to Alagille syndrome 1, OMIM:118450; Neonatal and Adult Cholestasis
Neonatal cholestasis v1.20 JAG1 Arina Puzriakova Phenotypes for gene: JAG1 were changed from Alagille syndrome; Neonatal and Adult Cholestasis; Alagille syndrome 1, 118450 to Alagille syndrome 1, OMIM:118450; Neonatal and Adult Cholestasis
Skeletal dysplasia v2.118 SPARC Arina Puzriakova Phenotypes for gene: SPARC were changed from Osteogenesis imperfecta, type XVII 616507 to Osteogenesis imperfecta, type XVII, OMIM:616507
Osteogenesis imperfecta v2.23 SPARC Arina Puzriakova Phenotypes for gene: SPARC were changed from Osteogenesis Imperfecta, Type XVII; Osteogenesis Imperfecta to Osteogenesis imperfecta, type XVII, OMIM:616507
Skeletal dysplasia v2.117 SPARC Arina Puzriakova Publications for gene: SPARC were set to 26027498
Osteogenesis imperfecta v2.22 SPARC Arina Puzriakova Publications for gene: SPARC were set to 26027498
Early onset or syndromic epilepsy v2.411 ARF1 Arina Puzriakova edited their review of gene: ARF1: Added comment: Added to this panel as seizures have been reported in 3/5 cases. Epilepsy is likely to arise in these cases prior to detection of cortical malformations and may prompt earlier genetic investigation. Inclusion on this panel could increase the likelihood of detecting cases and therefore a Green rating is warranted.; Changed rating: GREEN; Changed publications to: 28868155, 34353862; Changed phenotypes to: Periventricular nodular heterotopia 8, OMIM:618185; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Early onset or syndromic epilepsy v2.411 ARF1 Arina Puzriakova Entity copied from Malformations of cortical development v2.62
Early onset or syndromic epilepsy v2.411 ARF1 Arina Puzriakova gene: ARF1 was added
gene: ARF1 was added to Genetic epilepsy syndromes. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: ARF1.
Mode of inheritance for gene: ARF1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ARF1 were set to 28868155; 34353862
Phenotypes for gene: ARF1 were set to Periventricular nodular heterotopia 8, OMIM:618185
Intellectual disability v3.1252 ARF1 Arina Puzriakova edited their review of gene: ARF1: Added comment: Added to ID panel as developmental delay (especially in speech) is a reported feature in all cases (except for one individuals for which only limited clinical information was available). Although only one patient has been reported with a moderate ID diagnosis, developmental delay is likely to be noticed earlier in the course of disease than cortical malformations and may prompt genetic investigation. Inclusion on this panel could increase the likelihood of detecting cases and therefore a Green rating is warranted.; Changed rating: GREEN; Changed publications to: 28868155, 34353862; Changed phenotypes to: Periventricular nodular heterotopia 8, OMIM:618185; Changed mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.1252 ARF1 Arina Puzriakova Entity copied from Malformations of cortical development v2.62
Intellectual disability v3.1252 ARF1 Arina Puzriakova gene: ARF1 was added
gene: ARF1 was added to Intellectual disability. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: ARF1.
Mode of inheritance for gene: ARF1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ARF1 were set to 28868155; 34353862
Phenotypes for gene: ARF1 were set to Periventricular nodular heterotopia 8, OMIM:618185
Malformations of cortical development v2.62 ARF1 Arina Puzriakova Added comment: Comment on publications: Gana et al., 2021 (PMID: 34353862) - additional family identified with a 5-year-old girl who inherited a heterozygous nonsense variant in the ARF1 gene (c.234G>A; p.Trp78Ter) from her father. Both displayed periventricular nodular heterotopia on brain MRI but with milder clinical expression in the father.
Malformations of cortical development v2.62 ARF1 Arina Puzriakova Publications for gene: ARF1 were set to 28868155
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.51 GINS2 Arina Puzriakova gene: GINS2 was added
gene: GINS2 was added to Craniosynostosis. Sources: Literature
Mode of inheritance for gene: GINS2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GINS2 were set to 34353863
Phenotypes for gene: GINS2 were set to Meier-Gorlin syndrome with craniosynostosis
Review for gene: GINS2 was set to RED
Added comment: Sa et al., 2021 (PMID: 34353863) identified a patient presenting with prenatal and postnatal growth restriction, a craniofacial gestalt of MGORS and coronal craniosynostosis. A homozygous missense variant (c.341G>T, p.Arg114Leu) in GINS2 was identified that was heterozygous in both unaffected parents. Some supportive functional data included.

GINS2 is not currently not associated with any phenotype in OMIM or G2P and no additional cases have been identified to date. Rating Red, awaiting further evidence.
Sources: Literature
Arthrogryposis v3.119 FLNC Arina Puzriakova Added comment: Comment on publications: PMID: 33060286 - additional patient presenting at birth with mild arthrogryposis including hip dislocation, clenched hands, adducted thumbs.
Arthrogryposis v3.119 FLNC Arina Puzriakova Publications for gene: FLNC were set to 29858533
Congenital myaesthenic syndrome v2.38 GMPPB Sarah Leigh Added comment: Comment on phenotypes: This phenotype includes features of congenital myasthenic syndrome (in some patients) according to OMIM:615352.
Congenital myaesthenic syndrome v2.38 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Congenital Myasthenic Syndrome, MONDO:0018940 to Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Intellectual disability v3.1251 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 615350; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 615351; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 615352 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 OMIM:615350; muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14 MONDO:0014140; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 OMIM:615351; muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14 MONDO:0014141; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Likely inborn error of metabolism v2.180 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 OMIM:615350; muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14 MONDO:0014140; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 OMIM:615351; muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14 MONDO:0014141; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Undiagnosed metabolic disorders v1.486 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 OMIM:615350; muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14 MONDO:0014140; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 OMIM:615351; muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14 MONDO:0014141; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Congenital muscular dystrophy v2.16 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 OMIM:615350; muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14 MONDO:0014140; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 OMIM:615351; muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14 MONDO:0014141; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Congenital disorders of glycosylation v2.76 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 615350; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 615351; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 615352 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 OMIM:615350; muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14 MONDO:0014140; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B, 14 OMIM:615351; muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B14 MONDO:0014141; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Ataxia and cerebellar anomalies - narrow panel v2.234 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 14 OMIM:615350; muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A14 MONDO:0014140
Rhabdomyolysis and metabolic muscle disorders v1.56 GMPPB Sarah Leigh Tag Q3_21_rating tag was added to gene: GMPPB.
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.25 GMPPB Sarah Leigh reviewed gene: GMPPB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Rhabdomyolysis and metabolic muscle disorders v1.56 GMPPB Sarah Leigh edited their review of gene: GMPPB: Added comment: Associated with relevant phenotype in OMIM, but not associated with the phenotype in Gen2Phen (although it has a confirmed association with OMIM:615350). At least nine variants reported in at least eight cases, supportive functional studies were also presented (PMID 23768512;26133662).; Changed rating: GREEN
Rhabdomyolysis and metabolic muscle disorders v1.56 GMPPB Sarah Leigh Classified gene: GMPPB as Amber List (moderate evidence)
Rhabdomyolysis and metabolic muscle disorders v1.56 GMPPB Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Rhabdomyolysis and metabolic muscle disorders v1.56 GMPPB Sarah Leigh Gene: gmppb has been classified as Amber List (Moderate Evidence).
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.25 GMPPB Sarah Leigh Publications for gene: GMPPB were set to 28456886; 27874200; 25681410; 26133662; 23768512
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.24 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142 to Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Rhabdomyolysis and metabolic muscle disorders v1.55 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142 to Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Rhabdomyolysis and metabolic muscle disorders v1.54 GMPPB Sarah Leigh Publications for gene: GMPPB were set to 28456886; 27874200; 25681410; 26133662; 23768512
Congenital disorders of glycosylation v2.75 GMPPB Sarah Leigh Publications for gene: GMPPB were set to 23768512
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.23 GMPPB Sarah Leigh Publications for gene: GMPPB were set to
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.22 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type to Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Rhabdomyolysis and metabolic muscle disorders v1.53 GMPPB Sarah Leigh Publications for gene: GMPPB were set to 28456886; 27874200; 25681410
Rhabdomyolysis and metabolic muscle disorders v1.52 GMPPB Sarah Leigh Phenotypes for gene: GMPPB were changed from Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 MIM#615352; Limb myalgia; exercise intolerance; myoglobinuria to Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 14 OMIM:615352; autosomal recessive limb-girdle muscular dystrophy type 2T MONDO:0014142
Intellectual disability v3.1250 KMT2E Arina Puzriakova Added comment: Comment on publications: PMID: 34321323 - 18 additional patients from 17 families with genetically confirmed ODLURO
Intellectual disability v3.1250 KMT2E Arina Puzriakova Publications for gene: KMT2E were set to 31079897
Early onset or syndromic epilepsy v2.410 KMT2E Arina Puzriakova Publications for gene: KMT2E were set to 31079897
Intellectual disability v3.1249 MAP1B Arina Puzriakova Tag Q3_21_rating tag was added to gene: MAP1B.
Intellectual disability v3.1249 MAP1B Arina Puzriakova edited their review of gene: MAP1B: Added comment: MAP1B was flagged by a GLH following identification of some potential cases relating to variants in this gene and predominantly ID phenotypes within 100K data. Although these are pending confirmations (will request update once cases are validated), upon reassessment of MAP1B it was highlighted that inclusion on this panels may still be warranted to increase the likelihood of detecting cases, particularly given that DD/ID is more likely to be observed earlier in the course of disease albeit at varying severities.

For this reason, MAP1B should be promoted to Green status at the next GMS panel review (tagged Q3_21_rating); Changed rating: GREEN
Thoracic aortic aneurysm or dissection (GMS) v1.16 FOXE3 Eleanor Williams Added comment: Comment on mode of inheritance: All cases reported in PMID: 26854927 (Kuang et al 2016) are heterozygous so the MONOALLELIC mode of inheritance is appropriate for the Thoracic aortic aneurysms and acute aortic dissection phenotype.
Thoracic aortic aneurysm or dissection (GMS) v1.16 FOXE3 Eleanor Williams Mode of inheritance for gene: FOXE3 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Inherited white matter disorders v1.138 PI4KA Ivone Leong Classified gene: PI4KA as Green List (high evidence)
Inherited white matter disorders v1.138 PI4KA Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. There is enough evidence to support a gene-disease association.
Inherited white matter disorders v1.138 PI4KA Ivone Leong Gene: pi4ka has been classified as Green List (High Evidence).
Inherited white matter disorders v1.137 PI4KA Ivone Leong Tag Q3_21_rating was removed from gene: PI4KA.
Intellectual disability v3.1249 PI4KA Ivone Leong Entity copied from Ataxia and cerebellar anomalies - narrow panel v2.233
Intellectual disability v3.1249 PI4KA Ivone Leong gene: PI4KA was added
gene: PI4KA was added to Intellectual disability. Sources: Expert Review Amber
Q3_21_rating tags were added to gene: PI4KA.
Mode of inheritance for gene: PI4KA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PI4KA were set to 25855803; 34415322; 34415310
Phenotypes for gene: PI4KA were set to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531
Inherited white matter disorders v1.137 PI4KA Ivone Leong Entity copied from Ataxia and cerebellar anomalies - narrow panel v2.233
Inherited white matter disorders v1.137 PI4KA Ivone Leong gene: PI4KA was added
gene: PI4KA was added to Inherited white matter disorders. Sources: Expert Review Amber
Q3_21_rating tags were added to gene: PI4KA.
Mode of inheritance for gene: PI4KA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PI4KA were set to 25855803; 34415322; 34415310
Phenotypes for gene: PI4KA were set to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531
White matter disorders and cerebral calcification - narrow panel v1.198 PI4KA Ivone Leong Entity copied from Ataxia and cerebellar anomalies - narrow panel v2.233
White matter disorders and cerebral calcification - narrow panel v1.198 PI4KA Ivone Leong gene: PI4KA was added
gene: PI4KA was added to White matter disorders and cerebral calcification - narrow panel. Sources: Expert Review Amber
Q3_21_rating tags were added to gene: PI4KA.
Mode of inheritance for gene: PI4KA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PI4KA were set to 25855803; 34415322; 34415310
Phenotypes for gene: PI4KA were set to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531
Ataxia and cerebellar anomalies - narrow panel v2.233 PI4KA Ivone Leong Tag Q3_21_rating tag was added to gene: PI4KA.
Ataxia and cerebellar anomalies - narrow panel v2.233 PI4KA Ivone Leong Phenotypes for gene: PI4KA were changed from Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis , 616531 to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531
Ataxia and cerebellar anomalies - narrow panel v2.232 PI4KA Ivone Leong Publications for gene: PI4KA were set to 25855803
Ataxia and cerebellar anomalies - narrow panel v2.231 PI4KA Ivone Leong Classified gene: PI4KA as Amber List (moderate evidence)
Ataxia and cerebellar anomalies - narrow panel v2.231 PI4KA Ivone Leong Gene: pi4ka has been classified as Amber List (Moderate Evidence).
Ataxia and cerebellar anomalies - narrow panel v2.230 PI4KA Ivone Leong reviewed gene: PI4KA: Rating: GREEN; Mode of pathogenicity: None; Publications: 25855803, 34415322, 34415310; Phenotypes: ; Mode of inheritance: None
Cerebellar hypoplasia v1.59 PI4KA Ivone Leong Added comment: Comment on publications: PMID:34415322. 10 patients from 10 unrelated families with biallelic varaints in PI4KA. Patients showed a spectrum of severe global neurodevelopmental delay (8/10 moderate to severe ID), hypomyelination, cerebellar hyoplasia (1/10), cerebellar atrophy (5/10), bilateral perisylvian polymicrogyria (1/10), immunological problems (hypogammaglobulinaemia, lymphopaenia, and autoimmune neutorpaenia - 4/10), bowl dysfunction (4/10). Age of onset ranged from newborn to 17 years.

PMID: 34415310. 7 unrelated families. Family 1: Amish. Severe extensive multiple intestinal atresia, IBD and combined immunodeficiency (2/4). Families 3 - 8 all have 1 affected individual, (Turkish, Indian, German and Italian). Global developmental delay (all), ID (severe to mild), cerebellar and/or brainstem anomalies (3/6), spasticity (all), immature gyral pattern (1/6), leukodystrophy (6/6), multiple intestinal atresia (0/6), IBD (3/6), combined immunodeficiency (2/6). Early age of onset.
Cerebellar hypoplasia v1.59 PI4KA Ivone Leong Publications for gene: PI4KA were set to 25855803
Adult onset hereditary spastic paraplegia v1.72 L1CAM Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: L1CAM.
Adult onset hereditary spastic paraplegia v1.72 L1CAM Arina Puzriakova commented on gene: L1CAM
Arthrogryposis v3.118 L1CAM Arina Puzriakova Mode of inheritance for gene: L1CAM was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Cerebellar hypoplasia v1.58 PI4KA Ivone Leong Phenotypes for gene: PI4KA were changed from Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis , 616531 to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531
Malformations of cortical development v2.61 PI4KA Ivone Leong Tag watchlist tag was added to gene: PI4KA.
Malformations of cortical development v2.61 PI4KA Ivone Leong Classified gene: PI4KA as Amber List (moderate evidence)
Malformations of cortical development v2.61 PI4KA Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Malformations of cortical development v2.61 PI4KA Ivone Leong Gene: pi4ka has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.60 PI4KA Ivone Leong Phenotypes for gene: PI4KA were changed from Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, MIM# 616531 to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531
Adult onset hereditary spastic paraplegia v1.72 GJA1 Arina Puzriakova changed review comment from: Progressive neurological symptoms are occasionally seen in ODDD due to degeneration of the white matter tracts and can include spastic paraplegia. Gait disturbances due to spasticity can be a presenting feature for which patients initially seek medical attention. Typically signs of spasticity arise in adulthood (PMID: 18660473; 22214631; 29927410; 31023660; 33190326; 33612672); however, several adolescent onset cases (PMID: 18660473; 31023660) have also been described and I could only find a single childhood-onset case with spasticity arising at age 8 (PMID: 29927410).

Overall there is enough evidence to rate as Green on both the adult and childhood-onset HSP panels to ensure identification of all cases. >10 unrelated families reported in literature.; to: Progressive neurological symptoms are occasionally seen in ODDD due to degeneration of the white matter tracts and can include spastic paraplegia. Gait disturbances due to spasticity can be a presenting feature for which patients initially seek medical attention. Typically signs of spasticity arise in adulthood (PMID: 18660473; 22214631; 29927410; 31023660; 33190326; 33612672); however, several adolescent onset cases (PMID: 18660473; 31023660) have also been described and I could only find a single childhood-onset case with spasticity arising at age 8 (PMID: 29927410).

Overall there is enough evidence to rate as Green on the adult-onset HSP panel (>10 unrelated families reported in literature). I will seek further clinical opinion with regard to inclusion on the childhood-onset panel given the implications of carrier status being found incidentally for this primarily adult-onset condition.
Adult onset hereditary spastic paraplegia v1.72 GJA1 Arina Puzriakova Classified gene: GJA1 as Amber List (moderate evidence)
Adult onset hereditary spastic paraplegia v1.72 GJA1 Arina Puzriakova Gene: gja1 has been classified as Amber List (Moderate Evidence).
Adult onset hereditary spastic paraplegia v1.71 GJA1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: GJA1.
Adult onset hereditary spastic paraplegia v1.71 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Adult onset hereditary spastic paraplegia v1.70 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Hereditary spastic paraplegia; Oculodentodigital dysplasia, MIM#164200 to Oculodentodigital dysplasia, OMIM:164200; Spastic paraplegia
Adult onset hereditary spastic paraplegia v1.69 GJA1 Arina Puzriakova Publications for gene: GJA1 were set to 31023660
Adult onset hereditary spastic paraplegia v1.68 GJA1 Arina Puzriakova reviewed gene: GJA1: Rating: GREEN; Mode of pathogenicity: None; Publications: 18660473, 22214631, 29927410, 31023660, 33190326, 33612672; Phenotypes: Oculodentodigital dysplasia, OMIM:164200; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Adult onset neurodegenerative disorder v2.196 SOD1 Ivone Leong Publications for gene: SOD1 were set to 23687121; 24501761; 25439728
Adult onset neurodegenerative disorder v2.195 SOD1 Ivone Leong Tag Q3_21_MOI tag was added to gene: SOD1.
Adult onset neurodegenerative disorder v2.195 SOD1 Ivone Leong reviewed gene: SOD1: Rating: ; Mode of pathogenicity: None; Publications: 7647793, 9817920, 7647793, 18608106, 10809943, 12442272, 11284995, 11127534, 23062701, 11220750; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Amyotrophic lateral sclerosis/motor neuron disease v1.39 SOD1 Ivone Leong Phenotypes for gene: SOD1 were changed from Amyotrophic Lateral Sclerosis, Dominant; Amyotrophic lateral sclerosis 1, 105400; amyotrophic lateral sclerosis to Amyotrophic lateral sclerosis 1, OMIM:105400
Amyotrophic lateral sclerosis/motor neuron disease v1.38 SOD1 Ivone Leong Publications for gene: SOD1 were set to 23687121
Amyotrophic lateral sclerosis/motor neuron disease v1.37 SOD1 Ivone Leong Added comment: Comment on mode of inheritance: MOI changed from "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal".

PMID: 7647793 identified homozygous variants in SOD1 in 14 affected people from 4 unrelated families (some were consanguineous) from Sweden or Finland with ALS. All affected individuals are homozgyous for the the same variant (D90A). Heterozygous carriers were not affected.

PMID: 9817920 studied 28 pedigrees with D90A from around the world. The authors found that 20 recessive familes have the same founder haplotype as PMID:7647793, regardless of location, and that heterozygous carriers in these families were also unaffected. In the dominant families, 5 were sporadic (no family history of ALS) and 3 were familial and several founders existed for these families. This study shows that D90A can cause disease in a dominant fashion just like all other SOD1 variants.

Recessive inheritance of ALS caused by D90A has also been reported in families from Russia, Germany, Iran, Italy, France, Australia, Canada, and US (PMID: 18608106, 10809943, 12442272, 11284995, 11127534, 23062701).

PMID: 11220750 identified a French family with ALS, where the affected individuals were compound heterozygous for D90A and D96N in SOD1.
Amyotrophic lateral sclerosis/motor neuron disease v1.37 SOD1 Ivone Leong Mode of inheritance for gene: SOD1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1248 ASXL3 Arina Puzriakova Publications for gene: ASXL3 were set to 23383720
Intellectual disability v3.1247 ASXL3 Arina Puzriakova Phenotypes for gene: ASXL3 were changed from BAINBRIDGE-ROPERS SYNDROME; BRPS to Bainbridge-Ropers syndrome, OMIM:615485
Palmoplantar keratoderma and erythrokeratodermas v1.20 GJA1 Arina Puzriakova changed review comment from: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 4 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 20597923, 29902798) none have reported dermal abnormalities. It is possible that these may have been overlooked in the context of other more prominent features of the disorder - but this further emphasises the limited value of this panel for this particular phenotype.

MOI for GJA1 on the GMS Palmoplantar keratodermas (R166) panel was set to 'monoallelic' only in 2019, and so the MOI was updated on this panel to reflect this.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100); to: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 4 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 20597923, 29902798) none have reported dermal abnormalities. It is possible that these may have been overlooked in the context of other more prominent features of the disorder - but this further emphasises the limited value of this panel for this particular phenotype.

MOI for GJA1 on the GMS Palmoplantar keratodermas (R166) panel was set to 'monoallelic' in 2019, and so the MOI was also updated to 'monoallelic' on this panel to reflect this.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100)
Palmoplantar keratoderma and erythrokeratodermas v1.20 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Palmoplantar keratoderma and erythrokeratodermas v1.19 GJA1 Arina Puzriakova Tag Q3_21_MOI was removed from gene: GJA1.
Tag Q3_21_expert_review was removed from gene: GJA1.
Palmoplantar keratoderma and erythrokeratodermas v1.19 GJA1 Arina Puzriakova changed review comment from: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 3 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 29902798) none have reported dermal abnormalities. However, it is possible that these may have been overlooked in the context of other more prominent features of the disorder.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100)

GJA1 will be flagged for GMS expert review to determine whether the MOI should be changed on this panel (tagged).; to: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 4 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 20597923, 29902798) none have reported dermal abnormalities. It is possible that these may have been overlooked in the context of other more prominent features of the disorder - but this further emphasises the limited value of this panel for this particular phenotype.

MOI for GJA1 on the GMS Palmoplantar keratodermas (R166) panel was set to 'monoallelic' only in 2019, and so the MOI was updated on this panel to reflect this.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100)
Ichthyosis and erythrokeratoderma v1.66 GJA1 Arina Puzriakova Tag Q3_21_expert_review was removed from gene: GJA1.
Ichthyosis and erythrokeratoderma v1.66 GJA1 Arina Puzriakova changed review comment from: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 3 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 29902798) none have reported dermal abnormalities. However, it is possible that these may have been overlooked in the context of other more prominent features of the disorder.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100)

GJA1 will be flagged for GMS expert review to determine whether the MOI should be changed on this panel (tagged).; to: Comment on mode of inheritance: MOI should be changed from 'both mono- and biallelic' to 'monoallelic' only at the next GMS panel update.

GJA1 was imported to this panel from the 'Palmoplantar keratoderma and erythrokeratodermas' 100K panel and the MOI reflects the mixed inheritance pattern associated with GJA1 oculodentodigital dysplasia (ODDD) (dominant - MIM:164200; recessive - MIM:257850) which can manifest with PPK. Following the uncoupling of PPK and erythrokeratodermas into two separate GMS panels (R165 & R166), only monoallelic variants remain relevant to this particular panel.

Monoallelic variants can cause erythrokeratodermia variabilis et progressiva 3 (MIM: 617525). Erythematous palms and soles have also been described in cases of GJA1-related palmoplantar keratoderma (MIM:104100), also associated with heterozygous variants.
Clefting v2.47 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia,164200; ODDD to Oculodentodigital dysplasia, OMIM:164200
Skeletal dysplasia v2.116 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia 164200; Syndactyly, type III 186100; Erythrokeratodermia variabilis et progressiva 133200; Palmoplantar keratoderma with congenital alopecia 104100; Oculodentodigital dysplasia, autosomal recessive 257850; Craniometaphyseal dysplasia, autosomal recessive 218400; Hypoplastic left heart syndrome 1 241550 to Craniometaphyseal dysplasia, autosomal recessive, OMIM:218400; Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850; Syndactyly, type III, OMIM:186100
Limb disorders v2.57 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Craniometaphyseal dysplasia, autosomal recessive 218400; Erythrokeratodermia variabilis et progressiva 133200; Hypoplastic left heart syndrome 1 241550; Oculodentodigital dysplasia 164200; Oculodentodigital dysplasia, autosomal recessive 257850; Palmoplantar keratoderma with congenital alopecia 104100; Syndactyly, type III 186100 to Craniometaphyseal dysplasia, autosomal recessive, OMIM:218400; Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850; Syndactyly, type III, OMIM:186100
Primary lymphoedema v2.17 GJA1 Arina Puzriakova Publications for gene: GJA1 were set to 23550541
Primary lymphoedema v2.16 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia 164200 to Oculodentodigital dysplasia, OMIM:164200
Adult onset leukodystrophy v1.30 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia, 164200, Oculodentodigital dysplasia, autosomal recessive, 257850 to Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850
White matter disorders and cerebral calcification - narrow panel v1.197 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia, autosomal recessive 257850; Oculodentodigital dysplasia (AD) 164200 to Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850
Inherited white matter disorders v1.136 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia (AD) 164200; Oculodentodigital dysplasia, autosomal recessive 257850 to Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850
Corneal abnormalities v1.9 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia 164200; Oculodentodigital dysplasia, autosomal recessive 257850 to Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850
Monogenic hearing loss v2.181 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from to Craniometaphyseal dysplasia, autosomal recessive, OMIM:218400
Structural eye disease v1.80 GJA1 Arina Puzriakova Publications for gene: GJA1 were set to 15637728; 25976645; 21273537; 30628995; 24508941; 16816024; 29902798
Glaucoma (developmental) v1.38 GJA1 Arina Puzriakova Publications for gene: GJA1 were set to 25976645; 21273537
Glaucoma (developmental) v1.37 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital dysplasia; open angle glaucoma (OAG) and microcornea to Oculodentodigital dysplasia, OMIM:164200
Structural eye disease v1.79 GJA1 Arina Puzriakova Publications for gene: GJA1 were set to 15637728; 25976645; 21273537; 30628995; 24508941
Structural eye disease v1.78 GJA1 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: GJA1.
Structural eye disease v1.78 GJA1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be updated from 'monoallelic' only to 'both mono- and biallelic' at the next GMS panel update.

Ocular abnormalities including microphthalmia and microcornea are reported in GJA1-related oculodentodigital dysplasia, which can be dominantly (MIM:164200) or recessively (MIM:257850) inherited.
Structural eye disease v1.78 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Structural eye disease v1.77 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from open angle glaucoma (OAG) and microcornea; Oculodentodigital dysplasia to Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850
Bilateral congenital or childhood onset cataracts v2.78 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Oculodentodigital Dysplasia to Oculodentodigital dysplasia, OMIM:164200; Oculodentodigital dysplasia, autosomal recessive, OMIM:257850
Rare genetic inflammatory skin disorders v1.40 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Palmoplantar keratoderma with congenital alopecia, OMIM:104100; ERYTHROKERATODERMIA VARIABILIS ET PROGRESSIVA 3, OMIM:617525 to Erythrokeratodermia variabilis et progressiva 3, OMIM:617525
Rare genetic inflammatory skin disorders v1.39 GJA1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be changed from 'both mono- and biallelic' to 'monoallelic' only at the next GMS panel update.

EKVP3 (MIM: 617525) which manifests in transient erythematous patches is associated with monoallelic variants only. Biallelic variants are not pertinent to this panel.
Rare genetic inflammatory skin disorders v1.39 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Rare genetic inflammatory skin disorders v1.38 GJA1 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: GJA1.
Pigmentary skin disorders v1.15 GJA1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be changed from 'both mono- and biallelic' to 'monoallelic' only at the next GMS panel update.

Monoallelic variants can cause EKVP3 (MIM: 617525) which manifests in hyperpigmentation. Erythematous palms and soles have also been described in cases of GJA1-related palmoplantar keratoderma (MIM: 104100), also associated with heterozygous variants. Biallelic variants are not pertinent to this panel.
Pigmentary skin disorders v1.15 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Pigmentary skin disorders v1.14 GJA1 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: GJA1.
Ichthyosis and erythrokeratoderma v1.66 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Palmoplantar keratoderma with congenital alopecia, OMIM:104100; Erythrokeratodermia variabilis et progressiva 3, OMIM:617525 to Erythrokeratodermia variabilis et progressiva 3, OMIM:617525; Palmoplantar keratoderma with congenital alopecia, OMIM:104100
Pigmentary skin disorders v1.14 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from ERYTHROKERATODERMIA VARIABILIS ET PROGRESSIVA 3, 617525 to Erythrokeratodermia variabilis et progressiva 3, OMIM:617525; Palmoplantar keratoderma with congenital alopecia, OMIM:104100
Ichthyosis and erythrokeratoderma v1.65 GJA1 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: GJA1.
Tag Q3_21_expert_review tag was added to gene: GJA1.
Ichthyosis and erythrokeratoderma v1.65 GJA1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 3 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 29902798) none have reported dermal abnormalities. However, it is possible that these may have been overlooked in the context of other more prominent features of the disorder.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100)

GJA1 will be flagged for GMS expert review to determine whether the MOI should be changed on this panel (tagged).
Ichthyosis and erythrokeratoderma v1.65 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Palmoplantar keratoderma and erythrokeratodermas v1.19 GJA1 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: GJA1.
Tag Q3_21_expert_review tag was added to gene: GJA1.
Palmoplantar keratoderma and erythrokeratodermas v1.19 GJA1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI was set to 'both mono- and biallelic' in 2017 as PPK has been observed in some patients with oculodentodigital dysplasia (ODDD). Although GJA1-related ODDD can be dominantly (MIM:164200) or recessively (MIM:257850) inherited, of the 3 unrelated families published to date with confirmed recessive ODDD (PMID: 14981729, 16816024, 29902798) none have reported dermal abnormalities. However, it is possible that these may have been overlooked in the context of other more prominent features of the disorder.

Notably, heterozygous variants are also associated with other relevant phenotypes (MIM: 617525 & 104100)

GJA1 will be flagged for GMS expert review to determine whether the MOI should be changed on this panel (tagged).
Palmoplantar keratoderma and erythrokeratodermas v1.19 GJA1 Arina Puzriakova Mode of inheritance for gene: GJA1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Palmoplantar keratoderma and erythrokeratodermas v1.18 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Palmoplantar keratoderma with congenital alopecia, 104100; Erythrokeratodermia variabilis et progressiva 3, 617525; Erythrokeratoderma; Palmoplantar keratoderma; Oculodentodigital dysplasia (ODDD) with palmoplantar keratoderma; keratoderma, hypotrichosis and leukonychia to Erythrokeratodermia variabilis et progressiva 3, OMIM:617525; Palmoplantar keratoderma with congenital alopecia, OMIM:104100; Oculodentodigital dysplasia, OMIM:164200
Palmoplantar keratodermas v1.9 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Palmoplantar keratoderma to Erythrokeratodermia variabilis et progressiva 3, OMIM:617525; Palmoplantar keratoderma with congenital alopecia, OMIM:104100; Oculodentodigital dysplasia, OMIM:164200
Monogenic hearing loss v2.180 HARS2 Bill Newman reviewed gene: HARS2: Rating: GREEN; Mode of pathogenicity: None; Publications: (PMID:34406847, 34338890); Phenotypes: sensorineural hearing loss, primary ovarian insufficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary ovarian insufficiency v1.44 HARS2 Bill Newman reviewed gene: HARS2: Rating: GREEN; Mode of pathogenicity: None; Publications: (PMID:34406847, 34338890); Phenotypes: sensorineural hearing loss, primary ovarian insufficiency; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Familial non syndromic congenital heart disease v1.64 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Hypoplastic left heart syndrome 1; Hypoplastic Left Heart Syndrome to Hypoplastic left heart syndrome 1, OMIM:241550; Atrioventricular septal defect 3, OMIM:600309
Familial cicatricial alopecia v1.3 GJA1 Arina Puzriakova Phenotypes for gene: GJA1 were changed from Palmoplantar keratoderma with congenital alopecia, 104100 to Palmoplantar keratoderma with congenital alopecia, OMIM:104100
Childhood onset hereditary spastic paraplegia v2.82 SLC25A15 Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Zornitza Stark. There is enough evidence to support a gene-disease association. Spasticity can be a predominant presenting feature, and inclusion on the adult onset panel would ensure later onset, as well as edge cases are identified. SLC25A15 should be promoted to Green at the next GMS panel update.; to: Comment on list classification: New gene added by Zornitza Stark. There is enough evidence to support a gene-disease association. Spasticity can be a predominant presenting feature, particularly in early-onset cases. SLC25A15 should be promoted to Green at the next GMS panel update.
Childhood onset hereditary spastic paraplegia v2.82 SLC25A15 Arina Puzriakova Entity copied from Hereditary spastic paraplegia - adult onset v1.68
Childhood onset hereditary spastic paraplegia v2.82 SLC25A15 Arina Puzriakova gene: SLC25A15 was added
gene: SLC25A15 was added to Hereditary spastic paraplegia - childhood onset. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: SLC25A15.
Mode of inheritance for gene: SLC25A15 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC25A15 were set to 11355015; 16376511; 18978333; 22465082; 28592010; 33314525
Phenotypes for gene: SLC25A15 were set to Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970
Adult onset hereditary spastic paraplegia v1.68 SLC25A15 Arina Puzriakova Classified gene: SLC25A15 as Amber List (moderate evidence)
Adult onset hereditary spastic paraplegia v1.68 SLC25A15 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There is enough evidence to support a gene-disease association. Spasticity can be a predominant presenting feature, and inclusion on the adult onset panel would ensure later onset, as well as edge cases are identified. SLC25A15 should be promoted to Green at the next GMS panel update.
Adult onset hereditary spastic paraplegia v1.68 SLC25A15 Arina Puzriakova Gene: slc25a15 has been classified as Amber List (Moderate Evidence).
Adult onset hereditary spastic paraplegia v1.67 SLC25A15 Arina Puzriakova Publications for gene: SLC25A15 were set to 16376511; 22465082; 28592010
Adult onset hereditary spastic paraplegia v1.66 SLC25A15 Arina Puzriakova Tag Q3_21_rating tag was added to gene: SLC25A15.
Adult onset hereditary spastic paraplegia v1.66 SLC25A15 Arina Puzriakova reviewed gene: SLC25A15: Rating: GREEN; Mode of pathogenicity: None; Publications: 11355015, 16376511, 18978333, 22465082, 33314525; Phenotypes: Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Likely inborn error of metabolism v2.179 SLC25A15 Arina Puzriakova Phenotypes for gene: SLC25A15 were changed from Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, 238970; HHH syndrome (Urea cycle disorders and inherited hyperammonaemias) to Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970; HHH syndrome (Urea cycle disorders and inherited hyperammonaemias)
Adult onset hereditary spastic paraplegia v1.66 SLC25A15 Arina Puzriakova Phenotypes for gene: SLC25A15 were changed from Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome MIM#238970 to Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970
Intellectual disability v3.1246 SLC25A15 Arina Puzriakova Phenotypes for gene: SLC25A15 were changed from Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, 238970 -3; HYPERORNITHINEMIA-HYPERAMMONEMIA-HOMOCITRULLINURIA SYNDROME (HHH SYNDROME) to Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970
Undiagnosed metabolic disorders v1.485 SLC25A15 Arina Puzriakova Phenotypes for gene: SLC25A15 were changed from HHH syndrome (Urea cycle disorders and inherited hyperammonaemias); Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, 238970 to Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970; HHH syndrome (Urea cycle disorders and inherited hyperammonaemias)
Hyperammonaemia v1.12 SLC25A15 Arina Puzriakova Phenotypes for gene: SLC25A15 were changed from Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, 238970 to Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome, OMIM:238970
Severe microcephaly v2.220 TRAPPC10 Aleš Maver gene: TRAPPC10 was added
gene: TRAPPC10 was added to Severe microcephaly. Sources: Other
Mode of inheritance for gene: TRAPPC10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TRAPPC10 were set to PMID: 30167849
Penetrance for gene: TRAPPC10 were set to Complete
Review for gene: TRAPPC10 was set to RED
Added comment: This gene was originally reported in association with microcephalic NDD in PMID:30167849 (biallelic missense variant) and was replicated in a large family consanguineous family with a biallelic frameshift variant - reported at the ESHG2021 conference, talk C16.4 by Rawlins).
Sources: Other
Peroxisomal disorders v1.15 PEX6 Ivone Leong Phenotypes for gene: PEX6 were changed from Peroxisome biogenesis disorder 4A (Zellweger) 614862; Peroxisome biogenesis disorder 4B 614863 to Peroxisome biogenesis disorder 4A (Zellweger), OMIM:614862; Peroxisome biogenesis disorder 4B, OMIM:614863
Peroxisomal disorders v1.14 PEX6 Ivone Leong Publications for gene: PEX6 were set to
Unexplained kidney failure in young people v1.96 TRIM8 Ivone Leong Publications for gene: TRIM8 were set to 33508234
Unexplained kidney failure in young people v1.95 TRIM8 Ivone Leong Classified gene: TRIM8 as Green List (high evidence)
Unexplained kidney failure in young people v1.95 TRIM8 Ivone Leong Added comment: Comment on list classification: New gene added by Julia Baptista (Royal Devon and Exeter NHS Foundation Trust). This gene is associated with a phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene has been given a Green rating.
Unexplained kidney failure in young people v1.95 TRIM8 Ivone Leong Gene: trim8 has been classified as Green List (High Evidence).
Unexplained kidney failure in young people v1.94 TRIM8 Ivone Leong Phenotypes for gene: TRIM8 were changed from nephrotic syndrome; epilepsy to nephrotic syndrome; epilepsy; Focal segmental glomerulosclerosis and neurodevelopmental syndrome, OMIM:619428
Rare multisystem ciliopathy disorders v1.145 TBC1D32 Ivone Leong Phenotypes for gene: TBC1D32 were changed from No OMIM phenotype; Oro-facio-digital syndrome type IX (Adly (2014) Hum Mutat 35, 36) to Orofaciodigital syndrome, MONDO:0015375
Adult onset hereditary spastic paraplegia v1.65 GBE1 Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM. There is enough evidence to support a gene-disease association. GBE1 should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM. There is enough evidence to support a gene-disease association. Transgenic homozygous mice also display late-onset spastic paraplegia. GBE1 should be rated Green at the next review.
Adult onset hereditary spastic paraplegia v1.65 GBE1 Arina Puzriakova Publications for gene: GBE1 were set to 23034915
Adult onset hereditary spastic paraplegia v1.64 GBE1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: GBE1.
Adult onset hereditary spastic paraplegia v1.64 GBE1 Arina Puzriakova Classified gene: GBE1 as Amber List (moderate evidence)
Adult onset hereditary spastic paraplegia v1.64 GBE1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM. There is enough evidence to support a gene-disease association. GBE1 should be rated Green at the next review.
Adult onset hereditary spastic paraplegia v1.64 GBE1 Arina Puzriakova Gene: gbe1 has been classified as Amber List (Moderate Evidence).
Adult onset neurodegenerative disorder v2.195 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Polyglucosan body disease, adult form MIM#263570 to Polyglucosan body disease, adult form, OMIM:263570
Adult onset hereditary spastic paraplegia v1.63 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Polyglucosan body disease, adult form MIM#263570 to Polyglucosan body disease, adult form, OMIM:263570
Paediatric or syndromic cardiomyopathy v1.54 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from DCM; Glycogen Storage Disease Type IV; Hypertrophic-hypocontractile cardiomyopathy; Polyglucosan body disease, adult form, 263570; Glycogen Storage Disease; failure to thrive in addition to hepatomegaly van have neuromuscular adult form ( polyglucosan body ideas which presents with neurogenic bladder, gait difficulties; Glycogen storage disease type IV (brancher enzyme deficiency), neuromuscular form; hypotonia, exercise intolerance, polyglucosan bodies in affected tissues; Glycogen storage disease type IV, Andersen (Glycogen storage disorders); Glycogen Storage Disorders- Liver; Glycogen Storage Disorders- Muscle; Glycogen storage disease IV, 232500 to Glycogen storage disease IV, OMIM:232500
Fetal anomalies v1.708 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV; Polyglucosan body disease, adult form; Fetal akinesia deformation sequence to Glycogen storage disease IV, OMIM:232500; Fetal akinesia deformation sequence
Likely inborn error of metabolism v2.178 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV, 232500; Glycogen Storage Disease; Glycogen Storage Disorders- Liver; Glycogen storage disease type IV, Andersen (Glycogen storage disorders); Glycogen Storage Disorders- Muscle; Glycogen Storage Disease Type IV; failure to thrive in addition to hepatomegaly van have neuromuscular adult form ( polyglucosan body ideas which presents with neurogenic bladder, gait difficulties; Polyglucosan body disease, adult form, 263570 to Glycogen storage disease IV, OMIM:232500; Polyglucosan body disease, adult form, OMIM:263570
Undiagnosed metabolic disorders v1.484 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease type IV, Andersen (Glycogen storage disorders); failure to thrive in addition to hepatomegaly van have neuromuscular adult form ( polyglucosan body ideas which presents with neurogenic bladder, gait difficulties; Glycogen storage disease IV, 232500; Polyglucosan body disease, adult form, 263570; Glycogen Storage Disease Type IV; Glycogen Storage Disorders- Liver; Glycogen Storage Disorders- Muscle; Glycogen Storage Disease to Glycogen storage disease IV, OMIM:232500; Polyglucosan body disease, adult form, OMIM:263570
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.21 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV, 232500 to Glycogen storage disease IV, OMIM:232500
Arthrogryposis v3.117 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV 232500 to Glycogen storage disease IV, OMIM:232500
Inherited white matter disorders v1.135 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Polyglucosan Body Disease (PGBD); General Leukodystrophy & Mitochondrial Leukoencephalopathy; Polyglucosan body disease, adult form to Polyglucosan body disease, adult form, OMIM:263570; General Leukodystrophy & Mitochondrial Leukoencephalopathy
Glycogen storage disease v1.7 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV 232500 to Glycogen storage disease IV, OMIM:232500
Adult onset leukodystrophy v1.29 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Polyglucosan body disease, adult form, 263570 to Polyglucosan body disease, adult form, OMIM:263570
White matter disorders and cerebral calcification - narrow panel v1.196 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from General Leukodystrophy & Mitochondrial Leukoencephalopathy; Polyglucosan body disease, adult form; Polyglucosan Body Disease (PGBD) to Polyglucosan body disease, adult form, OMIM:263570; General Leukodystrophy & Mitochondrial Leukoencephalopathy
Rhabdomyolysis and metabolic muscle disorders v1.51 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV 232500 to Glycogen storage disease IV, OMIM:232500
Fetal hydrops v1.34 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV, 232500; GSD4; Fetal hydrops (in perinatal or congenital neuromuscular forms); Andersen disease to Glycogen storage disease IV, OMIM:232500; Fetal hydrops (in perinatal or congenital neuromuscular forms)
Neonatal cholestasis v1.19 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from Glycogen storage disease IV 232500 to Glycogen storage disease IV, OMIM:232500
Ketotic hypoglycaemia v1.5 GBE1 Arina Puzriakova Phenotypes for gene: GBE1 were changed from failure to thrive in addition to hepatomegaly van have neuromuscular adult form ( polyglucosan body ideas which presents with neurogenic bladder, gait difficulties; Glycogen storage disease IV, 232500; Polyglucosan body disease, adult form, 263570; Glycogen Storage Disease Type IV; Glycogen Storage Disorders- Liver; Glycogen Storage Disorders- Muscle; Glycogen Storage Disease to Glycogen storage disease IV, OMIM:232500; Polyglucosan body disease, adult form, OMIM:263570
Childhood onset hereditary spastic paraplegia v2.81 GALC Arina Puzriakova Classified gene: GALC as Amber List (moderate evidence)
Childhood onset hereditary spastic paraplegia v2.81 GALC Arina Puzriakova Added comment: Comment on list classification: This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Childhood onset hereditary spastic paraplegia v2.81 GALC Arina Puzriakova Gene: galc has been classified as Amber List (Moderate Evidence).
Childhood onset hereditary spastic paraplegia v2.80 GALC Arina Puzriakova gene: GALC was added
gene: GALC was added to Hereditary spastic paraplegia - childhood onset. Sources: Literature
Q3_21_rating tags were added to gene: GALC.
Mode of inheritance for gene: GALC was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GALC were set to 20886637; 21070211; 26396125; 28547031; 30089515; 31185936
Phenotypes for gene: GALC were set to Krabbe disease OMIM:245200
Review for gene: GALC was set to GREEN
Added comment: Biallelic variants in GALC are associated with Krabbe disease (MIM# 245200). Most patients present within the first 6 months of life with extreme irritability, spasticity, and developmental delay. A subset of cases also have later onset, including onset in the juvenile and adolescence period - all of which are relevant to this panel.
Sources: Literature
Adult onset hereditary spastic paraplegia v1.62 GALC Arina Puzriakova Tag Q3_21_rating tag was added to gene: GALC.
Adult onset hereditary spastic paraplegia v1.62 GALC Arina Puzriakova Classified gene: GALC as Amber List (moderate evidence)
Adult onset hereditary spastic paraplegia v1.62 GALC Arina Puzriakova Gene: galc has been classified as Amber List (Moderate Evidence).
Adult onset hereditary spastic paraplegia v1.61 GALC Arina Puzriakova Classified gene: GALC as Green List (high evidence)
Adult onset hereditary spastic paraplegia v1.61 GALC Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Adult onset hereditary spastic paraplegia v1.61 GALC Arina Puzriakova Gene: galc has been classified as Green List (High Evidence).
Adult onset hereditary spastic paraplegia v1.60 GALC Arina Puzriakova reviewed gene: GALC: Rating: GREEN; Mode of pathogenicity: None; Publications: 9272171, 11971051, 21070211, 22959700, 26915362, 32064984; Phenotypes: Krabbe disease, OMIM:245200; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder v1.54 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe. Spastic paraplegia, developmental delay, optic atrophy; Krabbe disease, 245200; adult onset has spastic paraplegia and sensory-motor axonal neuropathy with slow or normal conduction velocities, MRI shows leukodystrophy to Krabbe disease, OMIM:245200
Intellectual disability v3.1245 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from KRABBE DISEASE to Krabbe disease, OMIM:245200
Early onset or syndromic epilepsy v2.409 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease, 245200; seizures; CALC deficiency; Galactosylceramide beta-galactosidase deficiency to Krabbe disease, OMIM:245200
Hereditary neuropathy v1.406 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease, 245200; Krabbe. Spastic paraplegia, developmental delay, optic atrophy; adult onset has spastic paraplegia and sensory-motor axonal neuropathy with slow or normal conduction velocities, MRI shows leukodystrophy to Krabbe disease, OMIM:245200
Likely inborn error of metabolism v2.177 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease to Krabbe disease, OMIM:245200
Fetal anomalies v1.707 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from KRABBE DISEASE to Krabbe disease, OMIM:245200
Rare multisystem ciliopathy disorders v1.144 TBC1D32 Ivone Leong Publications for gene: TBC1D32 were set to 32573025; 31130284; 32060556
Undiagnosed metabolic disorders v1.483 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease 245200 to Krabbe disease, OMIM:245200
Inherited white matter disorders v1.134 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease 245200 to Krabbe disease, OMIM:245200
Adult onset leukodystrophy v1.28 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease, 245200 to Krabbe disease, OMIM:245200
Hereditary ataxia with onset in adulthood v2.85 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease, 245200 to Krabbe disease, OMIM:245200
Adult onset hereditary spastic paraplegia v1.60 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease MIM#245200 to Krabbe disease, OMIM:245200
White matter disorders and cerebral calcification - narrow panel v1.195 GALC Arina Puzriakova Phenotypes for gene: GALC were changed from Krabbe disease to Krabbe disease, OMIM:245200
Rare multisystem ciliopathy disorders v1.143 TBC1D32 Ivone Leong Publications for gene: TBC1D32 were set to
Fetal hydrops v1.33 ALG8 Arina Puzriakova Classified gene: ALG8 as Green List (high evidence)
Fetal hydrops v1.33 ALG8 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. There are sufficient unrelated cases with prenatal hydrops and variants in this gene to rate as Green on this panel. ALG8 is also already Green on the GMS Fetal anomalies (R21) panel.
Fetal hydrops v1.33 ALG8 Arina Puzriakova Gene: alg8 has been classified as Green List (High Evidence).
Fetal hydrops v1.32 ALG1 Arina Puzriakova Publications for gene: ALG1 were set to 9762608; 14973778
Fetal hydrops v1.31 ALG1 Arina Puzriakova Classified gene: ALG1 as Red List (low evidence)
Fetal hydrops v1.31 ALG1 Arina Puzriakova Added comment: Comment on list classification: Only a single individual reported to date with prenatal hydrops and so will maintain the current Red rating on this panel. However, ALG1 is already Green on the GMS Fetal anomalies panel so cases should still be picked up via that route.
Fetal hydrops v1.31 ALG1 Arina Puzriakova Gene: alg1 has been classified as Red List (Low Evidence).
Fetal hydrops v1.30 ALG1 Arina Puzriakova Mode of inheritance for gene: ALG1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia with onset in adulthood v2.84 CHP1 Arina Puzriakova Entity copied from Hereditary ataxia v1.241
Hereditary ataxia with onset in adulthood v2.84 CHP1 Arina Puzriakova gene: CHP1 was added
gene: CHP1 was added to Hereditary ataxia - adult onset. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: CHP1.
Mode of inheritance for gene: CHP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CHP1 were set to 23904602; 29379881; 32787936
Phenotypes for gene: CHP1 were set to Spastic ataxia 9, autosomal recessive, OMIM:618438
Ataxia and cerebellar anomalies - narrow panel v2.230 CHP1 Arina Puzriakova Entity copied from Hereditary ataxia v1.241
Ataxia and cerebellar anomalies - narrow panel v2.230 CHP1 Arina Puzriakova gene: CHP1 was added
gene: CHP1 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: CHP1.
Mode of inheritance for gene: CHP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CHP1 were set to 23904602; 29379881; 32787936
Phenotypes for gene: CHP1 were set to Spastic ataxia 9, autosomal recessive, OMIM:618438
Adult onset hereditary spastic paraplegia v1.59 CHP1 Arina Puzriakova Entity copied from Hereditary ataxia v1.241
Adult onset hereditary spastic paraplegia v1.59 CHP1 Arina Puzriakova gene: CHP1 was added
gene: CHP1 was added to Hereditary spastic paraplegia - adult onset. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: CHP1.
Mode of inheritance for gene: CHP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CHP1 were set to 23904602; 29379881; 32787936
Phenotypes for gene: CHP1 were set to Spastic ataxia 9, autosomal recessive, OMIM:618438
Childhood onset hereditary spastic paraplegia v2.79 CHP1 Arina Puzriakova Entity copied from Hereditary ataxia v1.241
Childhood onset hereditary spastic paraplegia v2.79 CHP1 Arina Puzriakova gene: CHP1 was added
gene: CHP1 was added to Hereditary spastic paraplegia - childhood onset. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: CHP1.
Mode of inheritance for gene: CHP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CHP1 were set to 23904602; 29379881; 32787936
Phenotypes for gene: CHP1 were set to Spastic ataxia 9, autosomal recessive, OMIM:618438
Hereditary ataxia v1.241 CHP1 Arina Puzriakova edited their review of gene: CHP1: Changed rating: AMBER; Changed publications to: 23904602, 29379881, 32787936; Changed phenotypes to: Spastic ataxia 9, autosomal recessive, OMIM:618438; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia v1.241 CHP1 Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Julia Baptista (RD&E_NHS). Rating Amber, awaiting further cases to better delineate phenotypes and for clarification regarding the age of onset.
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Two unrelated families, each with two affected sibs presenting ataxia, associated with different biallelic variants in the CHP1 gene (PMID: 29379881; 32787936). Other features include intellectual disability (3/4), cerebellar atrophy (3/4), spastic paraplegia (3/4), and neuropathy (2/4).

In vitro studies of one variant showed mutant CHP1 fails to integrate into functional complexes and impairs membrane localisation of the Na+/H+ transporter NHE1. Zebrafish and mouse models recapitulate human phenotypes such as movement defects (including ataxia), cerebellar hypoplasia, and axon abnormalities (PMID: 23904602; 29379881).

However, there are some notable differences between the two families. The age at onset differs considerably with one sib pair presenting with ataxia and cognitive decline in middle age (PMID: 32787936), in contrast to the other sibs who had infantile-onset ataxia and intellectual disability (PMID: 29379881).

CHP1 has been added to both adult and childhood-onset ataxia GMS panels, but currently the evidence only suffices for an Amber rating for each (added watchlist tag).; to: Comment on list classification: New gene added by Julia Baptista (RD&E_NHS). Rating Amber, awaiting further cases to better delineate phenotypes and for clarification regarding the age of onset.
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Two unrelated families, each with two affected sibs presenting ataxia, associated with different biallelic variants in the CHP1 gene (PMID: 29379881; 32787936). Other features include intellectual disability (3/4), cerebellar atrophy (3/4), spastic paraplegia (3/4), and neuropathy (2/4).

In vitro studies of one variant showed mutant CHP1 fails to integrate into functional complexes and impairs membrane localisation of the Na+/H+ transporter NHE1. Zebrafish and mouse models recapitulate human phenotypes such as movement defects (including ataxia), cerebellar hypoplasia, and axon abnormalities (PMID: 23904602; 29379881).

However, there are some notable differences between the two families. The age at onset differs considerably with one sib pair presenting with ataxia and cognitive decline in middle age (PMID: 32787936), in contrast to the other sibs who had infantile-onset ataxia and intellectual disability (PMID: 29379881).

CHP1 has been added to both adult and childhood-onset ataxia and spasticity GMS panels, but currently the evidence only suffices for an Amber rating for each (added watchlist tag).
Hereditary ataxia v1.241 CHP1 Arina Puzriakova Publications for gene: CHP1 were set to 32787936; 29379881
Hereditary ataxia v1.240 CHP1 Arina Puzriakova Tag watchlist tag was added to gene: CHP1.
Hereditary ataxia v1.240 CHP1 Arina Puzriakova Classified gene: CHP1 as Amber List (moderate evidence)
Hereditary ataxia v1.240 CHP1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Julia Baptista (RD&E_NHS). Rating Amber, awaiting further cases to better delineate phenotypes and for clarification regarding the age of onset.
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Two unrelated families, each with two affected sibs presenting ataxia, associated with different biallelic variants in the CHP1 gene (PMID: 29379881; 32787936). Other features include intellectual disability (3/4), cerebellar atrophy (3/4), spastic paraplegia (3/4), and neuropathy (2/4).

In vitro studies of one variant showed mutant CHP1 fails to integrate into functional complexes and impairs membrane localisation of the Na+/H+ transporter NHE1. Zebrafish and mouse models recapitulate human phenotypes such as movement defects (including ataxia), cerebellar hypoplasia, and axon abnormalities (PMID: 23904602; 29379881).

However, there are some notable differences between the two families. The age at onset differs considerably with one sib pair presenting with ataxia and cognitive decline in middle age (PMID: 32787936), in contrast to the other sibs who had infantile-onset ataxia and intellectual disability (PMID: 29379881).

CHP1 has been added to both adult and childhood-onset ataxia GMS panels, but currently the evidence only suffices for an Amber rating for each (added watchlist tag).
Hereditary ataxia v1.240 CHP1 Arina Puzriakova Gene: chp1 has been classified as Amber List (Moderate Evidence).
Hereditary ataxia v1.239 CHP1 Arina Puzriakova Phenotypes for gene: CHP1 were changed from ataxia; ID to Spastic ataxia 9, autosomal recessive, OMIM:618438
Primary ciliary disorders v1.32 NEK10 Arina Puzriakova Classified gene: NEK10 as Green List (high evidence)
Primary ciliary disorders v1.32 NEK10 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zerin Hyder. NEK10 is associated with a relevant phenotype in OMIM. There is enough evidence to support a gene-disease association and so this gene has been added as Green - sufficient number of unrelated cases (>3) and functional support.
Primary ciliary disorders v1.32 NEK10 Arina Puzriakova Gene: nek10 has been classified as Green List (High Evidence).
Primary ciliary disorders v1.31 NEK10 Arina Puzriakova Phenotypes for gene: NEK10 were changed from primary ciliary dyskinesia; bronchiectasis to Ciliary dyskinesia, primary, 44, OMIM:618781
Primary ciliary disorders v1.30 NEK10 Arina Puzriakova Publications for gene: NEK10 were set to 31959991
Intellectual disability v3.1244 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sjogren-Larsson syndrome, 270200; SJOEGREN-LARSSON SYNDROME (SLS) to Sjogren-Larsson syndrome, OMIM:270200
Likely inborn error of metabolism v2.176 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Intellectual disability; Sj gren - Larsson syndrome (Other disorders of lipid and lipoprotein metabolism); Inherited white matter disorders to Sjogren-Larsson syndrome, OMIM:270200
Undiagnosed metabolic disorders v1.482 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sj gren - Larsson syndrome (Other disorders of lipid and lipoprotein metabolism); Inherited white matter disorders; Intellectual disability to Sjogren-Larsson syndrome, OMIM:270200
Inherited white matter disorders v1.133 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sjogren Larsson syndrome; General Leukodystrophy & Mitochondrial Leukoencephalopathy to Sjogren-Larsson syndrome, OMIM:270200; General Leukodystrophy & Mitochondrial Leukoencephalopathy
Adult onset leukodystrophy v1.27 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sjogren-Larsson syndrome, 270200 to Sjogren-Larsson syndrome, OMIM:270200
Palmoplantar keratodermas v1.8 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sjogren-Larsson syndrome to Sjogren-Larsson syndrome, OMIM:270200
White matter disorders and cerebral calcification - narrow panel v1.194 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sjogren Larsson syndrome; General Leukodystrophy & Mitochondrial Leukoencephalopathy to Sjogren-Larsson syndrome, OMIM:270200; General Leukodystrophy & Mitochondrial Leukoencephalopathy
Ichthyosis and erythrokeratoderma v1.64 ALDH3A2 Arina Puzriakova changed review comment from: Comment on list classification: New gene added by Denise Williams (BWC_NHS). Ichthyosis is a feature of the condition associated with biallelic variants in this gene (MIM# 270200). Cutaneous abnormalities are often the first clinical sign to be noted. There are sufficient unrelated cases (>3) to rate as Green on this panel.; to: Comment on list classification: New gene added by Denise Williams (BWC_NHS). Ichthyosis is a feature of the condition associated with biallelic variants in this gene (MIM# 270200). Cutaneous abnormalities are often the first clinical sign to be noted. There are sufficient unrelated cases (>3) to rate as Green at the next GMS panel update.
Ichthyosis and erythrokeratoderma v1.64 ALDH3A2 Arina Puzriakova Classified gene: ALDH3A2 as Amber List (moderate evidence)
Ichthyosis and erythrokeratoderma v1.64 ALDH3A2 Arina Puzriakova Gene: aldh3a2 has been classified as Amber List (Moderate Evidence).
Ichthyosis and erythrokeratoderma v1.63 ALDH3A2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: ALDH3A2.
Ichthyosis and erythrokeratoderma v1.63 ALDH3A2 Arina Puzriakova Entity copied from Autosomal recessive congenital ichthyosis v1.13
Ichthyosis and erythrokeratoderma v1.63 ALDH3A2 Arina Puzriakova gene: ALDH3A2 was added
gene: ALDH3A2 was added to Ichthyosis and erythrokeratoderma. Sources: Expert Review Green,Expert Review
Mode of inheritance for gene: ALDH3A2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ALDH3A2 were set to 9829906; 16476818; 25784589; 27547594; 29071827; 29183715; 29375833; 29704247; 30157790; 30403285; 31273323; 31388754; 31944864; 32930514; 34082469; 34315315
Phenotypes for gene: ALDH3A2 were set to Sjogren-Larsson syndrome, OMIM:270200
Penetrance for gene: ALDH3A2 were set to Complete
Retinal disorders v2.206 ALDH3A2 Arina Puzriakova Classified gene: ALDH3A2 as Amber List (moderate evidence)
Retinal disorders v2.206 ALDH3A2 Arina Puzriakova Added comment: Comment on list classification: There are sufficient unrelated cases (>3) with retinal abnormalities associated with variants in this gene to warrant a Green rating at the next GMS panel update.
Retinal disorders v2.206 ALDH3A2 Arina Puzriakova Gene: aldh3a2 has been classified as Amber List (Moderate Evidence).
Retinal disorders v2.205 ALDH3A2 Arina Puzriakova gene: ALDH3A2 was added
gene: ALDH3A2 was added to Retinal disorders. Sources: Literature
Q3_21_rating tags were added to gene: ALDH3A2.
Mode of inheritance for gene: ALDH3A2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ALDH3A2 were set to 25784589; 29071827; 29183715; 31273323
Phenotypes for gene: ALDH3A2 were set to Sjogren-Larsson syndrome, OMIM:270200
Review for gene: ALDH3A2 was set to GREEN
Added comment: Biallelic variants in this gene are associated with Sjogren-Larsson syndrome (MIM# 270200). Some affected individuals exhibit ocular manifestations which include a distinctive retinal abnormality characterised by macular degeneration with perifoveal crystalline inclusions (also referred to as glistening white dots) which develop in the first few years of life. There are also some reports of patients with retinal pigmentary degeneration in the macular region and thinning of the retinal layers.
Sources: Literature
Childhood onset hereditary spastic paraplegia v2.78 ALDH3A2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: ALDH3A2.
Childhood onset hereditary spastic paraplegia v2.78 ALDH3A2 Arina Puzriakova Classified gene: ALDH3A2 as Amber List (moderate evidence)
Childhood onset hereditary spastic paraplegia v2.78 ALDH3A2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). Childhood-onset spastic paraparesis is a feature of the condition associated with biallelic variants in this gene (MIM# 270200). There are sufficient unrelated cases (>3) to rate as Green at the next GMS panel update.
Childhood onset hereditary spastic paraplegia v2.78 ALDH3A2 Arina Puzriakova Gene: aldh3a2 has been classified as Amber List (Moderate Evidence).
Childhood onset hereditary spastic paraplegia v2.77 ALDH3A2 Arina Puzriakova Publications for gene: ALDH3A2 were set to 8528251; 29704247
Autosomal recessive congenital ichthyosis v1.13 ALDH3A2 Arina Puzriakova Classified gene: ALDH3A2 as Green List (high evidence)
Autosomal recessive congenital ichthyosis v1.13 ALDH3A2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Denise Williams (BWC_NHS). Ichthyosis is a feature of the condition associated with biallelic variants in this gene (MIM# 270200). Cutaneous abnormalities are often the first clinical sign to be noted. There are sufficient unrelated cases (>3) to rate as Green on this panel.
Autosomal recessive congenital ichthyosis v1.13 ALDH3A2 Arina Puzriakova Gene: aldh3a2 has been classified as Green List (High Evidence).
Autosomal recessive congenital ichthyosis v1.12 ALDH3A2 Arina Puzriakova Publications for gene: ALDH3A2 were set to 31273323; 27547594; 9829906
Childhood onset hereditary spastic paraplegia v2.76 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from Sjogren-Larsson syndrome, MIM#270200 to Sjogren-Larsson syndrome, OMIM:270200
Autosomal recessive congenital ichthyosis v1.11 ALDH3A2 Arina Puzriakova Phenotypes for gene: ALDH3A2 were changed from congenital ichthyosis; intellectual disability; spastic diplegia, ocular anomalies. to Sjogren-Larsson syndrome, OMIM:270200
Childhood onset dystonia, chorea or related movement disorder v1.146 SLC16A2 Arina Puzriakova Classified gene: SLC16A2 as Amber List (moderate evidence)
Childhood onset dystonia, chorea or related movement disorder v1.146 SLC16A2 Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update.
Childhood onset dystonia, chorea or related movement disorder v1.146 SLC16A2 Arina Puzriakova Gene: slc16a2 has been classified as Amber List (Moderate Evidence).
Childhood onset dystonia, chorea or related movement disorder v1.145 SLC16A2 Arina Puzriakova Publications for gene: SLC16A2 were set to 31410843
Childhood onset dystonia, chorea or related movement disorder v1.144 SLC16A2 Arina Puzriakova Tag Q3_21_rating tag was added to gene: SLC16A2.
Childhood onset dystonia, chorea or related movement disorder v1.144 SLC16A2 Arina Puzriakova reviewed gene: SLC16A2: Rating: GREEN; Mode of pathogenicity: None; Publications: 20713192, 22805248, 23419639, 24170966, 25160547, 25755011, 25900139, 27212794, 31410843; Phenotypes: Allan-Herndon-Dudley syndrome, OMIM:300523; Mode of inheritance: None
Adult onset hereditary spastic paraplegia v1.58 SLC16A2 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: SLC16A2.
Childhood onset hereditary spastic paraplegia v2.75 SLC16A2 Arina Puzriakova Publications for gene: SLC16A2 were set to 12871948; 14661163; 19194886
Adult onset hereditary spastic paraplegia v1.58 SLC16A2 Arina Puzriakova Publications for gene: SLC16A2 were set to 14661163; 19194886
Adult onset hereditary spastic paraplegia v1.57 SLC16A2 Arina Puzriakova reviewed gene: SLC16A2: Rating: ; Mode of pathogenicity: None; Publications: 20713192, 22805248, 23419639, 24170966, 25755011, 25900139, 28742507, 31410843; Phenotypes: Allan-Herndon-Dudley syndrome, OMIM:300523; Mode of inheritance: None
Intellectual disability v3.1243 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Allan-Herndon-Dudley syndrome, 300523; MCT8 (SLC16A2)-SPECIFIC THYROID HORMONE CELL TRANSPORTER DEFICIENCY to Allan-Herndon-Dudley syndrome, OMIM:300523
Childhood onset dystonia, chorea or related movement disorder v1.144 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Allan-Herndon-Dudley syndrome, MIM# 300523 to Allan-Herndon-Dudley syndrome, OMIM:300523
Congenital hypothyroidism v2.5 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from MENTAL RETARDATION AND MUSCULAR ATROPHY; MCT8 (SLC16A2)-specific thyroid hormone cell transporter deficiency; monocarboxylate transporter 8 (MCT8) deficiency; ALLAN-HERNDON SYNDROME; Monocarboxylate transporter 8 (MCT8) defect; Allan-Herndon-Dudley syndrome; AHDS; MENTAL RETARDATION, X-LINKED, WITH HYPOTONIA; Allan_Herndon_Dudley Syndrome; mental retardation, X-linked, with hypotonia; MONOCARBOXYLATE TRANSPORTER 8 DEFICIENCY; Allan-Herndon-Dudley Syndrome; T3 RESISTANCE; TRIIODOTHYRONINE RESISTANCE; 300523; Allan-Herndon-Dudley syndrome, 300523; ALLAN-HERNDON-DUDLEY SYNDROME to Allan-Herndon-Dudley syndrome, OMIM:300523
Early onset or syndromic epilepsy v2.408 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Allan-Herndon-Dudley syndrome, 300523; AHDS to Allan-Herndon-Dudley syndrome, OMIM:300523
Adult onset neurodegenerative disorder v2.194 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from to Allan-Herndon-Dudley syndrome, OMIM:300523
Adult onset hereditary spastic paraplegia v1.57 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Allan-Herndon-Dudley syndrome, 300523, XL to Allan-Herndon-Dudley syndrome, OMIM:300523
Childhood onset hereditary spastic paraplegia v2.74 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Allan-Herndon-Dudley syndrome, 300523 to Allan-Herndon-Dudley syndrome, OMIM:300523
Hereditary spastic paraplegia v1.257 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from to Allan-Herndon-Dudley syndrome, OMIM:300523
Inherited white matter disorders v1.132 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Hypomyelinating Leukodystrophy & Pelizaeus-Merzbacher Disease; Allan-Herndon-Dudley syndrome; Monocarboxylate transporter 8 deficiency (MCT8); General Leukodystrophy & Mitochondrial Leukoencephalopathy to Allan-Herndon-Dudley syndrome, OMIM:300523; General Leukodystrophy & Mitochondrial Leukoencephalopathy; Hypomyelinating Leukodystrophy & Pelizaeus-Merzbacher Disease; Monocarboxylate transporter 8 deficiency (MCT8)
White matter disorders and cerebral calcification - narrow panel v1.193 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from General Leukodystrophy & Mitochondrial Leukoencephalopathy; Hypomyelinating Leukodystrophy & Pelizaeus-Merzbacher Disease; Monocarboxylate transporter 8 deficiency (MCT8); Allan-Herndon-Dudley syndrome to Allan-Herndon-Dudley syndrome, OMIM:300523; General Leukodystrophy & Mitochondrial Leukoencephalopathy; Hypomyelinating Leukodystrophy & Pelizaeus-Merzbacher Disease; Monocarboxylate transporter 8 deficiency (MCT8)
Hyperthyroidism v2.8 SLC16A2 Arina Puzriakova Phenotypes for gene: SLC16A2 were changed from Monocarboxylate transporter 8 (MCT8) defect; Allan-Herndon-Dudley syndrome; Allan_Herndon_Dudley Syndrome; AHDS; 300523; Allan-Herndon-Dudley syndrome, 300523; Allan-Herndon-Dudley Syndrome; ALLAN-HERNDON-DUDLEY SYNDROME; ALLAN-HERNDON SYNDROME; MONOCARBOXYLATE TRANSPORTER 8 DEFICIENCY; TRIIODOTHYRONINE RESISTANCE; T3 RESISTANCE; MENTAL RETARDATION, X-LINKED, WITH HYPOTONIA; MENTAL RETARDATION AND MUSCULAR ATROPHY; mental retardation, X-linked, with hypotonia; MCT8 (SLC16A2)-specific thyroid hormone cell transporter deficiency; monocarboxylate transporter 8 (MCT8) deficiency to Allan-Herndon-Dudley syndrome, OMIM:300523
Childhood onset hereditary spastic paraplegia v2.73 L1CAM Arina Puzriakova Phenotypes for gene: L1CAM were changed from Hereditary spastic paraplegia; X-linked hydrocephalus, MASA syndrome, 303350 to CRASH syndrome, OMIM:303350; MASA syndrome, OMIM:303350; Hydrocephalus due to aqueductal stenosis, OMIM:307000; Hydrocephalus with congential idiopathic intestinal pseudoobstruction, OMIM:307000; Hydrocephalus with Hirschsprung disease, OMIM:307000
Adult onset hereditary spastic paraplegia v1.56 L1CAM Arina Puzriakova Phenotypes for gene: L1CAM were changed from Hereditary spastic paraplegia, 308840; MASA syndrome, 303350; X-linked hydrocephalus, 307000 to CRASH syndrome, OMIM:303350; MASA syndrome, OMIM:303350; Hydrocephalus due to aqueductal stenosis, OMIM:307000; Hydrocephalus with congential idiopathic intestinal pseudoobstruction, OMIM:307000; Hydrocephalus with Hirschsprung disease, OMIM:307000
Hereditary spastic paraplegia v1.256 L1CAM Arina Puzriakova Phenotypes for gene: L1CAM were changed from X-linked hydrocephalus, MASA syndrome, Hereditary spastic paraplegia to CRASH syndrome, OMIM:303350; MASA syndrome, OMIM:303350; Hydrocephalus due to aqueductal stenosis, OMIM:307000; Hydrocephalus with congential idiopathic intestinal pseudoobstruction, OMIM:307000; Hydrocephalus with Hirschsprung disease, OMIM:307000
Intellectual disability v3.1242 L1CAM Arina Puzriakova Phenotypes for gene: L1CAM were changed from Hydrocephalus due to aqueductal stenosis, 307000MASA syndrome, 303350CRASH syndrome, 303350Hydrocephalus with Hirschsprung disease, 307000Hydrocephalus with congenital idiopathic intestinal pseudoobstruction, 307000Corpus callosum, partial agenesis of, 304100; MENTAL RETARDATION-APHASIA-SHUFFLING GAIT-ADDUCTED THUMBS SYNDROME (MASA) to Corpus callosum, partial agenesis of, OMIM:304100; CRASH syndrome, OMIM:303350; MASA syndrome, OMIM:303350; Hydrocephalus due to aqueductal stenosis, OMIM:307000; Hydrocephalus with congential idiopathic intestinal pseudoobstruction, OMIM:307000; Hydrocephalus with Hirschsprung disease, OMIM:307000
Rare multisystem ciliopathy disorders v1.142 LAMA1 John Sayer commented on gene: LAMA1: PMID: 34423300 PMCID: PMC8374969 DOI: 10.1093/braincomms/fcab163

These patients with LAMA1 may be misdiagnosed as Joubert Syndrome
Rare multisystem ciliopathy disorders v1.142 LAMA1 John Sayer commented on gene: LAMA1: PMID: 34423300 PMCID: PMC8374969 DOI: 10.1093/braincomms/fcab163

These patients with LAMA1 may be misdiagnosed as Joubert Syndrome
Hereditary neuropathy or pain disorder v1.53 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Retinal disorders v2.204 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Retinal disorders v2.203 C12orf65 Arina Puzriakova Mode of inheritance for gene: C12orf65 was changed from to BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.51 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Combined oxidative phosphorylation deficiency 7, 613559; Spastic paraplegia 55, autosomal recessive, 615035 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Intellectual disability v3.1241 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 7 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Hereditary neuropathy v1.405 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Likely inborn error of metabolism v2.175 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Spastic paraplegia 55, autosomal recessive, 615035; Combined oxidative phosphorylation deficiency 7, 613559 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035; Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis)
Possible mitochondrial disorder - nuclear genes v1.53 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Combined oxidative phosphorylation deficiency 7, 613559; Spastic paraplegia 55, autosomal recessive, 615035 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Undiagnosed metabolic disorders v1.481 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Combined oxidative phosphorylation deficiency 7, 613559; Spastic paraplegia 55, autosomal recessive, 615035 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035; Required for mitochondrial gene expression (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis)
Adult onset hereditary spastic paraplegia v1.55 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035 to Spastic paraplegia 55, autosomal recessive, OMIM:615035
Adult onset hereditary spastic paraplegia v1.54 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from optic atrophy and spasticity, tibial muscle weakness and atrophy, peripheral neuropathy; Combined oxidative phosphorylation deficiency 7, 613559; Spastic paraplegia 55, autosomal recessive, 615035 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Optic neuropathy v2.50 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from SPASTIC PARAPLEGIA 55, AUTOSOMAL RECESSIVE, 615035 to Combined oxidative phosphorylation deficiency 7, OMIM:613559; Spastic paraplegia 55, autosomal recessive, OMIM:615035
Optic neuropathy v2.49 C12orf65 Arina Puzriakova Publications for gene: C12orf65 were set to 28091420; 25995486; 23188110; 24198383; 24284555; 24424123
Adult onset hereditary spastic paraplegia v1.53 C12orf65 Arina Puzriakova Publications for gene: C12orf65 were set to 23188110; 24424123
Adult onset hereditary spastic paraplegia v1.52 C12orf65 Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: C12orf65.
Tag Q3_21_phenotype tag was added to gene: C12orf65.
Adult onset hereditary spastic paraplegia v1.52 C12orf65 Arina Puzriakova reviewed gene: C12orf65: Rating: AMBER; Mode of pathogenicity: None; Publications: 23188110, 24080142, 24198383, 24284555, 24424123, 25995486, 26380172; Phenotypes: Spastic paraplegia 55, autosomal recessive, OMIM:615035; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Adult onset neurodegenerative disorder v2.193 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Spasticparaplegia55,autosomalrecessive,615035 to Spastic paraplegia 55, autosomal recessive, OMIM:615035
Childhood onset hereditary spastic paraplegia v2.72 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Spastic paraplegia 55, autosomal recessive, 615035; optic atrophy and spasticity, tibial muscle weakness and atrophy, peripheral neuropathy; Combined oxidative phosphorylation deficiency 7, 613559 to Spastic paraplegia 55, autosomal recessive, OMIM:615035
Hereditary spastic paraplegia v1.255 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from Spasticparaplegia55,autosomalrecessive,615035 to Spastic paraplegia 55, autosomal recessive, OMIM:615035
Arthrogryposis v3.116 C12orf65 Arina Puzriakova Phenotypes for gene: C12orf65 were changed from to Spastic paraplegia 55, autosomal recessive, OMIM:615035
Arthrogryposis v3.115 C12orf65 Arina Puzriakova Mode of inheritance for gene: C12orf65 was changed from to BIALLELIC, autosomal or pseudoautosomal
Arthrogryposis v3.114 C12orf65 Arina Puzriakova Publications for gene: C12orf65 were set to
Childhood onset dystonia, chorea or related movement disorder v1.143 C12orf65 Arina Puzriakova Mode of inheritance for gene: C12orf65 was changed from to BIALLELIC, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v1.52 WDR45B Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: WDR45B.
Adult onset hereditary spastic paraplegia v1.52 WDR45B Arina Puzriakova reviewed gene: WDR45B: Rating: ; Mode of pathogenicity: None; Publications: 28503735; Phenotypes: Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset hereditary spastic paraplegia v2.71 WDR45B Arina Puzriakova Phenotypes for gene: WDR45B were changed from profound developmental delay, early-onset refractory epilepsy, progressive spastic quadriplegia and contractures, and brain malformations.; Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, 617977 to Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977
Hereditary spastic paraplegia v1.254 WDR45B Arina Puzriakova Phenotypes for gene: WDR45B were changed from profound developmental delay, early-onset refractory epilepsy, progressive spastic quadriplegia and contractures, and brain malformations. to Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977
Adult onset hereditary spastic paraplegia v1.52 WDR45B Arina Puzriakova Phenotypes for gene: WDR45B were changed from Profound developmental delay, early-onset refractory epilepsy, progressive spastic quadriplegia and contractures, and brain malformations. Omim-Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, 617977 to Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977
Intellectual disability v3.1240 WDR45B Arina Puzriakova Phenotypes for gene: WDR45B were changed from AUTOSOMAL RECESSIVE MENTAL RETARDATION; Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, 617977 to Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977
Early onset or syndromic epilepsy v2.407 WDR45B Arina Puzriakova Phenotypes for gene: WDR45B were changed from Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, 617977; profound developmental delay, early-onset refractory epilepsy, progressive spastic quadriplegia and contractures, and brain malformations to Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977
Adult onset neurodegenerative disorder v2.192 WDR45B Arina Puzriakova Phenotypes for gene: WDR45B were changed from profound developmental delay, early-onset refractory epilepsy, progressive spastic quadriplegia and contractures, and brain malformations. to Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977
Optic neuropathy v2.48 TFG Arina Puzriakova Classified gene: TFG as Amber List (moderate evidence)
Optic neuropathy v2.48 TFG Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update.
Optic neuropathy v2.48 TFG Arina Puzriakova Gene: tfg has been classified as Amber List (Moderate Evidence).
Optic neuropathy v2.47 TFG Arina Puzriakova gene: TFG was added
gene: TFG was added to Optic neuropathy. Sources: Literature
Q3_21_rating tags were added to gene: TFG.
Mode of inheritance for gene: TFG was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TFG were set to 23479643; 27492651; 29971521; 30467354
Phenotypes for gene: TFG were set to Spastic paraplegia 57, autosomal recessive, OMIM:615658
Review for gene: TFG was set to GREEN
Added comment: Biallelic variants cause a HSP (MIM# 615658) which has been shown to involve early-onset optic atrophy in complex cases. At least 4 unrelated families reported with optic atrophy and variants in this gene (PMIDs: 23479643; 27492651; 29971521; 30467354).

Note that monoallelic variants are associated with different phenotype comprising adult-onset neuropathy (MIM# 604484)
Sources: Literature
Hereditary neuropathy or pain disorder v1.52 TFG Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be assessed at the next GMS panel review. If the decision is made to include genes on this panel that are associated with neuropathy as part of a more complex phenotype, rather than isolated neuropathy, the MOI should be updated from 'monoallelic' only to 'both mono- and biallelic' .
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Monoallelic variants are associated with an adult-onset motor and sensory neuropathy (MIM# 604484), a disorder that is relevant to this panel. Biallelic variants cause a HSP (MIM# 615658) which also has been shown to involve peripheral neuropathy in complex cases. Both phenotypes have a sufficient number of unrelated cases (>3) reported to warrant a Green rating (updated publications list).
Hereditary neuropathy or pain disorder v1.52 TFG Arina Puzriakova Mode of inheritance for gene: TFG was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Hereditary neuropathy or pain disorder v1.51 TFG Arina Puzriakova Publications for gene: TFG were set to
Hereditary neuropathy v1.404 TFG Arina Puzriakova Publications for gene: TFG were set to
Hereditary neuropathy or pain disorder v1.50 TFG Arina Puzriakova Tag Q3_21_MOI tag was added to gene: TFG.
Tag Q3_21_expert_review tag was added to gene: TFG.
Hereditary neuropathy v1.403 TFG Arina Puzriakova Added comment: Comment on mode of inheritance: Updated MOI from 'monoallelic' only to 'both mono- and biallelic'

Monoallelic variants are associated with an adult-onset motor and sensory neuropathy (MIM# 604484), a disorder that is relevant to this panel. Biallelic variants cause a HSP (MIM# 615658) which also has been shown to involve peripheral neuropathy in complex cases. Both phenotypes have a sufficient number of unrelated cases (>3) reported to warrant a Green rating (updated publications list).
Hereditary neuropathy v1.403 TFG Arina Puzriakova Mode of inheritance for gene: TFG was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder v1.50 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from Hereditary motor and sensory neuropathy, Okinawa type; Chondrosarcoma, extraskeletal myxoid, 612237; Hereditary motor and sensory neuropathy, proximal type, 604484 to Hereditary motor and sensory neuropathy, Okinawa type, OMIM:604484; Spastic paraplegia 57, autosomal recessive, OMIM:615658
Hereditary neuropathy v1.402 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from Hereditary motor and sensory neuropathy, proximal type, 604484; Chondrosarcoma, extraskeletal myxoid, 612237; Hereditary motor and sensory neuropathy, Okinawa type to Hereditary motor and sensory neuropathy, Okinawa type, OMIM:604484; Spastic paraplegia 57, autosomal recessive, OMIM:615658
Adult onset neurodegenerative disorder v2.191 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from to Spastic paraplegia 57, autosomal recessive, OMIM:615658
Childhood onset hereditary spastic paraplegia v2.70 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from ?Spastic paraplegia 57, autosomal recessive, 615658, AR; Hereditary motor and sensory neuropathy, Okinawa type, 604484, AD to Spastic paraplegia 57, autosomal recessive, OMIM:615658
Hereditary spastic paraplegia v1.253 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from Hereditary spastic paraplegia - childhood onset; Intellectual disability; Hereditary spastic paraplegia - adult onset; neuropathy to Spastic paraplegia 57, autosomal recessive, OMIM:615658
Adult onset hereditary spastic paraplegia v1.51 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from Hereditary motor and sensory neuropathy, Okinawa type, 604484, AD; ?Spastic paraplegia 57, autosomal recessive 615658,AR to Spastic paraplegia 57, autosomal recessive, OMIM:615658
Childhood onset hereditary spastic paraplegia v2.69 TFG Arina Puzriakova Publications for gene: TFG were set to Beetz et al. (2013); 23479643; 27492651; 27601211; 28124177
Hereditary spastic paraplegia v1.252 TFG Arina Puzriakova Publications for gene: TFG were set to 23479643; 27601211; 28124177; 27492651
Adult onset hereditary spastic paraplegia v1.50 TFG Arina Puzriakova Publications for gene: TFG were set to Beetz (2013); 23479643; 27601211; 28124177; 27492651
Adult onset hereditary spastic paraplegia v1.49 TFG Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: TFG.
Adult onset hereditary spastic paraplegia v1.49 TFG Arina Puzriakova reviewed gene: TFG: Rating: ; Mode of pathogenicity: None; Publications: 23479643, 27492651, 27601211, 28124177, 29971521, 30467354, 33767317; Phenotypes: Spastic paraplegia 57, autosomal recessive, OMIM:615658; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1239 TFG Arina Puzriakova Phenotypes for gene: TFG were changed from Hereditary motor and sensory neuropathy, proximal type, 604484; ?Spastic paraplegia 57, autosomal recessive, 615658 to Spastic paraplegia 57, autosomal recessive, OMIM:615658
Childhood onset hereditary spastic paraplegia v2.68 TFG Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be changed from 'both mono- and biallelic' to 'biallelic' only at the next GMS panel update.

Monoallelic variants are associated with an adult onset neuropathy (MIM# 604484), a disorder that does not include spasticity and is therefore not relevant to this panel.
Childhood onset hereditary spastic paraplegia v2.68 TFG Arina Puzriakova Mode of inheritance for gene: TFG was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Childhood onset hereditary spastic paraplegia v2.67 TFG Arina Puzriakova Tag Q3_21_MOI tag was added to gene: TFG.
Intellectual disability v3.1238 WDR11 Konstantinos Varvagiannis reviewed gene: WDR11: Rating: AMBER; Mode of pathogenicity: None; Publications: 34413497; Phenotypes: Intellectual disability, Microcephaly, Short stature; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset hereditary spastic paraplegia v2.67 SPART Arina Puzriakova Publications for gene: SPART were set to 12134148; 18413476; 26003402; 20301556
Hereditary spastic paraplegia v1.251 SPART Arina Puzriakova Publications for gene: SPART were set to Patel et al. (2002
Adult onset hereditary spastic paraplegia v1.49 SPART Arina Puzriakova Publications for gene: SPART were set to 12134148; 18413476; 26003402; 20301556
Adult onset hereditary spastic paraplegia v1.48 SPART Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: SPART.
Adult onset hereditary spastic paraplegia v1.48 SPART Arina Puzriakova reviewed gene: SPART: Rating: ; Mode of pathogenicity: None; Publications: 12134148, 18413476, 20301556, 20437587, 27112432, 28679690; Phenotypes: Troyer syndrome, OMIM:275900; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset hereditary spastic paraplegia v2.66 SPART Arina Puzriakova Phenotypes for gene: SPART were changed from Troyer syndrome, 275900; Spastic paraplegia 20 to Troyer syndrome, OMIM:275900; Spastic paraplegia 20
Hereditary spastic paraplegia v1.250 SPART Arina Puzriakova Phenotypes for gene: SPART were changed from to Troyer syndrome, OMIM:275900; Spastic paraplegia 20
Hereditary neuropathy or pain disorder v1.49 SPART Arina Puzriakova Mode of inheritance for gene: SPART was changed from to BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1238 SPART Arina Puzriakova Phenotypes for gene: SPART were changed from Troyer syndrome; MIM:275900; developmental delay to Troyer syndrome, OMIM:275900
Hereditary neuropathy v1.401 SPART Arina Puzriakova Mode of inheritance for gene: SPART was changed from to BIALLELIC, autosomal or pseudoautosomal
Adult onset neurodegenerative disorder v2.190 SPART Arina Puzriakova Phenotypes for gene: SPART were changed from to Troyer syndrome, OMIM:275900
Adult onset hereditary spastic paraplegia v1.48 SPART Arina Puzriakova Phenotypes for gene: SPART were changed from Troyer syndrome; Spastic paraplegia 20, autosomal recessive to Troyer syndrome, OMIM:275900; Spastic paraplegia 20
Hereditary ataxia v1.238 CHP1 Julia Baptista gene: CHP1 was added
gene: CHP1 was added to Hereditary ataxia. Sources: Literature
Mode of inheritance for gene: CHP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CHP1 were set to 32787936; 29379881
Phenotypes for gene: CHP1 were set to ataxia; ID
Review for gene: CHP1 was set to AMBER
Added comment: Only 2 families reported to date. One additional unpublished family with ID, spasticity and severe disease course.
Sources: Literature
Adult onset hereditary spastic paraplegia v1.47 SERAC1 Arina Puzriakova changed review comment from: Review of literature did not reveal any adult onset cases - disorder presents at birth and severe spasticity becomes apparent, typically with disease progression during the infantile or childhood period.

The 'Q3_21_phenotype' tag has been added to highlight that this is a childhood onset condition. Leaving the rating as Green, but with a recommendation for review at the next GMS panel update. This gene is already Green on the 'Hereditary spastic paraplegia - childhood onset v.2.18' panel.; to: Review of literature did not reveal any adult onset cases - disorder presents at birth and severe spasticity becomes apparent, typically with disease progression, during the infantile or childhood period.

The 'Q3_21_phenotype' tag has been added to highlight that this is a childhood onset condition. Leaving the rating as Green, but with a recommendation for review at the next GMS panel update. This gene is already Green on the 'Hereditary spastic paraplegia - childhood onset v.2.18' panel.
Adult onset hereditary spastic paraplegia v1.47 SERAC1 Arina Puzriakova reviewed gene: SERAC1: Rating: ; Mode of pathogenicity: None; Publications: 16527507, 22683713, 23918762, 27186703, 28778788, 29205472; Phenotypes: 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Likely inborn error of metabolism v2.174 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from Disorders of mitochondrial membrane lipids (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis); Methylglutaconic aciduria with deafness, encephalopathy and Leigh-like syndrome (MEGDEL) (Organic acidurias); 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739 to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739; Disorders of mitochondrial membrane lipids (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis)
Undiagnosed metabolic disorders v1.480 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from Methylglutaconic aciduria with deafness, encephalopathy and Leigh-like syndrome (MEGDEL) (Organic acidurias); Disorders of mitochondrial membrane lipids (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis); 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739 to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739; Disorders of mitochondrial membrane lipids (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Multiple respiratory chain complex deficiencies (disorders of protein synthesis)
Adult onset hereditary spastic paraplegia v1.47 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, Autosomal dominant, 614739; MEGDHEL syndrome to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Childhood onset dystonia, chorea or related movement disorder v1.142 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from Lesions in the basal ganglia; MEGDEL syndrome; MEGDHEL syndrome; Dystonia; 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Adult onset dystonia, chorea or related movement disorder v1.123 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from MEGDEL syndrome; Dystonia; MEGDHEL syndrome; 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; Lesions in the basal ganglia to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Mitochondrial disorders v2.50 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from Multiple respiratory chain complex deficiencies (disorders of protein synthesis); 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739 to Multiple respiratory chain complex deficiencies (disorders of protein synthesis); 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Intellectual disability v3.1237 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome; Intellectual disability to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Monogenic hearing loss v2.180 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Possible mitochondrial disorder - nuclear genes v1.52 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739 to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Adult onset neurodegenerative disorder v2.189 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from Dystonia; 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDEL syndrome; MEGDHEL syndrome to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Childhood onset hereditary spastic paraplegia v2.65 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Hereditary spastic paraplegia v1.249 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739
Structural basal ganglia disorders v1.19 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome; Lesions in the basal ganglia to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739; Lesions in the basal ganglia
Early onset dystonia v1.89 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome; Dystonia to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739; Dystonia
Hyperammonaemia v1.11 SERAC1 Arina Puzriakova Phenotypes for gene: SERAC1 were changed from 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, 614739; MEGDEL syndrome; 3-MEthylGlutaconic aciduria, Dystonia-Deafness, Hepatopathy, Encephalopathy, Leigh-like syndrome; MEGDHEL syndrome; Hypoglycemia to 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739; Hypoglycemia
Hereditary spastic paraplegia v1.248 REEP2 Arina Puzriakova Classified gene: REEP2 as Green List (high evidence)
Hereditary spastic paraplegia v1.248 REEP2 Arina Puzriakova Added comment: Comment on list classification: Upgraded from Amber to Green as there are now sufficient unrelated cases (>3) of spasticity associated with variants in this gene (updated references in publications list). REEP2 is also already Green on the GMS-equivalent HSP panels.
Hereditary spastic paraplegia v1.248 REEP2 Arina Puzriakova Gene: reep2 has been classified as Green List (High Evidence).
Hereditary spastic paraplegia v1.247 KIF1C Arina Puzriakova changed review comment from: Comment on list classification: Upgraded from Amber to Green as there are now sufficient unrelated cases (>3) of spasticity associated with variants in this gene (updated references in publications list). KDM5C is also already Green on the GMS-equivalent HSP panels.; to: Comment on list classification: Upgraded from Amber to Green as there are now sufficient unrelated cases (>3) of spasticity associated with variants in this gene (updated references in publications list). KIF1C is also already Green on the GMS-equivalent HSP panels.
Childhood onset hereditary spastic paraplegia v2.64 REEP2 Arina Puzriakova Publications for gene: REEP2 were set to 24388663; 28491902; 24482476
Hereditary spastic paraplegia v1.247 REEP2 Arina Puzriakova Publications for gene: REEP2 were set to 24388663
Adult onset hereditary spastic paraplegia v1.46 REEP2 Arina Puzriakova Publications for gene: REEP2 were set to 24388663; 28491902; 24482476
Adult onset hereditary spastic paraplegia v1.45 REEP2 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: REEP2.
Adult onset hereditary spastic paraplegia v1.45 REEP2 Arina Puzriakova reviewed gene: REEP2: Rating: ; Mode of pathogenicity: None; Publications: 24388663, 24482476, 28491902, 33526816; Phenotypes: Spastic paraplegia 72, autosomal recessive, OMIM:615625, Spastic paraplegia 72, autosomal dominant, OMIM:615625; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v1.45 NT5C2 Arina Puzriakova edited their review of gene: NT5C2: Changed publications to: 19415352, 24482476, 28327087, 28884889, 29123918, 32153630
Adult onset hereditary spastic paraplegia v1.45 NT5C2 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: NT5C2.
Childhood onset hereditary spastic paraplegia v2.63 NT5C2 Arina Puzriakova Publications for gene: NT5C2 were set to 19415352; 24482476; 2832708; 28884889; 29123918; 32153630
Adult onset hereditary spastic paraplegia v1.45 NT5C2 Arina Puzriakova Publications for gene: NT5C2 were set to 19415352; 24482476; 2832708; 28884889; 29123918; 32153630
Childhood onset hereditary spastic paraplegia v2.62 NT5C2 Arina Puzriakova Publications for gene: NT5C2 were set to 28327087; 28884889; 24482476; 29123918
Adult onset hereditary spastic paraplegia v1.44 NT5C2 Arina Puzriakova Publications for gene: NT5C2 were set to 28327087; 28884889; 24482476; 29123918
Adult onset hereditary spastic paraplegia v1.43 NT5C2 Arina Puzriakova reviewed gene: NT5C2: Rating: ; Mode of pathogenicity: None; Publications: 19415352, 24482476, 2832708, 28884889, 29123918, 32153630; Phenotypes: Spastic paraplegia 45, autosomal recessive, OMIM:613162; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v1.43 NT5C2 Arina Puzriakova Phenotypes for gene: NT5C2 were changed from Spasticparaplegia45, autosomal recessive, 613162; Spastic paraplegia 45, autosomal recessive, 613162, AR to Spastic paraplegia 45, autosomal recessive, 613162
Skeletal dysplasia v2.115 DLX5 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: DLX5.
Adult onset neurodegenerative disorder v2.188 SORL1 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: SORL1.
Adult onset neurodegenerative disorder v2.188 FIG4 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: FIG4.
Hereditary neuropathy or pain disorder v1.48 SORD Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: SORD.
Hereditary neuropathy or pain disorder v1.48 VWA1 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: VWA1.
Adult onset hereditary spastic paraplegia v1.42 NKX6-2 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: NKX6-2.
Adult onset hereditary spastic paraplegia v1.42 NKX6-2 Arina Puzriakova reviewed gene: NKX6-2: Rating: ; Mode of pathogenicity: None; Publications: 28969374, 29388673, 28575651, 31509304, 32004679, 32246862; Phenotypes: Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, OMIM:617560; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset hereditary spastic paraplegia v2.61 NKX6-2 Arina Puzriakova Phenotypes for gene: NKX6-2 were changed from Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, 617560 to Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, 617560
Hereditary spastic paraplegia v1.246 NKX6-2 Arina Puzriakova Phenotypes for gene: NKX6-2 were changed from Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy 617560 to Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, OMIM:617560
Hereditary ataxia v1.238 NKX6-2 Arina Puzriakova Phenotypes for gene: NKX6-2 were changed from Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy 617560 to Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, OMIM:617560
Ataxia and cerebellar anomalies - narrow panel v2.229 NKX6-2 Arina Puzriakova Phenotypes for gene: NKX6-2 were changed from Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy to Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, OMIM:617560
White matter disorders and cerebral calcification - narrow panel v1.192 NKX6-2 Arina Puzriakova Phenotypes for gene: NKX6-2 were changed from Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy to Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, OMIM:617560
Intellectual disability v3.1236 KDM5C Arina Puzriakova Tag Q3_21_MOI tag was added to gene: KDM5C.
Hereditary spastic paraplegia v1.245 KIF1C Arina Puzriakova Classified gene: KIF1C as Green List (high evidence)
Hereditary spastic paraplegia v1.245 KIF1C Arina Puzriakova Added comment: Comment on list classification: Upgraded from Amber to Green as there are now sufficient unrelated cases (>3) of spasticity associated with variants in this gene (updated references in publications list). KDM5C is also already Green on the GMS-equivalent HSP panels.
Hereditary spastic paraplegia v1.245 KIF1C Arina Puzriakova Gene: kif1c has been classified as Green List (High Evidence).
Hereditary spastic paraplegia v1.244 KIF1C Arina Puzriakova Tag watchlist was removed from gene: KIF1C.
Hereditary spastic paraplegia v1.244 KIF1C Arina Puzriakova Publications for gene: KIF1C were set to 24482476; 24319291; 24482476; 17273843
Hereditary ataxia with onset in adulthood v2.83 KIF1C Arina Puzriakova Publications for gene: KIF1C were set to
Ataxia and cerebellar anomalies - narrow panel v2.228 KIF1C Arina Puzriakova Publications for gene: KIF1C were set to
Hereditary ataxia v1.237 KIF1C Arina Puzriakova Publications for gene: KIF1C were set to
Childhood onset hereditary spastic paraplegia v2.60 KIF1C Arina Puzriakova Publications for gene: KIF1C were set to 24482476; 17273843; 24319291
Adult onset hereditary spastic paraplegia v1.42 KIF1C Arina Puzriakova Publications for gene: KIF1C were set to 24482476; 24319291; 17273843; 24808017
Adult onset hereditary spastic paraplegia v1.41 KIF1C Arina Puzriakova reviewed gene: KIF1C: Rating: GREEN; Mode of pathogenicity: None; Publications: 24319291, 24482476, 24808017, 29544888, 31413903; Phenotypes: Spastic ataxia 2, autosomal recessive, OMIM:611302; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder v1.141 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2, autosomal recessive, 611302 to Spastic ataxia 2, autosomal recessive, OMIM:611302
Hereditary ataxia with onset in adulthood v2.82 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2,autosomal recessive; Autosomal recessive spastic ataxia 2, 611302 to Spastic ataxia 2, autosomal recessive, OMIM:611302
Intellectual disability v3.1236 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2, autosomal recessive, 611302 to Spastic ataxia 2, autosomal recessive, OMIM:611302
Adult onset neurodegenerative disorder v2.188 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2,autosomal recessive to Spastic ataxia 2, autosomal recessive, OMIM:611302
Childhood onset hereditary spastic paraplegia v2.59 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2, autosomal recessive, 611302 to Spastic ataxia 2, autosomal recessive, OMIM:611302
Hereditary spastic paraplegia v1.243 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2,autosomal recessive to Spastic ataxia 2, autosomal recessive, OMIM:611302
Hereditary ataxia v1.236 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2,autosomal recessive to Spastic ataxia 2, autosomal recessive, OMIM:611302
Ataxia and cerebellar anomalies - narrow panel v2.227 KIF1C Arina Puzriakova Phenotypes for gene: KIF1C were changed from Spastic ataxia 2,autosomal recessive to Spastic ataxia 2, autosomal recessive, OMIM:611302
Nephrocalcinosis or nephrolithiasis v2.24 MOCOS Eleanor Williams Tag Q3_21_NHS_review tag was added to gene: MOCOS.
Renal ciliopathies v1.42 DLG5 Eleanor Williams Tag Q3_21_NHS_review tag was added to gene: DLG5.
Proteinuric renal disease v2.55 CD151 Eleanor Williams Tag Q3_21_NHS_review tag was added to gene: CD151.
Adult onset hereditary spastic paraplegia v1.41 KIDINS220 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: KIDINS220.
Intellectual disability v3.1235 KIDINS220 Arina Puzriakova Publications for gene: KIDINS220 were set to 27005418
Hereditary spastic paraplegia v1.242 KIDINS220 Arina Puzriakova Publications for gene: KIDINS220 were set to
Osteogenesis imperfecta v2.21 UNC45A Eleanor Williams Tag Q3_21_NHS_review tag was added to gene: UNC45A.
Childhood onset hereditary spastic paraplegia v2.58 KIDINS220 Arina Puzriakova Publications for gene: KIDINS220 were set to 27005418; 29667355
Adult onset hereditary spastic paraplegia v1.41 KIDINS220 Arina Puzriakova Publications for gene: KIDINS220 were set to 27005418; 29667355
Adult onset hereditary spastic paraplegia v1.40 KIDINS220 Arina Puzriakova reviewed gene: KIDINS220: Rating: ; Mode of pathogenicity: None; Publications: 27005418, 29667355, 31630374; Phenotypes: Spastic paraplegia, intellectual disability, nystagmus, and obesity, OMIM:617296; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Limb disorders v2.56 MECOM Eleanor Williams Tag Q3_21_NHS_review tag was added to gene: MECOM.
Amelogenesis imperfecta v2.14 PEX26 Eleanor Williams Classified gene: PEX26 as Amber List (moderate evidence)
Amelogenesis imperfecta v2.14 PEX26 Eleanor Williams Added comment: Comment on list classification: Leaving rating as amber for now, but with recommendation for green rating following GMS review. 3 cases now reported with a syndromic amelogenesis imperfecta phenotype.
Amelogenesis imperfecta v2.14 PEX26 Eleanor Williams Gene: pex26 has been classified as Amber List (Moderate Evidence).
Amelogenesis imperfecta v2.13 PEX26 Eleanor Williams Phenotypes for gene: PEX26 were changed from Peroxisome biogenesis disorder 7A (Zellweger), 614872; Peroxisome biogenesis disorder 7B, 614873; Heimler syndrome; Amelogenesis imperfecta; enamel dysplasia to Amelogenesis Imperfecta, MONDO:0019507; Heimler syndrome
Amelogenesis imperfecta v2.12 PEX26 Eleanor Williams Publications for gene: PEX26 were set to 28944237
Amelogenesis imperfecta v2.11 PEX26 Eleanor Williams Tag watchlist was removed from gene: PEX26.
Tag Q3_21_rating tag was added to gene: PEX26.
Amelogenesis imperfecta v2.11 PEX26 Eleanor Williams commented on gene: PEX26
Amelogenesis imperfecta v2.11 SP6 Eleanor Williams Classified gene: SP6 as Amber List (moderate evidence)
Amelogenesis imperfecta v2.11 SP6 Eleanor Williams Added comment: Comment on list classification: Leaving rating as amber, but with recommendation for green rating following GMS review. 2 unrelated cases, plus animal model.
Amelogenesis imperfecta v2.11 SP6 Eleanor Williams Gene: sp6 has been classified as Amber List (Moderate Evidence).
Amelogenesis imperfecta v2.10 SP6 Eleanor Williams Phenotypes for gene: SP6 were changed from Amelogenesis Imperfecta to Amelogenesis Imperfecta, MONDO:0019507
Intellectual disability v3.1234 KDM5C Arina Puzriakova Publications for gene: KDM5C were set to
Amelogenesis imperfecta v2.9 SP6 Eleanor Williams Publications for gene: SP6 were set to 32167558; 18156176; 18297738; 22676574
Amelogenesis imperfecta v2.8 SP6 Eleanor Williams Tag Q3_21_rating tag was added to gene: SP6.
Intellectual disability v3.1233 KDM5C Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be updated from 'X-linked.. biallelic in females' to 'X-linked.. monoallelic in females may cause disease' at the next GMS panel update.

A subset of female carriers have been shown to have impaired intellectual development and/or developmental delay (PMIDs: 10982473; 16538222; 18697827; 19826449; 21575681; 32279304)

This also reflects the current MOI on all other relevant panels.
Intellectual disability v3.1233 KDM5C Arina Puzriakova Mode of inheritance for gene: KDM5C was changed from X-LINKED: hemizygous mutation in males, biallelic mutations in females to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Amelogenesis imperfecta v2.8 SP6 Eleanor Williams edited their review of gene: SP6: Added comment: Additional case from Korea reported in PMID: 33652941 (Kim et al 2021) has the same nucleotide positions affected as in previous case (c.817_818delinsAT, p.(Ala273Met)) in the SP6 gene. The variant was de novo and the child showed unusual root development, taurodontism, and severe hypoplastic AI.; Changed rating: GREEN
Hereditary spastic paraplegia v1.241 KDM5C Arina Puzriakova Publications for gene: KDM5C were set to 10982473; 15586325; 26919706
Hereditary spastic paraplegia v1.240 KDM5C Arina Puzriakova Classified gene: KDM5C as Green List (high evidence)
Hereditary spastic paraplegia v1.240 KDM5C Arina Puzriakova Added comment: Comment on list classification: Upgraded from Amber to Green as there are now sufficient unrelated cases (>3) of spastic paraplegia with variants in this gene (updated references in publications list). KDM5C is also already Green on the GMS-equivalent HSP panels.
Hereditary spastic paraplegia v1.240 KDM5C Arina Puzriakova Gene: kdm5c has been classified as Green List (High Evidence).
Hereditary spastic paraplegia v1.239 KDM5C Arina Puzriakova Tag watchlist was removed from gene: KDM5C.
Childhood onset hereditary spastic paraplegia v2.57 KDM5C Arina Puzriakova Publications for gene: KDM5C were set to 10982473; 26919706; 15586325; 18697827
Adult onset hereditary spastic paraplegia v1.40 KDM5C Arina Puzriakova Publications for gene: KDM5C were set to 10982473; 26919706; 15586325; 18697827
Adult onset hereditary spastic paraplegia v1.39 KDM5C Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: KDM5C.
Tag Q3_21_phenotype tag was added to gene: KDM5C.
Adult onset hereditary spastic paraplegia v1.39 KDM5C Arina Puzriakova reviewed gene: KDM5C: Rating: AMBER; Mode of pathogenicity: None; Publications: 10982473, 15586325, 18697827, 19826449, 26919706, 32279304; Phenotypes: Mental retardation, X-linked, syndromic, Claes-Jensen type, OMIM:300534; Mode of inheritance: X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Nephrocalcinosis or nephrolithiasis v2.24 MOCOS Eleanor Williams Classified gene: MOCOS as Amber List (moderate evidence)
Nephrocalcinosis or nephrolithiasis v2.24 MOCOS Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber, with a recommendation for green rating following GMS review. 2 cases where urolithiasis is part of the Xanthinuria type 2 phenotype. Additional evidence from animal models.
Nephrocalcinosis or nephrolithiasis v2.24 MOCOS Eleanor Williams Gene: mocos has been classified as Amber List (Moderate Evidence).
Nephrocalcinosis or nephrolithiasis v2.23 MOCOS Eleanor Williams Phenotypes for gene: MOCOS were changed from Xanthinuria type II (MIM603592) to Xanthinuria, type II, OMIM:603592
Nephrocalcinosis or nephrolithiasis v2.22 MOCOS Eleanor Williams Publications for gene: MOCOS were set to PMID: 11302742; 17368066; 14624414; 25967871; 34356852; 32073534; 30758870; 27919260
Nephrocalcinosis or nephrolithiasis v2.21 MOCOS Eleanor Williams Tag Q3_21_rating tag was added to gene: MOCOS.
Nephrocalcinosis or nephrolithiasis v2.21 MOCOS Eleanor Williams reviewed gene: MOCOS: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Xanthinuria, type II, OMIM:603592; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 DCLRE1B Zornitza Stark edited their review of gene: DCLRE1B: Changed mode of inheritance: Unknown
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 DCLRE1B Zornitza Stark reviewed gene: DCLRE1B: Rating: RED; Mode of pathogenicity: None; Publications: 20479256, 21647296; Phenotypes: Dyskeratosis congenita and Hoyeraal-Hreidarsson (HH) syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Renal ciliopathies v1.42 DLG5 Eleanor Williams Classified gene: DLG5 as Amber List (moderate evidence)
Renal ciliopathies v1.42 DLG5 Eleanor Williams Added comment: Comment on list classification: Green review from Julia Baptista (Royal Devon and Exeter NHS Foundation Trust) suggesting mode of inheritance of both biallelic and monoallelic further supports promotion to green rating.
Renal ciliopathies v1.42 DLG5 Eleanor Williams Gene: dlg5 has been classified as Amber List (Moderate Evidence).
Proteinuric renal disease v2.55 CD151 Eleanor Williams Classified gene: CD151 as Amber List (moderate evidence)
Proteinuric renal disease v2.55 CD151 Eleanor Williams Added comment: Comment on list classification: Further case reported by Natalie Forrester from the South West Genomic Laboratory Hub, which supports the recommendation for a green rating.
Proteinuric renal disease v2.55 CD151 Eleanor Williams Gene: cd151 has been classified as Amber List (Moderate Evidence).
Proteinuric renal disease v2.54 CD151 Eleanor Williams Publications for gene: CD151 were set to 15265795; 17015618; 29138120
Proteinuric renal disease v2.53 CD151 Eleanor Williams Phenotypes for gene: CD151 were changed from Nephropathy with pretibial epidermolysis bullosa and deafness #609057 to Nephropathy with pretibial epidermolysis bullosa and deafness, OMIM:609057; nephrotic syndrome - deafness - pretibial epidermolysis bullosa syndrome, MONDO:0012190
Osteogenesis imperfecta v2.21 UNC45A Eleanor Williams Phenotypes for gene: UNC45A were changed from cholestasis; congenital diarrhea; impaired hearing; bone fragility to Osteootohepatoenteric syndrome, OMIM:619377
Osteogenesis imperfecta v2.20 UNC45A Eleanor Williams Classified gene: UNC45A as Amber List (moderate evidence)
Osteogenesis imperfecta v2.20 UNC45A Eleanor Williams Gene: unc45a has been classified as Amber List (Moderate Evidence).
Osteogenesis imperfecta v2.19 UNC45A Eleanor Williams Classified gene: UNC45A as No list
Osteogenesis imperfecta v2.19 UNC45A Eleanor Williams Added comment: Comment on list classification: Promoting this gene from grey to amber, with recommendation for green rating following GMS review. 2 unrelated families with bone fragility and biallelic variants in this gene reported in the literature, plus another case reported by an NHS laboratory.
Osteogenesis imperfecta v2.19 UNC45A Eleanor Williams Gene: unc45a has been removed from the panel.
Osteogenesis imperfecta v2.18 UNC45A Eleanor Williams Tag Q3_21_rating tag was added to gene: UNC45A.
Osteogenesis imperfecta v2.18 UNC45A Eleanor Williams reviewed gene: UNC45A: Rating: GREEN; Mode of pathogenicity: None; Publications: 29429573; Phenotypes: Osteootohepatoenteric syndrome, OMIM:619377; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Limb disorders v2.56 HOXA11 Eleanor Williams Classified gene: HOXA11 as Red List (low evidence)
Limb disorders v2.56 HOXA11 Eleanor Williams Added comment: Comment on list classification: Leaving the rating as red as there are only 2 cases reported, each with the same variant, and only 2 genes were looked at in the analyses of these patients.
Limb disorders v2.56 HOXA11 Eleanor Williams Gene: hoxa11 has been classified as Red List (Low Evidence).
Limb disorders v2.55 HOXA11 Eleanor Williams gene: HOXA11 was added
gene: HOXA11 was added to Limb disorders. Sources: Literature
Mode of inheritance for gene: HOXA11 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: HOXA11 were set to 11101832
Phenotypes for gene: HOXA11 were set to Radioulnar synostosis with amegakaryocytic thrombocytopenia 1, OMIM:605432; radioulnar synostosis with amegakaryocytic thrombocytopenia 1, MONDO:0024558
Review for gene: HOXA11 was set to AMBER
Added comment: Associated with Radioulnar synostosis with amegakaryocytic thrombocytopenia 1 #605432 (AD) in OMIM.

2 unrelated cases reported in PMID: 11101832 - Thompson and Nguyen 2000. In both families the fathers and all affected children show proximal fusion of the radius and ulna. 3 out of the 4 children, but not the fathers had symptomatic thrombocytopenia. Only the HOXA10 and HOXA11 genes were analysed. The same single base-pair deletion in a highly conserved region encoding the homeodomain was found in HOXA11 in affected individuals.

A PubMed search does not find any further reported cases.
Sources: Literature
Limb disorders v2.54 MECOM Eleanor Williams Classified gene: MECOM as Amber List (moderate evidence)
Limb disorders v2.54 MECOM Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber, with a recommendation for green rating following GMS review. There are sufficient cases with a radioulnar synostosis phenotype to rate this gene green.
Limb disorders v2.54 MECOM Eleanor Williams Gene: mecom has been classified as Amber List (Moderate Evidence).
Limb disorders v2.53 MECOM Eleanor Williams Phenotypes for gene: MECOM were changed from Radioulnar synostosis; Brachymesophalangia to Radioulnar synostosis with amegakaryocytic thrombocytopenia 2, OMIM:616738; radioulnar synostosis with amegakaryocytic thrombocytopenia 2, MONDO:0014758
Limb disorders v2.52 MECOM Eleanor Williams Publications for gene: MECOM were set to
Limb disorders v2.51 MECOM Eleanor Williams Tag Q3_21_rating tag was added to gene: MECOM.
Limb disorders v2.51 MECOM Eleanor Williams reviewed gene: MECOM: Rating: GREEN; Mode of pathogenicity: None; Publications: 26581901, 29200407, 30536840; Phenotypes: Radioulnar synostosis with amegakaryocytic thrombocytopenia 2, OMIM:616738, radioulnar synostosis with amegakaryocytic thrombocytopenia 2, MONDO:0014758; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability v3.1232 KDM5C Arina Puzriakova Phenotypes for gene: KDM5C were changed from Mental retardation, X-linked, syndromic, Claes-Jensen type, 300534 -3; MENTAL RETARDATION SYNDROMIC X-LINKED JARID1C-RELATED (MRXSJ) to Mental retardation, X-linked, syndromic, Claes-Jensen type, OMIM:300534
Intellectual disability v3.1231 HACE1 Arina Puzriakova Publications for gene: HACE1 were set to
Hereditary spastic paraplegia v1.239 HACE1 Arina Puzriakova Publications for gene: HACE1 were set to 26424145; 26437029
Early onset or syndromic epilepsy v2.406 HACE1 Arina Puzriakova Publications for gene: HACE1 were set to 26437029; 26424145
Childhood onset hereditary spastic paraplegia v2.56 HACE1 Arina Puzriakova Publications for gene: HACE1 were set to 26424145; 26437029
Adult onset hereditary spastic paraplegia v1.39 HACE1 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: HACE1.
Adult onset hereditary spastic paraplegia v1.39 HACE1 Arina Puzriakova Publications for gene: HACE1 were set to 26424145; 26437029
Adult onset hereditary spastic paraplegia v1.38 HACE1 Arina Puzriakova reviewed gene: HACE1: Rating: ; Mode of pathogenicity: None; Publications: 26424145, 26437029, 29423242, 31321300, 33813722; Phenotypes: Spastic paraplegia and psychomotor retardation with or without seizures, OMIM:616756; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v1.38 FBXO7 Arina Puzriakova Classified gene: FBXO7 as Amber List (moderate evidence)
Adult onset hereditary spastic paraplegia v1.38 FBXO7 Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update (tagged)
Adult onset hereditary spastic paraplegia v1.38 FBXO7 Arina Puzriakova Gene: fbxo7 has been classified as Amber List (Moderate Evidence).
Adult onset hereditary spastic paraplegia v1.37 FBXO7 Arina Puzriakova Phenotypes for gene: FBXO7 were changed from Parkinson disease 15, autosomal recessive MIM#260300 to Parkinson disease 15, autosomal recessive, OMIM:260300
Adult onset hereditary spastic paraplegia v1.36 FBXO7 Arina Puzriakova Publications for gene: FBXO7 were set to 18513678; 19038853
Adult onset hereditary spastic paraplegia v1.35 FBXO7 Arina Puzriakova Tag Q3_21_rating tag was added to gene: FBXO7.
Adult onset hereditary spastic paraplegia v1.35 FBXO7 Arina Puzriakova reviewed gene: FBXO7: Rating: GREEN; Mode of pathogenicity: None; Publications: 19038853, 18513678, 26882974, 34144229; Phenotypes: Parkinson disease 15, autosomal recessive, OMIM:260300; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Rhabdomyolysis and metabolic muscle disorders v1.50 FDX2 Sarah Leigh Tag Q3_21_rating tag was added to gene: FDX2.
Rhabdomyolysis and metabolic muscle disorders v1.50 FDX2 Sarah Leigh edited their review of gene: FDX2: Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least three variants reported in three unrelated cases that included rhabdomyolysis (PMID: 24281368; 30010796; 28803783).; Changed rating: GREEN
Rhabdomyolysis and metabolic muscle disorders v1.50 FDX2 Sarah Leigh Classified gene: FDX2 as Amber List (moderate evidence)
Rhabdomyolysis and metabolic muscle disorders v1.50 FDX2 Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Rhabdomyolysis and metabolic muscle disorders v1.50 FDX2 Sarah Leigh Gene: fdx2 has been classified as Amber List (Moderate Evidence).
Mitochondrial disorders v2.49 FDX2 Sarah Leigh Phenotypes for gene: FDX2 were changed from Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy, 251900 to Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714
Undiagnosed metabolic disorders v1.479 FDX2 Sarah Leigh Phenotypes for gene: FDX2 were changed from Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy 251900 to Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714
Possible mitochondrial disorder - nuclear genes v1.51 FDX2 Sarah Leigh Phenotypes for gene: FDX2 were changed from Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy, 251900 to Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714
Rhabdomyolysis and metabolic muscle disorders v1.49 FDX2 Sarah Leigh Phenotypes for gene: FDX2 were changed from Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714 to Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714
Rhabdomyolysis and metabolic muscle disorders v1.49 FDX2 Sarah Leigh Phenotypes for gene: FDX2 were changed from Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MIM#251900 to Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714
Likely inborn error of metabolism v2.173 FDX2 Sarah Leigh Phenotypes for gene: FDX2 were changed from Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy 251900 to Mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy OMIM:251900; mitochondrial myopathy, episodic, with optic atrophy and reversible leukoencephalopathy MONDO:0020714
Cerebellar hypoplasia v1.57 B4GAT1 Ivone Leong Classified gene: B4GAT1 as Green List (high evidence)
Cerebellar hypoplasia v1.57 B4GAT1 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. Hydrocephalus is part of the phenotype. This gene should be rated Green at the next review.

This gene is also recommended for promotion to Green status on the Malformations of cortical development (v2.59) panel. With the following review from Zornitza Stark:
"Two families and two animal models. Extensive brain abnormalities reported.
Zornitza Stark (Australian Genomics), 24 Aug 2020"
Cerebellar hypoplasia v1.57 B4GAT1 Ivone Leong Gene: b4gat1 has been classified as Green List (High Evidence).
Cerebellar hypoplasia v1.56 B4GAT1 Ivone Leong Phenotypes for gene: B4GAT1 were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13, 615287 ; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), typeA, 13, 615287 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13, OMIM:615287
Cerebellar hypoplasia v1.55 B4GAT1 Ivone Leong Publications for gene: B4GAT1 were set to 23359570
Hydrocephalus v2.116 B4GAT1 Ivone Leong changed review comment from: Comment on list classification: This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. Hydrocephalus is part of the phenotype. This gene should be rated Green at the next review.
Hydrocephalus v2.116 B4GAT1 Ivone Leong Entity copied from Malformations of cortical development v2.59
Hydrocephalus v2.116 B4GAT1 Ivone Leong gene: B4GAT1 was added
gene: B4GAT1 was added to Hydrocephalus. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: B4GAT1.
Mode of inheritance for gene: B4GAT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: B4GAT1 were set to 23359570; 23877401; 23217742
Phenotypes for gene: B4GAT1 were set to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13, OMIM:615287
Penetrance for gene: B4GAT1 were set to Complete
Malformations of cortical development v2.59 B4GAT1 Ivone Leong Tag Q3_21_rating tag was added to gene: B4GAT1.
Malformations of cortical development v2.59 B4GAT1 Ivone Leong Classified gene: B4GAT1 as Amber List (moderate evidence)
Malformations of cortical development v2.59 B4GAT1 Ivone Leong Added comment: Comment on list classification: This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Malformations of cortical development v2.59 B4GAT1 Ivone Leong Gene: b4gat1 has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.58 B4GAT1 Ivone Leong Publications for gene: B4GAT1 were set to 23359570; 23877401; 23359570; 23217742
Malformations of cortical development v2.57 B4GAT1 Ivone Leong Phenotypes for gene: B4GAT1 were changed from Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13 615287 to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 13, OMIM:615287
Malformations of cortical development v2.56 B4GAT1 Ivone Leong Publications for gene: B4GAT1 were set to 23359570
Radial dysplasia v1.15 FIG4 Sarah Leigh commented on gene: FIG4: Amyotrophic lateral sclerosis 11 OMIM:612577 is not relevant to this panel, so bialellic mode of inheritance is appropriate.
Malformations of cortical development v2.55 ARF1 Ivone Leong Tag Q3_21_rating tag was added to gene: ARF1.
Malformations of cortical development v2.55 ARF1 Ivone Leong Classified gene: ARF1 as Amber List (moderate evidence)
Malformations of cortical development v2.55 ARF1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Malformations of cortical development v2.55 ARF1 Ivone Leong Gene: arf1 has been classified as Amber List (Moderate Evidence).
Limb disorders v2.51 FIG4 Sarah Leigh commented on gene: FIG4: Amyotrophic lateral sclerosis 11 OMIM:612577 is not relevant to this panel, so bialellic mode of inheritance is appropriate.
Amyotrophic lateral sclerosis/motor neuron disease v1.36 FIG4 Sarah Leigh Mode of inheritance for gene: FIG4 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Malformations of cortical development v2.54 ARF1 Ivone Leong Phenotypes for gene: ARF1 were changed from Periventricular nodular heterotopia 8, MIM# 618185 to Periventricular nodular heterotopia 8, OMIM:618185
Malformations of cortical development v2.53 MCF2 Ivone Leong Classified gene: MCF2 as Red List (low evidence)
Malformations of cortical development v2.53 MCF2 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is currently not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Malformations of cortical development v2.53 MCF2 Ivone Leong Gene: mcf2 has been classified as Red List (Low Evidence).
Amyotrophic lateral sclerosis/motor neuron disease v1.35 FIG4 Sarah Leigh reviewed gene: FIG4: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Malformations of cortical development v2.52 MCF2 Ivone Leong Phenotypes for gene: MCF2 were changed from Perisylvian polymicrogyria to Perisylvian polymicrogyria; bilateral perisylvian polymicrogyria, MONDO:0020340
Amyotrophic lateral sclerosis/motor neuron disease v1.35 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Amyotrophic Lateral Sclerosis, Dominant; Charcot-Marie-Tooth disease, type 4J, 611228 to Amyotrophic lateral sclerosis 11 OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640; Yunis Varon syndrome OMIM:216340; Yunis-Varon syndrome MONDO:0008995
Radial dysplasia v1.15 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Yunis-Varon syndrome, 216340; Aplastic/hypoplastic thumbs; absent thumbs to Yunis Varon syndrome OMIM:216340; Yunis-Varon syndrome MONDO:0008995
Limb disorders v2.51 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Aplastic/hypoplastic thumbs; Yunis-Varon syndrome, 216340; absent thumbs to Yunis Varon syndrome OMIM:216340; Yunis-Varon syndrome MONDO:0008995
Skeletal dysplasia v2.115 FIG4 Sarah Leigh Added comment: Comment on phenotypes: Amyotrophic lateral sclerosis 11 OMIM:612577 is not relevant to this panel
Skeletal dysplasia v2.115 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Yunis-Varon syndrome 216340; Amyotrophic lateral sclerosis 11 612577; Yunis-Varon syndrome 216340 to Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640; Yunis Varon syndrome OMIM:216340; Yunis-Varon syndrome MONDO:0008995
Intellectual disability v3.1230 FIG4 Sarah Leigh Tag Q3_21_MOI was removed from gene: FIG4.
Intellectual disability v3.1230 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from CHARCOT-MARIE-TOOTH DISEASE, TYPE 4J to Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640; Yunis Varon syndrome OMIM:216340; Yunis-Varon syndrome MONDO:0008995
Malformations of cortical development v2.51 EMX2 Ivone Leong Phenotypes for gene: EMX2 were changed from Schizencephaly, 269160 to Schizencephaly, OMIM:269160
Malformations of cortical development v2.50 EMX2 Ivone Leong Publications for gene: EMX2 were set to 8528262; 9359037
Intellectual disability v3.1229 FIG4 Sarah Leigh Publications for gene: FIG4 were set to 17572665
Intellectual disability v3.1228 FIG4 Sarah Leigh Tag Q3_21_MOI tag was added to gene: FIG4.
Hereditary neuropathy v1.400 FIG4 Sarah Leigh Mode of inheritance for gene: FIG4 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Hereditary neuropathy v1.399 FIG4 Sarah Leigh reviewed gene: FIG4: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v1.35 FARS2 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: FARS2.
Adult onset hereditary spastic paraplegia v1.35 FARS2 Arina Puzriakova reviewed gene: FARS2: Rating: ; Mode of pathogenicity: None; Publications: 30250868, 26553276, 29126765; Phenotypes: Spastic paraplegia 77, autosomal recessive, OMIM:617046; Mode of inheritance: None
Hereditary neuropathy or pain disorder v1.48 FIG4 Sarah Leigh reviewed gene: FIG4: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder v1.48 FIG4 Sarah Leigh Deleted their review
Hereditary neuropathy or pain disorder v1.48 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Amyotrophic lateral sclerosis 11 OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640; Yunis Varon syndrome OMIM:216340; Yunis-Varon syndromeMONDO:0008995 to Amyotrophic lateral sclerosis 11 OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640; Yunis Varon syndrome OMIM:216340; Yunis-Varon syndrome MONDO:0008995
Hereditary neuropathy or pain disorder v1.47 FIG4 Sarah Leigh Publications for gene: FIG4 were set to 17572665; 19118816 23888880 21705420
Hereditary neuropathy or pain disorder v1.46 FIG4 Sarah Leigh Deleted their comment
Hereditary neuropathy or pain disorder v1.46 FIG4 Sarah Leigh Publications for gene: FIG4 were set to 17572665
Hereditary neuropathy or pain disorder v1.45 FIG4 Sarah Leigh Added comment: Comment on phenotypes: Amyotrophic lateral sclerosis 11 OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640;Yunis Varon syndrome OMIM:216340;Yunis-Varon syndromeMONDO:0008995
Hereditary neuropathy or pain disorder v1.45 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Charcot Marie Tooth disease, type 4J, 611228; Amyotrophic lateral sclerosis 11, 612577; Yunis Varon syndrome, 216340 to Amyotrophic lateral sclerosis 11 OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640; Yunis Varon syndrome OMIM:216340; Yunis-Varon syndromeMONDO:0008995
Hereditary neuropathy or pain disorder v1.44 FIG4 Sarah Leigh Tag Q3_21_MOI tag was added to gene: FIG4.
Adult onset hereditary spastic paraplegia v1.35 ERLIN1 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: ERLIN1.
Adult onset hereditary spastic paraplegia v1.35 ERLIN1 Arina Puzriakova commented on gene: ERLIN1
Limb disorders v2.50 DLX5 Ivone Leong Phenotypes for gene: DLX5 were changed from Split-hand/foot malformation 1 with sensorineural hearing loss, 220600 to ?Split-hand/foot malformation 1 with sensorineural hearing loss, OMIM:220600; Split-hand/foot malformation 1, OMIM:183600
Skeletal dysplasia v2.114 DLX5 Ivone Leong Phenotypes for gene: DLX5 were changed from Split-hand/foot malformation 1 with sensorineural hearing loss 220600 to ?Split-hand/foot malformation 1 with sensorineural hearing loss, OMIM:220600; Split-hand/foot malformation 1, OMIM:183600
Limb disorders v2.49 DLX5 Ivone Leong Tag Q3_21_MOI tag was added to gene: DLX5.
Limb disorders v2.49 DLX5 Ivone Leong reviewed gene: DLX5: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Skeletal dysplasia v2.113 DLX5 Ivone Leong Tag Q3_21_MOI tag was added to gene: DLX5.
Skeletal dysplasia v2.113 DLX5 Ivone Leong reviewed gene: DLX5: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Adult onset neurodegenerative disorder v2.187 FIG4 Sarah Leigh changed review comment from: The Q3_21_MOI tag has been added as Amyotrophic lateral sclerosis 11 (OMIM:612577) is monoallelic Charcot-Marie-Tooth disease, type 4J (OMIM:611228) is biallelic.; to: The Q3_21_MOI tag has been added as Amyotrophic lateral sclerosis 11 (OMIM:612577) is monoallelic and Charcot-Marie-Tooth disease, type 4J (OMIM:611228) is biallelic, therefore the mode of inheritance should be - BOTH monoallelic and biallelic, autosomal or pseudoautosomal for this gene on this panel.
Intellectual disability v3.1228 HNMT Ivone Leong Phenotypes for gene: HNMT were changed from Mental retardation, autosomal recessive 51, MIM#616739 to Mental retardation, autosomal recessive 51, OMIM:616739
Intellectual disability v3.1227 HNMT Ivone Leong reviewed gene: HNMT: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.1227 HNMT Ivone Leong Tag watchlist was removed from gene: HNMT.
Tag Q3_21_rating tag was added to gene: HNMT.
Tag Q3_21_NHS_review tag was added to gene: HNMT.
Intellectual disability v3.1227 HNMT Ivone Leong Publications for gene: HNMT were set to 26206890; 30744146
Adult onset hereditary spastic paraplegia v1.35 ENTPD1 Arina Puzriakova Phenotypes for gene: ENTPD1 were changed from Spasticparaplegia 64, 615683 to Spastic paraplegia 64, autosomal recessive, OMIM:615683
Adult onset neurodegenerative disorder v2.187 ENTPD1 Arina Puzriakova Publications for gene: ENTPD1 were set to Novarino et al. (2014)
Adult onset neurodegenerative disorder v2.186 ENTPD1 Arina Puzriakova Phenotypes for gene: ENTPD1 were changed from Spasticparaplegia64,615683 to Spastic paraplegia 64, autosomal recessive, OMIM:615683
Hereditary spastic paraplegia v1.238 ENTPD1 Arina Puzriakova Phenotypes for gene: ENTPD1 were changed from Spasticparaplegia64,615683 to Spastic paraplegia 64, autosomal recessive, OMIM:615683
Hereditary spastic paraplegia v1.237 ENTPD1 Arina Puzriakova Publications for gene: ENTPD1 were set to Novarino et al. (2014)
Hereditary spastic paraplegia v1.236 ENTPD1 Arina Puzriakova Classified gene: ENTPD1 as Green List (high evidence)
Hereditary spastic paraplegia v1.236 ENTPD1 Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Green as there are sufficient unrelated cases (>3) to support this gene-disease association. ENTPD1 is also already Green on the GMS-equivalent HSP panels.
Hereditary spastic paraplegia v1.236 ENTPD1 Arina Puzriakova Gene: entpd1 has been classified as Green List (High Evidence).
Hereditary spastic paraplegia v1.235 ENTPD1 Arina Puzriakova reviewed gene: ENTPD1: Rating: GREEN; Mode of pathogenicity: None; Publications: 30652007; Phenotypes: Spastic paraplegia 64, autosomal recessive, OMIM:615683; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1226 ENTPD1 Arina Puzriakova Classified gene: ENTPD1 as Amber List (moderate evidence)
Intellectual disability v3.1226 ENTPD1 Arina Puzriakova Added comment: Comment on list classification: Upgraded from Red to Amber as there is some evidence of cognitive impairment associated with SPG64, but perhaps too mild in most cases to warrant inclusion on this panel. Cases are expected to be picked up via the HSP route which presents a more prominent feature of this disorder.
Intellectual disability v3.1226 ENTPD1 Arina Puzriakova Gene: entpd1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1225 ENTPD1 Arina Puzriakova Publications for gene: ENTPD1 were set to 21937992
Intellectual disability v3.1224 ENTPD1 Arina Puzriakova Phenotypes for gene: ENTPD1 were changed from AUTOSOMAL RECESSIVE MENTAL RETARDATION to Spastic paraplegia 64, autosomal recessive, OMIM:615683
Intellectual disability v3.1223 ENTPD1 Arina Puzriakova reviewed gene: ENTPD1: Rating: AMBER; Mode of pathogenicity: None; Publications: 24482476, 29691679, 30652007; Phenotypes: Spastic paraplegia 64, autosomal recessive, OMIM:615683; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Childhood onset hereditary spastic paraplegia v2.55 ENTPD1 Arina Puzriakova Publications for gene: ENTPD1 were set to Novarino et al. (2014); 24482476; 29691679
Adult onset hereditary spastic paraplegia v1.34 ENTPD1 Arina Puzriakova Publications for gene: ENTPD1 were set to Novarino et al. (2014); 24482476; 29691679
Adult onset hereditary spastic paraplegia v1.33 ENTPD1 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: ENTPD1.
Adult onset hereditary spastic paraplegia v1.33 ENTPD1 Arina Puzriakova changed review comment from: Review of literature revealed 4 unrelated families with SPG64 - all of which presented in childhood.

The 'Q3_21_phenotype' tag has been added to highlight that this is a childhood onset condition. Leaving the rating as Green, but with a recommendation for review at the next GMS panel update. This gene is already Green on the 'Hereditary spastic paraplegia - childhood onset v.2.18' panel.; to: Review of literature revealed 4 unrelated families with SPG64 - all of which presented during childhood.

The 'Q3_21_phenotype' tag has been added to highlight that this is a childhood onset condition. Leaving the rating as Green, but with a recommendation for review at the next GMS panel update. This gene is already Green on the 'Hereditary spastic paraplegia - childhood onset v.2.18' panel.
Adult onset hereditary spastic paraplegia v1.33 ENTPD1 Arina Puzriakova reviewed gene: ENTPD1: Rating: ; Mode of pathogenicity: None; Publications: 24482476, 29691679, 30652007; Phenotypes: Spastic paraplegia 64, autosomal recessive, OMIM:615683; Mode of inheritance: None
Childhood onset hereditary spastic paraplegia v2.54 ENTPD1 Arina Puzriakova Phenotypes for gene: ENTPD1 were changed from Spasticparaplegia 64, 615683 to Spastic paraplegia 64, autosomal recessive, OMIM:615683
Adult onset hereditary spastic paraplegia v1.33 ARG1 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: ARG1.
Adult onset hereditary spastic paraplegia v1.33 ARG1 Arina Puzriakova commented on gene: ARG1
Intellectual disability v3.1223 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininemia, 207800; ARGININEMIA (ARGIN) to Argininemia, OMIM:207800
Early onset or syndromic epilepsy v2.405 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininemia 207800 to Argininemia, OMIM:207800
Likely inborn error of metabolism v2.172 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininaemia (Urea cycle disorders and inherited hyperammonaemias); Argininemia 207800 to Argininaemia (Urea cycle disorders and inherited hyperammonaemias); Argininemia, OMIM:207800
Undiagnosed metabolic disorders v1.478 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininaemia (Urea cycle disorders and inherited hyperammonaemias); Argininemia 207800 to Argininaemia (Urea cycle disorders and inherited hyperammonaemias); Argininemia, OMIM:207800
Adult onset neurodegenerative disorder v2.185 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininaemia, 207800; Progressive spastic tetraplegia to Argininemia, OMIM:207800
Childhood onset hereditary spastic paraplegia v2.53 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Progressive spastic tetraplegia; Argininaemia, 207800 to Argininemia, OMIM:207800
Hereditary spastic paraplegia v1.235 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininaemia, 207800; Progressive spastic tetraplegia to Argininemia, OMIM:207800
Neonatal cholestasis v1.18 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininemia 207800 to Argininemia, OMIM:207800
Hyperammonaemia v1.10 ARG1 Arina Puzriakova Phenotypes for gene: ARG1 were changed from Argininemia 207800 to Argininemia, OMIM:207800
Adult onset hereditary spastic paraplegia v1.33 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353; Spastic paralysis, infantile onset ascending, OMIM:607225 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353
Adult onset hereditary spastic paraplegia v1.32 ALS2 Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: ALS2.
Tag Q3_21_phenotype tag was added to gene: ALS2.
Adult onset hereditary spastic paraplegia v1.32 ALS2 Arina Puzriakova commented on gene: ALS2
Intellectual disability v3.1222 RNF220 Konstantinos Varvagiannis gene: RNF220 was added
gene: RNF220 was added to Intellectual disability. Sources: Literature,Other
Mode of inheritance for gene: RNF220 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNF220 were set to 33964137; 10881263
Phenotypes for gene: RNF220 were set to Leukodystrophy; CNS hypomyelination; Ataxia; Intellectual disability; Sensorineural hearing impairment; Elevated hepatic transaminases; Hepatic fibrosis; Dilated cardiomyopathy; Spastic paraplegia; Dysarthria; Abnormality of the corpus callosum
Penetrance for gene: RNF220 were set to Complete
Review for gene: RNF220 was set to GREEN
Added comment: Sferra et al (2021 - PMID: 33964137) provide extensive evidence that biallelic RNF220 mutations cause a disorder characterized by hypomyelinating leukodystrophy, ataxia (9/9 - onset 1-5y), borderline intellectual functioning (3/9) / intellectual disability (5/9 - in most cases mild), sensorineural deafness (9/9) with complete hearing loss in the first decade of life, hepatopathy (9/9) with associated periportal fibrosis, and dilated cardiomyopathy (9/9) which was fatal.

Other neurologic manifestations apart from ataxia incl. hyperreflexia (8/8), spastic paraplegia (9/9), dysarthria (9/9), peripheral neuropathy (4/9), seizures in one case (1/9). Upon brain MRI there was thin corpus callosum (9/9) or cerebellar atrophy in some (2/9).

The authors identified homozygosity for 2 recurrent missense RNF220 variants in affected members belonging to these 5 broad consanguineous pedigrees (7 families), namely NM_018150.4:c.1094G>A / p.Arg365Gly in 4 Roma families in the context of a shared haplotype (/founder effect) as well as c.1088G>A / p.Arg363Gly in a large pedigree from southern Italy initially reported by Leuzzi et al (2000 - PMID: 10881263).

Extensive segregation analyses were carried out including several affected and unaffected members.

RNF220 encodes ring finger protein 220, which functions as an E3 ubiquitin ligase. Previous studies have shown among others a role in modulation of Sonic hedgehog/GLI signaling and cerebellar development

Evidence for the role of RNF220 included relevant expression, localization within the cell, interaction partners (lamin B1, 20S proteasome), similarities with other laminopathies in terms of phenotype, etc :
*RNF220 has a relevant expression pattern in CNS (based on qRT-PCR analyses in human brain, cerebellum, cerebral cortex / mRNA levels in human fetal CNS with higher expression in cerebellum, spinal cord and cortex / previous GTEx data / protein levels in mouse CNS)
*The protein displays nuclear localization based on iPSC cells differentiated to motor neurons (also supported by data from the Human Protein Atlas). Transfection of COS-1 cells demonstrated localization primarily to the nucleus (as also previously demonstrated in HEK293T cells) in vesicle like structures with ASF2/SF2 colocalization suggesting enrichment in nuclear speckles. There was also partial co-distribution with the 20S proteasome. R363Q and R365Q additionally coalesced in the cytoplasm forming protein aggregates/inclusions.
*Immunofluorescence studies in patient fibroblasts also confirmed abnormal increase of the protein in the cytoplasm and increased fluorescence with the 20S proteasome.
*Proteomic identification of RNF220-interacting proteins in transfected HEK293T cells demonstrated enrichment for all members of the lamin protein family (incl . lamin B1, AC, B2).
*RNAi-mediated downregulation of RNF222 in Drosophila suggested altered subcellular localization and accumulation of the fly orthologue for human lamin B1.
*Immunoprecipitation of lamin B1 from the nuclear matrix of cerebellar cells suggested significant interaction of endogenous lamin B1 with RNF220, while transfection studies in HEK293T cells for wt/mt suggested reduced binding to endogenous lamin B1 for RNF220 mt compared to wt (more prominent for R365Q). RNF220 mutants also reduced ubiquitination of nuclear lamin B1 compared to wt.
*Patient fibroblasts immunostained with different nuclear envelope markers displayed abnormal nuclear shapes with multiple invaginations and lobulations, findings also observed in laminopathies.

There is currently no associated phenotype in OMIM or G2P. SysID includes RNF220 among the current primary ID genes.

Consider inclusion in panels for leukodystrophies, childhood onset ataxia, sensorineural hearing loss, corpus callosum anomalies, cardiomyopathies, hepatopathies, etc in all cases with green rating.
Sources: Literature, Other
Intellectual disability v3.1222 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from ALS2-RELATED DISORDERS; Amyotrophic lateral sclerosis 2, juvenile, 205100 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353; Spastic paralysis, infantile onset ascending, OMIM:607225
Amyotrophic lateral sclerosis/motor neuron disease v1.34 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from Amyotrophic Lateral Sclerosis, Recessive; Amyotrophic lateral sclerosis 2, juvenile, 205100; Primary lateral sclerosis, juvenile, 606353; Spastic paralysis, infantile onset ascending, 607225 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353
Adult onset neurodegenerative disorder v2.184 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from Primary lateral sclerosis, juvenile, 606353; Spastic paralysis, infantile onset ascending, 607225; Amyotrophic lateral sclerosis 2, juvenile, 205100 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353
Adult onset hereditary spastic paraplegia v1.32 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from Spastic paralysis, infantile onset ascending,autosomal recessive, 607225; Primary lateral sclerosis, juvenile, autosomal recessive, 606353; Amyotrophic lateral sclerosis 2, autosomal recessive, juvenile, 205100 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353; Spastic paralysis, infantile onset ascending, OMIM:607225
Childhood onset hereditary spastic paraplegia v2.52 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from Spastic paralysis, infantile onset ascending,autosomal recessive, 607225; Primary lateral sclerosis, juvenile, autosomal recessive, 606353; Amyotrophic lateral sclerosis 2, autosomal recessive, juvenile, 205100 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353; Spastic paralysis, infantile onset ascending, OMIM:607225
Hereditary spastic paraplegia v1.234 ALS2 Arina Puzriakova Phenotypes for gene: ALS2 were changed from 607225 to Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100; Primary lateral sclerosis, juvenile, OMIM:606353; Spastic paralysis, infantile onset ascending, OMIM:607225
Childhood onset hereditary spastic paraplegia v2.51 AIMP1 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: AIMP1.
Childhood onset hereditary spastic paraplegia v2.51 AIMP1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be updated from 'both mono- and biallelic' to 'biallelic' only at the next GMS panel update (tagged Q3_21_MOI).

Literature review showed that all affected individuals harbour biallelic variants, while heterozygous variant carriers are asymptomatic. The MOI is also biallelic in OMIM, Gen2Phen, and all other relevant panels.
Childhood onset hereditary spastic paraplegia v2.51 AIMP1 Arina Puzriakova Mode of inheritance for gene: AIMP1 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v1.31 AIMP1 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: AIMP1.
Adult onset hereditary spastic paraplegia v1.31 AIMP1 Arina Puzriakova Classified gene: AIMP1 as Green List (high evidence)
Adult onset hereditary spastic paraplegia v1.31 AIMP1 Arina Puzriakova Added comment: Comment on list classification: Review of literature did not reveal any adult onset cases - infantile and childhood onset only.

The 'Q3_21_phenotype' tag has been added to highlight that this is a childhood onset condition. Leaving the rating as Green, but with a recommendation for review at the next GMS panel update. This gene is already Green on the 'Hereditary spastic paraplegia - childhood onset v.2.18' panel.
Adult onset hereditary spastic paraplegia v1.31 AIMP1 Arina Puzriakova Gene: aimp1 has been classified as Green List (High Evidence).
Hereditary ataxia with onset in adulthood v2.81 ABCB7 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: ABCB7.
Intellectual disability v3.1221 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating, 3, 260600; LEUKODYSTROPHY, HYPOMYELINATING, 3 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Adult onset hereditary spastic paraplegia v1.30 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating, 3, OMIM:260600 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Early onset or syndromic epilepsy v2.404 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating 3 260600 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Adult onset hereditary spastic paraplegia v1.29 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating, 3, autosomomal recessive, 260600 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Childhood onset hereditary spastic paraplegia v2.50 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating, 3, 260600 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Hereditary spastic paraplegia v1.233 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from 260600 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Inherited white matter disorders v1.131 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating, 3 260600 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
White matter disorders and cerebral calcification - narrow panel v1.191 AIMP1 Arina Puzriakova Phenotypes for gene: AIMP1 were changed from Leukodystrophy, hypomyelinating, 3 to Leukodystrophy, hypomyelinating, 3, OMIM:260600
Early onset or syndromic epilepsy v2.403 ARF3 Konstantinos Varvagiannis gene: ARF3 was added
gene: ARF3 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: ARF3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ARF3 were set to 34346499
Phenotypes for gene: ARF3 were set to Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system
Penetrance for gene: ARF3 were set to unknown
Added comment: Sakamoto et al (2021 - PMID: 34346499) provide some evidence that monoallelic ARF3 pathogenic variants may be associated with a NDD with brain abnormality.

Using trio exome sequencing, the authors identified 2 individuals with NDD harboring de novo ARF3 variants, namely: NM_001659.2:c.200A>T / p.Asp67Val and c.296G>T / p.Arg99Leu.

Individual 1 (with Asp67Val / age : 4y10m), appeared to be more severelely affected with prenatal onset progressive microcephaly, severe global DD, epilepsy. Upon MRI there was cerebellar and brainstem atrophy. Individual 2 (Arg99Leu / 14y) had severe DD and ID (IQ of 23), epilepsy and upon MRI cerebellar hypoplasia. This subject did not exhibit microcephaly. Common facial features incl. broad nose, full cheeks, small philtrum, strabismus, thin upper lips and abnormal jaw. There was no evidence of systemic involvement in both.

ARF3 encodes ADP-ribosylation factor 3. Adenosine diphosphate ribosylation factors (ARFs) are key proteins for regulation of cargo sorting at the Golgi network, with ARF3 mainly working at the trans-Golgi network. ARFs belong to the small GTP-binding protein (G protein) superfamily. ARF3 switches between an active GTP-bound form and an inactive GDP-bound form, regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) respectively.

Members of the ARF superfamily regulate various aspects of membrane traffic, among others in neurons.

There are 5 homologs of ARF families, divided in 3 classes. ARF3 and ARF1 belong to class I. Monoallelic ARF1 mutations are associated with Periventricular nodular heterotopia 8 (MIM 618185).

In vivo, in vitro and in silico studies for the 2 variants suggest that both impair the Golgi transport system although each variant most likely exerts a different effect (gain-of-function for Arg99Leu vs loss-of-function/dominant-negative for Asp67Val).

This was also reflected in somewhat different phenotype of the subjects with the respective variants. Common features included severe DD, epilepsy and brain abnormalities although Asp67Val was associated with diffuse brain atrophy as well as congenital microcephaly and Arg99Leu with cerebellar hypoplasia.

Evidence to support the effect of each variant include:

Arg99Leu:
Had identical Golgi localization to that of wt
Had increased binding activity with GGA1, a protein recruited by the GTP-bound active form of ARF3 to the TGN membrane (supporting GoF)
In silico structural analysis suggested it may fail to stabilize the conformation of Asp26, resulting in impaired GTP hydrolysis (GoF).
In transgenic fruit flies, evaluation of the ARF3 variant toxicity using the rough eye phenotype this variant was associated with increased severity of the r-e phenotype similar to a previously studied GoF variant (Gln71Leu)

Asp67Val:
Did not show a Golgi-like pattern of localization (similar to Thr31Asn a previously studied dominant-negative variant)
Displayed decreased protein stability
In silico structural analysis suggested that Asp67Val may lead to compromised binding of GTP or GDP (suggestive of LoF)
In transgenic Drosophila eye-specific expression of Asp67Val (similar to Thr31Asn, a known dominant-negative variant) was lethal possibly due to high toxicity in very small amounts in tissues outside the eye.

There is no associated phenotype in OMIM, G2P or SysID.
Sources: Literature
Intellectual disability v3.1220 ARF3 Konstantinos Varvagiannis gene: ARF3 was added
gene: ARF3 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ARF3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ARF3 were set to 34346499
Phenotypes for gene: ARF3 were set to Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system
Penetrance for gene: ARF3 were set to unknown
Review for gene: ARF3 was set to AMBER
Added comment: Sakamoto et al (2021 - PMID: 34346499) provide some evidence that monoallelic ARF3 pathogenic variants may be associated with a NDD with brain abnormality.

Using trio exome sequencing, the authors identified 2 individuals with NDD harboring de novo ARF3 variants, namely: NM_001659.2:c.200A>T / p.Asp67Val and c.296G>T / p.Arg99Leu.

Individual 1 (with Asp67Val / age : 4y10m), appeared to be more severelely affected with prenatal onset progressive microcephaly, severe global DD, epilepsy. Upon MRI there was cerebellar and brainstem atrophy. Individual 2 (Arg99Leu / 14y) had severe DD and ID (IQ of 23), epilepsy and upon MRI cerebellar hypoplasia. This subject did not exhibit microcephaly. Common facial features incl. broad nose, full cheeks, small philtrum, strabismus, thin upper lips and abnormal jaw. There was no evidence of systemic involvement in both.

ARF3 encodes ADP-ribosylation factor 3. Adenosine diphosphate ribosylation factors (ARFs) are key proteins for regulation of cargo sorting at the Golgi network, with ARF3 mainly working at the trans-Golgi network. ARFs belong to the small GTP-binding protein (G protein) superfamily. ARF3 switches between an active GTP-bound form and an inactive GDP-bound form, regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) respectively.

Members of the ARF superfamily regulate various aspects of membrane traffic, among others in neurons.

There are 5 homologs of ARF families, divided in 3 classes. ARF3 and ARF1 belong to class I. Monoallelic ARF1 mutations are associated with Periventricular nodular heterotopia 8 (MIM 618185).

In vivo, in vitro and in silico studies for the 2 variants suggest that both impair the Golgi transport system although each variant most likely exerts a different effect (gain-of-function for Arg99Leu vs loss-of-function/dominant-negative for Asp67Val).

This was also reflected in somewhat different phenotype of the subjects with the respective variants. Common features included severe DD, epilepsy and brain abnormalities although Asp67Val was associated with diffuse brain atrophy as well as congenital microcephaly and Arg99Leu with cerebellar hypoplasia.

Evidence to support the effect of each variant include:

Arg99Leu:
Had identical Golgi localization to that of wt
Had increased binding activity with GGA1, a protein recruited by the GTP-bound active form of ARF3 to the TGN membrane (supporting GoF)
In silico structural analysis suggested it may fail to stabilize the conformation of Asp26, resulting in impaired GTP hydrolysis (GoF).
In transgenic fruit flies, evaluation of the ARF3 variant toxicity using the rough eye phenotype this variant was associated with increased severity of the r-e phenotype similar to a previously studied GoF variant (Gln71Leu)

Asp67Val:
Did not show a Golgi-like pattern of localization (similar to Thr31Asn a previously studied dominant-negative variant)
Displayed decreased protein stability
In silico structural analysis suggested that Asp67Val may lead to compromised binding of GTP or GDP (suggestive of LoF)
In transgenic Drosophila eye-specific expression of Asp67Val (similar to Thr31Asn, a known dominant-negative variant) was lethal possibly due to high toxicity in very small amounts in tissues outside the eye.

There is no associated phenotype in OMIM, G2P or SysID.
Sources: Literature
Intellectual disability v3.1220 PLXNA2 Konstantinos Varvagiannis changed review comment from: Altuame et al (2021 - PMID: 34327814) describe 3 individuals from 2 consanguineous Arab families with biallelic PLXNA2 variants.

The index patient from the 1st family presented with CHD (hypoplastic right ventricle, ASD), DD and moderate ID (IQ of 40), failure to thrive as well as some dysmorphic features (obtuse mandibular angle, mild overbite, synophrys with downslanting p-f, strabismus, etc). There were additional features (eg. postaxial polydactyly) which were found in other affected and unaffected family members.

Exome sequencing with autozygome analysis revealed homozygosity for a PLXNA2 stopgain variant (NM_025179:c.3603C>A / p.(Cys1201*)).

Sanger confirmation was carried out and segregation analyses confirmed carrier status of the unaffected parents and a sib as well as a brother homozygous for the same variant. Clinical evaluation of the latter, following this finding revealed borderline intellectual functioning, ADHD, failure to thrive. There was no mandibular anomaly or overbite and no clinical evidence of CHD (no echo performed).

The index patient from the 2nd consanguineous family was evaluated for ID (IQ of 63), with previous borderline motor development, ADHD and some dysmorphic features (obtuse mandibular angle and overbite). There was no clinical evidence of CHD (no echo performed).

Exome sequencing with autozygosity mapping revealed a homozygous missense PLXNA2 variant (c.3073G>A / p.(Asp1025Asn), present only once in gnomAD (htz), with rather non-concordant in silico predictions SIFT 0.22, PolyPhen 0.682 and CADD 23.5. The aa was however highly conserved.

Segregation analysis confirmed carrier state of the parents and 2 unaffected sibs, with a 3rd sib homozygous for the wt allele.

As the authors discuss:
*PLXNA2 belongs to the plexin family of genes, encoding transmbembrane proteins functioning as semaphorin receptors. It has predominant expression in neural tissue. The protein is thought to bind semaphorin-3A, -3C or -5 followed by plexin A2 dimerization, activation of its GTPase-activating protein domain, negative regulation of Rap1B GTPase and initiation of a signal transduction cascade mediating axonal repulsion/guidance, dendritic guidance, neuronal migration.
*Murine Plxna2 knockout models display structural brain defects. In addition they display congenital heart defects incl. persistent truncus arteriosus and interrupted aortic arch.
*Rare CNVs in adult humans with tetralogy of Fallot have suggested a potential role of PLXNA2 in cardiac development and CHD.
*Expression and the role of PLXNA2 in human chondrocytes as well as a GWAS in 240 japanese patients with mandibular prognathism where PLXNA2 was suggested as a susceptibility locus.

Overall, the authors recognize some common features (as for cognitive functioning, some dysmorphic features incl. obtuse mandibular angle and overbite in 2 unrelated subjects, failure to thrive 3/3) and provide plausible explanations for the variability / discordance of others eg:
- Cyanotic heart disease explaining discordance in cognitive outcome among sibs
- Incomplete penetrance for CHD (and/or ID or mandibular anomaly) as for few AR disorders and/or
- Additional pathogenic variants explaining the CHD in the first subject.

There is no associated phenotype in OMIM or G2P. SysID includes PLXNA2 among the candidate ID genes.
Sources: Literature, Other; to: Altuame et al (2021 - PMID: 34327814) describe 3 individuals from 2 consanguineous Arab families with biallelic PLXNA2 variants.

The index patient from the 1st family presented with CHD (hypoplastic right ventricle, ASD), DD and moderate ID (IQ of 40), failure to thrive as well as some dysmorphic features (obtuse mandibular angle, mild overbite, synophrys with downslanting p-f, strabismus, etc). There were additional features (eg. postaxial polydactyly) which were found in other affected and unaffected family members.

Exome sequencing with autozygome analysis revealed homozygosity for a PLXNA2 stopgain variant (NM_025179:c.3603C>A / p.(Cys1201*)).

Sanger confirmation was carried out and segregation analyses confirmed carrier status of the unaffected parents and a sib as well as a brother homozygous for the same variant. Clinical evaluation of the latter, following this finding revealed borderline intellectual functioning, ADHD, failure to thrive. There was no mandibular anomaly or overbite and no clinical evidence of CHD (no echo performed).

The index patient from the 2nd consanguineous family was evaluated for ID (IQ of 63), with previous borderline motor development, ADHD and some dysmorphic features (obtuse mandibular angle and overbite). There was no clinical evidence of CHD (no echo performed).

Exome sequencing with autozygosity mapping revealed a homozygous missense PLXNA2 variant (c.3073G>A / p.(Asp1025Asn), present only once in gnomAD (htz), with rather non-concordant in silico predictions SIFT 0.22, PolyPhen 0.682 and CADD 23.5. The aa was however highly conserved.

Segregation analysis confirmed carrier state of the parents and 2 unaffected sibs, with a 3rd sib homozygous for the wt allele.

As the authors discuss:
*PLXNA2 belongs to the plexin family of genes, encoding transmbembrane proteins functioning as semaphorin receptors. It has predominant expression in neural tissue. The protein is thought to bind semaphorin-3A, -3C or -5 followed by plexin A2 dimerization, activation of its GTPase-activating protein domain, negative regulation of Rap1B GTPase and initiation of a signal transduction cascade mediating axonal repulsion/guidance, dendritic guidance, neuronal migration.
*Murine Plxna2 knockout models display structural brain defects. In addition they display congenital heart defects incl. persistent truncus arteriosus and interrupted aortic arch.
*Rare CNVs in adult humans with tetralogy of Fallot have suggested a potential role of PLXNA2 in cardiac development and CHD.
*Expression and the role of PLXNA2 in human chondrocytes as well as a GWAS in 240 japanese patients with mandibular prognathism where PLXNA2 was suggested as a susceptibility locus.

Overall, the authors recognize some common features (as for cognitive functioning, some dysmorphic features incl. obtuse mandibular angle and overbite in 2 unrelated subjects, failure to thrive 3/3) and provide plausible explanations for the variability / discordance of others eg:
- Cyanotic heart disease explaining discordance in cognitive outcome among sibs
- Incomplete penetrance for CHD (and/or ID or mandibular anomaly) as for few AR disorders and/or
- Additional pathogenic variants possibly explaining the CHD in the first subject.

There is no associated phenotype in OMIM or G2P. SysID includes PLXNA2 among the candidate ID genes.
Sources: Literature, Other
Intellectual disability v3.1220 PLXNA2 Konstantinos Varvagiannis gene: PLXNA2 was added
gene: PLXNA2 was added to Intellectual disability. Sources: Literature,Other
Mode of inheritance for gene: PLXNA2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PLXNA2 were set to 34327814
Phenotypes for gene: PLXNA2 were set to Intellectual disability; Abnormality of the face; Failure to thrive; Abnormal heart morphology
Penetrance for gene: PLXNA2 were set to Incomplete
Review for gene: PLXNA2 was set to AMBER
Added comment: Altuame et al (2021 - PMID: 34327814) describe 3 individuals from 2 consanguineous Arab families with biallelic PLXNA2 variants.

The index patient from the 1st family presented with CHD (hypoplastic right ventricle, ASD), DD and moderate ID (IQ of 40), failure to thrive as well as some dysmorphic features (obtuse mandibular angle, mild overbite, synophrys with downslanting p-f, strabismus, etc). There were additional features (eg. postaxial polydactyly) which were found in other affected and unaffected family members.

Exome sequencing with autozygome analysis revealed homozygosity for a PLXNA2 stopgain variant (NM_025179:c.3603C>A / p.(Cys1201*)).

Sanger confirmation was carried out and segregation analyses confirmed carrier status of the unaffected parents and a sib as well as a brother homozygous for the same variant. Clinical evaluation of the latter, following this finding revealed borderline intellectual functioning, ADHD, failure to thrive. There was no mandibular anomaly or overbite and no clinical evidence of CHD (no echo performed).

The index patient from the 2nd consanguineous family was evaluated for ID (IQ of 63), with previous borderline motor development, ADHD and some dysmorphic features (obtuse mandibular angle and overbite). There was no clinical evidence of CHD (no echo performed).

Exome sequencing with autozygosity mapping revealed a homozygous missense PLXNA2 variant (c.3073G>A / p.(Asp1025Asn), present only once in gnomAD (htz), with rather non-concordant in silico predictions SIFT 0.22, PolyPhen 0.682 and CADD 23.5. The aa was however highly conserved.

Segregation analysis confirmed carrier state of the parents and 2 unaffected sibs, with a 3rd sib homozygous for the wt allele.

As the authors discuss:
*PLXNA2 belongs to the plexin family of genes, encoding transmbembrane proteins functioning as semaphorin receptors. It has predominant expression in neural tissue. The protein is thought to bind semaphorin-3A, -3C or -5 followed by plexin A2 dimerization, activation of its GTPase-activating protein domain, negative regulation of Rap1B GTPase and initiation of a signal transduction cascade mediating axonal repulsion/guidance, dendritic guidance, neuronal migration.
*Murine Plxna2 knockout models display structural brain defects. In addition they display congenital heart defects incl. persistent truncus arteriosus and interrupted aortic arch.
*Rare CNVs in adult humans with tetralogy of Fallot have suggested a potential role of PLXNA2 in cardiac development and CHD.
*Expression and the role of PLXNA2 in human chondrocytes as well as a GWAS in 240 japanese patients with mandibular prognathism where PLXNA2 was suggested as a susceptibility locus.

Overall, the authors recognize some common features (as for cognitive functioning, some dysmorphic features incl. obtuse mandibular angle and overbite in 2 unrelated subjects, failure to thrive 3/3) and provide plausible explanations for the variability / discordance of others eg:
- Cyanotic heart disease explaining discordance in cognitive outcome among sibs
- Incomplete penetrance for CHD (and/or ID or mandibular anomaly) as for few AR disorders and/or
- Additional pathogenic variants explaining the CHD in the first subject.

There is no associated phenotype in OMIM or G2P. SysID includes PLXNA2 among the candidate ID genes.
Sources: Literature, Other
Intellectual disability v3.1220 VPS50 Konstantinos Varvagiannis gene: VPS50 was added
gene: VPS50 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: VPS50 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS50 were set to 34037727
Phenotypes for gene: VPS50 were set to Neonatal cholestatic liver disease; Failure to thrive; Profound global developmental delay; Postnatal microcephaly; Seizures; Abnormality of the corpus callosum
Penetrance for gene: VPS50 were set to Complete
Review for gene: VPS50 was set to AMBER
Added comment: Schneeberger et al (2021 - PMID: 34037727) describe the phenotype of 2 unrelated individuals with biallelic VPS50 variants.

Common features included transient neonatal cholestasis, failure to thrive, severe DD with failure to achieve milestones (last examination at 2y and 2y2m respectively), postnatal microcephaly, seizures (onset at 6m and 25m) and irritability. There was corpus callosum hypoplasia on brain imaging.

Both individuals were homozygous for variants private to each family (no/not known consanguinity applying to each case). The first individual was homozygous for a splicing variant (NM_017667.4:c.1978-1G>T) and had a similarly unaffected sister deceased with no available DNA for testing. The other individual was homozygous for an in-frame deletion (c.1823_1825delCAA / p.(Thr608del)).

VPS50 encodes a critical component of the endosome-associated recycling protein (EARP) complex, which functions in recycling endocytic vesicles back to the plasma membrane [OMIM based on Schindler et al]. The complex contains VPS50, VPS51, VPS52, VPS53, the three latter also being components of GARP (Golgi-associated-retrograde protein) complex. GARP contains VPS54 instead of VPS50 and is required for trafficking of proteins to the trans-golgi network. Thus VPS50 (also named syndetin) and VPS54 function in the EARP and GARP complexes, to define directional movement of their endocytic vesicles [OMIM based on Schindler et al]. The VPS50 subunit is required for recycling of the transferrin receptor.

As discussed by Schneeberger et al (refs provided in text):
- VPS50 has a high expression in mouse and human brain as well as throughout mouse brain development.
- Mice deficient for Vps50 have not been reported. vps50 knockdown in zebrafish results in severe developmental defects of the body axis. Knockout mice for other proteins of the EARP/GARP complex (e.g. Vps52, 53 and 54) display embryonic lethality.

Studies performed by Schneeberger et al included:
- Transcript analysis for the 1st variant demonstrated skipping of ex21 (in patient derived fabriblasts) leading to an in frame deletion of 81 bp (r.1978_2058del) with predicted loss of 27 residues (p.Leu660_Leu686del).
- Similar VPS50 mRNA levels but significant reduction of protein levels (~5% and ~8% of controls) were observed in fibroblasts from patients 1 and 2. Additionally, significant reductions in the amounts of VPS52 and VPS53 protein levels were observed despite mRNA levels similar to controls. Overall, this suggested drastic reduction of functional EARP complex levels.
- Lysosomes appeared to have similar morphology, cellular distribution and likely unaffected function in patient fibroblasts.
- Transferrin receptor recycling was shown to be delayed in patient fibroblasts suggestive of compromise of endocytic-recycling function.

As the authors comment, the phenotype of both individuals with biallelic VPS50 variants overlaps with the corresponding phenotype reported in 15 subjects with biallelic VPS53 or VPS51 mutations notably, severe DD/ID, microcephaly and early onset epilepsy, CC anomalies. Overall, for this group, they propose the term "GARP and/or EARP deficiency disorders".

There is no VPS50-associated phenotype in OMIM or G2P. SysID includes VPS50 among the ID candidate genes.

Consider inclusion in other relevant gene panels (e.g. for neonatal cholestasis, epilepsy, microcephaly, growth failure in early infancy, corpus callosum anomalies, etc) with amber rating pending further reports.
Sources: Literature
Early onset or syndromic epilepsy v2.403 VPS50 Konstantinos Varvagiannis gene: VPS50 was added
gene: VPS50 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: VPS50 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: VPS50 were set to 34037727
Phenotypes for gene: VPS50 were set to Neonatal cholestatic liver disease; Failure to thrive; Profound global developmental delay; Postnatal microcephaly; Seizures; Abnormality of the corpus callosum
Penetrance for gene: VPS50 were set to Complete
Review for gene: VPS50 was set to AMBER
Added comment: Schneeberger et al (2021 - PMID: 34037727) describe the phenotype of 2 unrelated individuals with biallelic VPS50 variants.

Common features included transient neonatal cholestasis, failure to thrive, severe DD with failure to achieve milestones (last examination at 2y and 2y2m respectively), postnatal microcephaly, seizures (onset at 6m and 25m) and irritability. There was corpus callosum hypoplasia on brain imaging.

Both individuals were homozygous for variants private to each family (no/not known consanguinity applying to each case). The first individual was homozygous for a splicing variant (NM_017667.4:c.1978-1G>T) and had a similarly unaffected sister deceased with no available DNA for testing. The other individual was homozygous for an in-frame deletion (c.1823_1825delCAA / p.(Thr608del)).

VPS50 encodes a critical component of the endosome-associated recycling protein (EARP) complex, which functions in recycling endocytic vesicles back to the plasma membrane [OMIM based on Schindler et al]. The complex contains VPS50, VPS51, VPS52, VPS53, the three latter also being components of GARP (Golgi-associated-retrograde protein) complex. GARP contains VPS54 instead of VPS50 and is required for trafficking of proteins to the trans-golgi network. Thus VPS50 (also named syndetin) and VPS54 function in the EARP and GARP complexes, to define directional movement of their endocytic vesicles [OMIM based on Schindler et al]. The VPS50 subunit is required for recycling of the transferrin receptor.

As discussed by Schneeberger et al (refs provided in text):
- VPS50 has a high expression in mouse and human brain as well as throughout mouse brain development.
- Mice deficient for Vps50 have not been reported. vps50 knockdown in zebrafish results in severe developmental defects of the body axis. Knockout mice for other proteins of the EARP/GARP complex (e.g. Vps52, 53 and 54) display embryonic lethality.

Studies performed by Schneeberger et al included:
- Transcript analysis for the 1st variant demonstrated skipping of ex21 (in patient derived fabriblasts) leading to an in frame deletion of 81 bp (r.1978_2058del) with predicted loss of 27 residues (p.Leu660_Leu686del).
- Similar VPS50 mRNA levels but significant reduction of protein levels (~5% and ~8% of controls) were observed in fibroblasts from patients 1 and 2. Additionally, significant reductions in the amounts of VPS52 and VPS53 protein levels were observed despite mRNA levels similar to controls. Overall, this suggested drastic reduction of functional EARP complex levels.
- Lysosomes appeared to have similar morphology, cellular distribution and likely unaffected function in patient fibroblasts.
- Transferrin receptor recycling was shown to be delayed in patient fibroblasts suggestive of compromise of endocytic-recycling function.

As the authors comment, the phenotype of both individuals with biallelic VPS50 variants overlaps with the corresponding phenotype reported in 15 subjects with biallelic VPS53 or VPS51 mutations notably, severe DD/ID, microcephaly and early onset epilepsy, CC anomalies. Overall, for this group, they propose the term "GARP and/or EARP deficiency disorders".

There is no VPS50-associated phenotype in OMIM or G2P. SysID includes VPS50 among the ID candidate genes.

Consider inclusion in other relevant gene panels (e.g. for neonatal cholestasis, epilepsy, microcephaly, growth failure in early infancy, corpus callosum anomalies, etc) with amber rating pending further reports.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 MCM4 Arina Puzriakova Classified gene: MCM4 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 MCM4 Arina Puzriakova Added comment: Comment on list classification: Gene was reassessed following a recent Amber review by Zornitza Stark. Although there has only been a single founder variant reported to date, the rating was based on multiple Green GMS expert reviews and the functional support was deemed sufficiently compelling. Therefore, the Green gene rating will be maintained on this panel.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.458 MCM4 Arina Puzriakova Gene: mcm4 has been classified as Green List (High Evidence).
Adult onset neurodegenerative disorder v2.183 SORL1 Sarah Leigh Classified gene: SORL1 as Amber List (moderate evidence)
Adult onset neurodegenerative disorder v2.183 SORL1 Sarah Leigh Added comment: Comment on list classification: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. The cited publications give evidence for a role for SORL1 in the development of Alzheimers disease (PMIDs 28537274; 22472873; 28595629; 32587946).
Adult onset neurodegenerative disorder v2.183 SORL1 Sarah Leigh Gene: sorl1 has been classified as Amber List (Moderate Evidence).
Adult onset neurodegenerative disorder v2.182 FIG4 Sarah Leigh commented on gene: FIG4: The Q3_21_MOI tag has been added as Amyotrophic lateral sclerosis 11 (OMIM:612577) is monoallelic Charcot-Marie-Tooth disease, type 4J (OMIM:611228) is biallelic.
Adult onset neurodegenerative disorder v2.182 FIG4 Sarah Leigh Tag Q3_21_MOI tag was added to gene: FIG4.
Adult onset neurodegenerative disorder v2.182 FIG4 Sarah Leigh edited their review of gene: FIG4: Added comment: Associated with relevant phenotype in OMIM, but not associated with Amyotrophic lateral sclerosis 11 (OMIM:612577) or Charcot-Marie-Tooth disease, type 4J (OMIM:611228) in Gen2Phen. At least three variants reported in three cases of Amyotrophic lateral sclerosis 11 (OMIM:612577)(PMID: 19118816), and two variants in at least one case of Charcot-Marie-Tooth disease, type 4J (OMIM:611228)(PMID: 21705420).; Changed rating: GREEN; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1220 HNMT Sarah Graham reviewed gene: HNMT: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 26206890, 33310825, 33739554; Phenotypes: Intellectual disability, 616739; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Adult onset neurodegenerative disorder v2.182 FIG4 Sarah Leigh Added comment: Comment on phenotypes: Amyotrophic lateral sclerosis 11 OMIM:612577 is associated with this panel (Neurodegenerative disorders - adult onset) as it is an adult onset condition. Charcot-Marie-Tooth disease, type 4J, 611228 is predominantly a childhood condition, however, some adult cases have been reported (PMID: 21705420).
Adult onset neurodegenerative disorder v2.182 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Amyotrophic lateral sclerosis 11, OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640 to Amyotrophic lateral sclerosis 11 OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640
Adult onset neurodegenerative disorder v2.181 FIG4 Sarah Leigh Publications for gene: FIG4 were set to 19118816; 23888880
Adult onset neurodegenerative disorder v2.180 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Amyotrophic lateral sclerosis 11, OMIM:612577 to Amyotrophic lateral sclerosis 11, OMIM:612577; amyotrophic lateral sclerosis type 11 MONDO:0012945; Charcot-Marie-Tooth disease, type 4J, OMIM:611228; Charcot-Marie-Tooth disease type 4J MONDO:0012640
Malformations of cortical development v2.49 FIG4 Sarah Leigh Classified gene: FIG4 as Amber List (moderate evidence)
Malformations of cortical development v2.49 FIG4 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with ?Polymicrogyria, bilateral temporooccipital OMIM:612691 in Gen2Phen. A single missense variant has been reported in a large consanguineous Moroccan family, supportive functional studies were also reported (PMID: 24598713).
Malformations of cortical development v2.49 FIG4 Sarah Leigh Gene: fig4 has been classified as Amber List (Moderate Evidence).
Malformations of cortical development v2.48 FIG4 Sarah Leigh Added comment: Comment on phenotypes: FIG4 variants also are associated with Amyotrophic lateral sclerosis 11 OMIM:612577; Charcot-Marie-Tooth disease, type 4J OMIM:611228 and Yunis-Varon syndrome OMIM:216340, but these phenotypes are not appropriate for this panel.
Malformations of cortical development v2.48 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from ?Polymicrogyria, bilateral temporooccipital OMIM:612691; bilateral parasagittal parieto-occipital polymicrogyria MONDO:0012986 to ?Polymicrogyria, bilateral temporooccipital OMIM:612691; bilateral parasagittal parieto-occipital polymicrogyria MONDO:0012986
Malformations of cortical development v2.47 FIG4 Sarah Leigh Phenotypes for gene: FIG4 were changed from Polymicrogyria with epilepsy MIM# 612691 to ?Polymicrogyria, bilateral temporooccipital OMIM:612691; bilateral parasagittal parieto-occipital polymicrogyria MONDO:0012986
Amelogenesis imperfecta v2.8 SP6 Zornitza Stark reviewed gene: SP6: Rating: GREEN; Mode of pathogenicity: None; Publications: 33652941; Phenotypes: Amelogenesis imperfecta; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Amelogenesis imperfecta v2.8 PEX26 Zornitza Stark reviewed gene: PEX26: Rating: GREEN; Mode of pathogenicity: None; Publications: 33926089; Phenotypes: Heimler syndrome; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1220 CTC1 Arina Puzriakova Phenotypes for gene: CTC1 were changed from CEREBRORETINAL MICROANGIOPATHY WITH CALCIFICATIONS AND CYSTS to Cerebroretinal microangiopathy with calcifications and cysts, OMIM:612199
Intellectual disability v3.1219 CTC1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: CTC1.
Intellectual disability v3.1219 CTC1 Arina Puzriakova Classified gene: CTC1 as Green List (high evidence)
Intellectual disability v3.1219 CTC1 Arina Puzriakova Added comment: Comment on list classification: This gene should be demoted from Green to Amber, as per the recent review by Zornitza Stark. The disorder is primarily characterised by intracranial calcifications to which cognitive decline is secondary. Some individuals have normal cognition.
Intellectual disability v3.1219 CTC1 Arina Puzriakova Gene: ctc1 has been classified as Green List (High Evidence).
Severe early-onset obesity v2.41 PGM2L1 Arina Puzriakova Entity copied from Intellectual disability v3.1218
Severe early-onset obesity v2.41 PGM2L1 Arina Puzriakova gene: PGM2L1 was added
gene: PGM2L1 was added to Severe early-onset obesity. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: PGM2L1.
Mode of inheritance for gene: PGM2L1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PGM2L1 were set to 33979636
Phenotypes for gene: PGM2L1 were set to Neurodevelopmental disorder
Early onset or syndromic epilepsy v2.403 PGM2L1 Arina Puzriakova Entity copied from Intellectual disability v3.1218
Early onset or syndromic epilepsy v2.403 PGM2L1 Arina Puzriakova gene: PGM2L1 was added
gene: PGM2L1 was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: PGM2L1.
Mode of inheritance for gene: PGM2L1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PGM2L1 were set to 33979636
Phenotypes for gene: PGM2L1 were set to Neurodevelopmental disorder
Intellectual disability v3.1218 PGM2L1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: PGM2L1.
Intellectual disability v3.1218 PGM2L1 Arina Puzriakova Classified gene: PGM2L1 as Amber List (moderate evidence)
Intellectual disability v3.1218 PGM2L1 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 (tagged).

Morava et al. 2021 (PMID: 33979636) identified 4 unrelated individuals with different biallelic protein-truncating variants in the PGM2L1 gene. All had severe GDD/ID. Other features that reach the threshold for inclusion on the relevant panels (observed in at least 3 cases) are epilepsy and early obesity (99th centile at ages 2 to 3). Some functional data included.
Intellectual disability v3.1218 PGM2L1 Arina Puzriakova Gene: pgm2l1 has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy v1.399 SORD Sarah Leigh Classified gene: SORD as Green List (high evidence)
Hereditary neuropathy v1.399 SORD Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 7 variants reported in unrelated cases. Functional studies showed undetectable SORD protein levels and increased intracellular sorbitol accumulation in patient fibroblasts compared to controls (PMID 32367058).
Hereditary neuropathy v1.399 SORD Sarah Leigh Gene: sord has been classified as Green List (High Evidence).
Hereditary neuropathy v1.398 SORD Sarah Leigh Publications for gene: SORD were set to PMID: 32367058
Hereditary neuropathy or pain disorder v1.44 SORD Sarah Leigh Publications for gene: SORD were set to 32367058; 33314640; 33397963
Hereditary neuropathy or pain disorder v1.43 SORD Sarah Leigh Phenotypes for gene: SORD were changed from Neuropathy to Sorbitol dehydrogenase deficiency with peripheral neuropathy OMIM:618912; sorbitol dehydrogenase deficiency with peripheral neuropathy MONDO:0030055
Hereditary neuropathy v1.397 SORD Sarah Leigh Phenotypes for gene: SORD were changed from CMT2 to Sorbitol dehydrogenase deficiency with peripheral neuropathy OMIM:618912; sorbitol dehydrogenase deficiency with peripheral neuropathy MONDO:0030055
Hereditary neuropathy v1.396 VWA1 Sarah Leigh Publications for gene: VWA1 were set to 33559681; 33459760
Hereditary neuropathy or pain disorder v1.42 VWA1 Sarah Leigh Publications for gene: VWA1 were set to 33559681; 33459760
Hereditary neuropathy or pain disorder v1.41 VWA1 Sarah Leigh Classified gene: VWA1 as Amber List (moderate evidence)
Hereditary neuropathy or pain disorder v1.41 VWA1 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 v1.41 VWA1 Sarah Leigh Gene: vwa1 has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy or pain disorder v1.40 VWA1 Sarah Leigh reviewed gene: VWA1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Hereditary neuropathy or pain disorder v1.40 VWA1 Sarah Leigh Tag Q3_21_rating tag was added to gene: VWA1.
Hereditary neuropathy v1.395 VWA1 Sarah Leigh Classified gene: VWA1 as Green List (high evidence)
Hereditary neuropathy v1.395 VWA1 Sarah Leigh Added comment: Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least five variants reported in numerous unrelated cases (PMID 33559681; 33459760). Supportive Zebra fish morpholino studies have also been presented (PMID 33559681; 33015062).
Hereditary neuropathy v1.395 VWA1 Sarah Leigh Gene: vwa1 has been classified as Green List (High Evidence).
Hereditary neuropathy v1.394 VWA1 Sarah Leigh Publications for gene: VWA1 were set to 33459760
Hereditary neuropathy or pain disorder v1.40 VWA1 Sarah Leigh Publications for gene: VWA1 were set to 33559681
Hereditary neuropathy v1.393 VWA1 Sarah Leigh Publications for gene: VWA1 were set to PMID: 33459760
Hereditary neuropathy or pain disorder v1.39 VWA1 Sarah Leigh Publications for gene: VWA1 were set to PMID: 33559681
Hereditary neuropathy or pain disorder v1.38 VWA1 Sarah Leigh Phenotypes for gene: VWA1 were changed from axonal hereditary motor neuropathy; myopathy to Neuropathy, hereditary motor, with myopathic features OMIM:619216; neuropathy, hereditary motor, with myopathic features MONDO:0030977
Hereditary neuropathy v1.392 VWA1 Sarah Leigh Phenotypes for gene: VWA1 were changed from hereditary motor neuropathy to Neuropathy, hereditary motor, with myopathic features OMIM:619216; neuropathy, hereditary motor, with myopathic features MONDO:0030977
Primary immunodeficiency or monogenic inflammatory bowel disease v2.457 GIMAP5 Arina Puzriakova Phenotypes for gene: GIMAP5 were changed from lymphopenia; autoimmunity; immunodeficiency; liver disease to Portal hypertension, noncirrhotic, 2, OMIM:619463; lymphopenia; autoimmunity; immunodeficiency; liver disease
Primary immunodeficiency or monogenic inflammatory bowel disease v2.456 GIMAP5 Arina Puzriakova Publications for gene: GIMAP5 were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.455 GIMAP5 Arina Puzriakova commented on gene: GIMAP5: Cannot access new publication identified by Zornitza Stark (PMID:33956074) - free text will be available from 05/01/2022. OMIM entry states that "some patients may have recurrent infections or features suggestive of an immunodeficiency" but it is unclear how many individuals were affected and to what extent. Liver dysfunction (portal hypertension, liver failure) seems to be the more prominent phenotype in these cases but currently there are no relevant PanelApp panels for this. Therefore, I will maintain the Amber rating at this time, until publications become available or further evidence emerges.
Childhood solid tumours v2.23 NYNRIN Arina Puzriakova Classified gene: NYNRIN as Amber List (moderate evidence)
Childhood solid tumours v2.23 NYNRIN Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. The NYNRIN gene is currently not listed in OMIM or G2P.

Mahamdallie et al. 2019 (PMID: 30885698) report 2 families with 3 affected children with Wilms tumour who harboured distinct compound het protein-truncating variants in this gene. To date, there have been no further reports linking NYNRIN with disease and little is known about its functions. Rating Amber as two families have been identified but additional cases/functional evidence are required to validate pathogenicity.
Childhood solid tumours v2.23 NYNRIN Arina Puzriakova Gene: nynrin has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.706 WDR91 Arina Puzriakova Publications for gene: WDR91 were set to 32732226
Fetal anomalies v1.705 PRKD1 Arina Puzriakova Added comment: Comment on mode of inheritance: MOI was reassessed following a recent review by Zornitza Stark highlighting the potential involvement of biallelic variants. Currently the evidence for biallelic inheritance only suffices for an Amber rating and so I have kept the MOI as monoallelic but with a 'watchlist_MOI' tag to monitor for additional evidence. The Genomics England pipeline would still pick up biallelic cases under the current MOI.
Fetal anomalies v1.705 PRKD1 Arina Puzriakova Mode of inheritance for gene: PRKD1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Fetal anomalies v1.704 PRKD1 Arina Puzriakova Publications for gene: PRKD1 were set to
Fetal anomalies v1.703 PRKD1 Arina Puzriakova Tag watchlist_moi tag was added to gene: PRKD1.
Intellectual disability v3.1217 TCF7L2 Konstantinos Varvagiannis reviewed gene: TCF7L2: Rating: AMBER; Mode of pathogenicity: None; Publications: 34003604; Phenotypes: Global developmental delay, Intellectual disability, Autism, Attention deficit hyperactivity disorder, Myopia, Abnormality of skeletal system; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Beckwith-Wiedemann syndrome (BWS) and other congenital overgrowth disorders v1.115 EZH2 Ivone Leong Tag for-review was removed from gene: EZH2.
Beckwith-Wiedemann syndrome (BWS) and other congenital overgrowth disorders v1.115 EZH2 Ivone Leong Added comment: Comment on mode of inheritance: MOI changed from "MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed)" to "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown" as advised by Sarah Leigh (Genomics England Curator)
Beckwith-Wiedemann syndrome (BWS) and other congenital overgrowth disorders v1.115 EZH2 Ivone Leong Mode of inheritance for gene: EZH2 was changed from MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed) to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Nephrocalcinosis or nephrolithiasis v2.21 MOCOS Detlef Bockenhauer gene: MOCOS was added
gene: MOCOS was added to Nephrocalcinosis or nephrolithiasis. Sources: Literature
Mode of inheritance for gene: MOCOS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MOCOS were set to PMID: 11302742; 17368066; 14624414; 25967871; 34356852; 32073534; 30758870; 27919260
Phenotypes for gene: MOCOS were set to Xanthinuria type II (MIM603592)
Penetrance for gene: MOCOS were set to Incomplete
Review for gene: MOCOS was set to GREEN
Added comment: This gene had not been previously included in this panel, but there is good evidence from several publications that recessive loss-of-function variants in MOCOS are associated with Xanthinuria type 2. There is also a good pathophysiologic basis: MOCOS encodes a necessary co-factor for the 2 enzymes that degrade Xanthine, XDH and AOX1.
Moreover, there are spontaneous animal models, with MOCOS variants identified in a goat (PMID 30758870) and Tyrolean grey cattle (PMID 27919260).
Sources: Literature
Mitochondrial disorder with complex I deficiency v1.14 NDUFC2 Ivone Leong Tag Q2_21_rating tag was added to gene: NDUFC2.
Mitochondrial disorder with complex IV deficiency v1.12 COX4I1 Ivone Leong Tag Q2_21_rating tag was added to gene: COX4I1.
Mitochondrial disorder with complex IV deficiency v1.12 SQOR Ivone Leong Tag Q2_21_rating tag was added to gene: SQOR.
Early onset or syndromic epilepsy v2.402 PIDD1 Konstantinos Varvagiannis changed review comment from: There is enough evidence to include this gene in the current panel with green rating.

Biallelic PIDD1 pathogenic variants have been reported in 26 individuals (11 families) with DD (all), variable degrees of ID (mild to severe), behavioral (eg. aggression/self-mutilation in several, ADHD) and/or psychiatric abnormalities (ASD, psychosis in 5 belonging to 3 families), well-controlled epilepsy is some (9 subjects from 6 families) and MRI abnormalities notably abnormal gyration pattern (pachygyria with predominant anterior gradient) as well as corpus callosum anomalies (commonly thinning) in several. Dysmorphic features have been reported in almost all, although there has been no specific feature suggested.

The first reports on the phenotype associated with biallelic PIDD1 mutations were made by Harripaul et al (2018 - PMID: 28397838) and Hu et al (2019 - PMID: 29302074) [both studies investigating large cohorts of individuals with ID from consanguineous families].

Sheikh et al (2021 - PMID: 33414379) provided details on the phenotype of 15 individuals from 5 families including those from the previous 2 reports and studied provided evidence on the role of PIDD1 and the effect of variants.

Zaki et al (2021 - PMID: 34163010) reported 11 additional individuals from 6 consanguineous families, summarize the features of all subjects published in the literature and review the neuroradiological features of the disorder.

PIDD1 encodes p53-induced death domain protein 1. The protein is part of the PIDDosome, a multiprotein complex also composed of the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 and induces apoptosis in response to DNA damage.

There are 5 potential PIDD1 mRNA transcript variants with NM_145886.4 corresponding to the longest. Similar to the protein encoded by CRADD, PIDD1 contains a death domain (DD - aa 774-893). Constitutive post-translational processing gives PIDD1-N, PIDD1-C the latter further processed into PIDD1-CC (by auto-cleavage). Serine residues at pos. 446 and 588 are involved in this autoprocessing generating PIDD1-C (aa 446-910) and PIDD1-CC (aa 774-893). The latter is needed for caspase-2 activation.

Most (if not all) individuals belonged to consanguineous families of different origins and harbored pLoF or missense variants.

Variants reported so far include : c.2587C>T; p.Gln863* / c.1909C>T ; p.Arg637* / c.2443C>T / p.Arg815Trp / c.2275-1G>A which upon trap assay was shown to lead to skipping of ex15 with direct splicing form exon14 to the terminal exon 16 (resulting to p.Arg759Glyfs*1 with exlcusion of the entire DD) / c.2584C>T; p.Arg862Trp / c.1340G>A; p.Trp447* / c.2116_2120del; p.Val706His*, c.1564_1565del; p.Gly602fs*26

Evidence so far provided includes:
- Biallelic CRADD variants cause a NDD disorder and a highly similar gyration pattern.
- Confirmation of splicing effect (eg. for c.2275-1G>A premature stop in position 760) or poor expression (NM_145886.3:c.2587C>T; p.Gln863*). Arg815Trp did not affect autoprocessing or protein stability.
- Abnormal localization pattern, loss of interaction with CRADD and failure to activate caspase-2 (MDM2 cleavage assay) [p.Gln863* and Arg815Trp]
- Available expression data from GTEx (PIDD1 having broad expression in multiple tissues, but higher in brain cerebellum) as well as BrainSpan and PsychEncode studies suggesting high coexpression of PIDD1, CRADD and CASP2 in many regions in the developing human brain.
- Variants in other genes encoding proteins interacting with PIDD1 (MADD, FADD, DNAJ, etc) are associated with NDD.

Pidd-1 ko mice (ex3-15 removal) lack however CNS-related phenotypes. These show decreased anxiety but no motor anomalies. This has also been the case with Cradd-/- mice displaying no significant CNS phenotypes without lamination defects.

There is currently no associated phenotype in OMIM, PanelApp Australia. PIDD1 is listed in the DD panel of G2P (PIDD1-relared NDD / biallelic / loss of function / probable) . SysID includes PIDD1 among the current primary ID genes.

Overall the gene appears to be relevant for the epilepsy panel, panels for gyration and/or corpus callosum anomalies etc.
Sources: Literature, Other; to: There is enough evidence to include this gene in the current panel with green rating.

Biallelic PIDD1 pathogenic variants have been reported in 26 individuals (11 families) with DD (all), variable degrees of ID (mild to severe), behavioral (eg. aggression/self-mutilation in several, ADHD) and/or psychiatric abnormalities (ASD, psychosis in 5 belonging to 3 families), well-controlled epilepsy is some (9 subjects from 6 families) and MRI abnormalities notably abnormal gyration pattern (pachygyria with predominant anterior gradient) as well as corpus callosum anomalies (commonly thinning) in several. Dysmorphic features have been reported in almost all, although there has been no specific feature suggested.

The first reports on the phenotype associated with biallelic PIDD1 mutations were made by Harripaul et al (2018 - PMID: 28397838) and Hu et al (2019 - PMID: 29302074) [both studies investigating large cohorts of individuals with ID from consanguineous families].

Sheikh et al (2021 - PMID: 33414379) provided details on the phenotype of 15 individuals from 5 families including those from the previous 2 reports and studied provided evidence on the role of PIDD1 and the effect of variants.

Zaki et al (2021 - PMID: 34163010) reported 11 additional individuals from 6 consanguineous families, summarize the features of all subjects published in the literature and review the neuroradiological features of the disorder.

PIDD1 encodes p53-induced death domain protein 1. The protein is part of the PIDDosome, a multiprotein complex also composed of the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 and induces apoptosis in response to DNA damage.

There are 5 potential PIDD1 mRNA transcript variants with NM_145886.4 corresponding to the longest. Similar to the protein encoded by CRADD, PIDD1 contains a death domain (DD - aa 774-893). Constitutive post-translational processing gives PIDD1-N, PIDD1-C the latter further processed into PIDD1-CC (by auto-cleavage). Serine residues at pos. 446 and 588 are involved in this autoprocessing generating PIDD1-C (aa 446-910) and PIDD1-CC (aa 774-893). The latter is needed for caspase-2 activation.

Most (if not all) individuals belonged to consanguineous families of different origins and harbored pLoF or missense variants.

Variants reported so far include : c.2587C>T; p.Gln863* / c.1909C>T ; p.Arg637* / c.2443C>T / p.Arg815Trp / c.2275-1G>A which upon trap assay was shown to lead to skipping of ex15 with direct splicing form exon14 to the terminal exon 16 (resulting to p.Arg759Glyfs*1 with exlcusion of the entire DD) / c.2584C>T; p.Arg862Trp / c.1340G>A; p.Trp447* / c.2116_2120del; p.Val706His*, c.1564_1565del; p.Gly602fs*26

Evidence so far provided includes:
- Biallelic CRADD variants cause a NDD disorder and a highly similar gyration pattern.
- Confirmation of splicing effect (eg. for c.2275-1G>A premature stop in position 760) or poor expression (NM_145886.3:c.2587C>T; p.Gln863*). Arg815Trp did not affect autoprocessing or protein stability.
- Abnormal localization pattern, loss of interaction with CRADD and failure to activate caspase-2 (MDM2 cleavage assay) [p.Gln863* and Arg815Trp]
- Available expression data from GTEx (PIDD1 having broad expression in multiple tissues, but higher in brain cerebellum) as well as BrainSpan and PsychEncode studies suggesting high coexpression of PIDD1, CRADD and CASP2 in many regions in the developing human brain.
- Variants in other genes encoding proteins interacting with PIDD1 (MADD, FADD, DNAJ, etc) are associated with NDD.

Pidd-1 ko mice (ex3-15 removal) lack however CNS-related phenotypes. These show decreased anxiety but no motor anomalies. This has also been the case with Cradd-/- mice displaying no significant CNS phenotypes without lamination defects.

There is currently no associated phenotype in OMIM, PanelApp Australia. PIDD1 is listed in the DD panel of G2P (PIDD1-related NDD / biallelic / loss of function / probable) . SysID includes PIDD1 among the current primary ID genes.

Overall the gene appears to be relevant for the epilepsy panel, panels for gyration and/or corpus callosum anomalies etc.
Sources: Literature, Other
Intellectual disability v3.1217 PIDD1 Konstantinos Varvagiannis changed review comment from: There is enough evidence to include this gene in the current panel with green rating.

Biallelic PIDD1 pathogenic variants have been reported in 26 individuals (11 families) with DD (all), variable degrees of ID (mild to severe), behavioral (eg. aggression/self-mutilation in several, ADHD) and/or psychiatric abnormalities (ASD, psychosis in 5 belonging to 3 families), well-controlled epilepsy is some (9 subjects from 6 families) and MRI abnormalities notably abnormal gyration pattern (pachygyria with predominant anterior gradient) as well as corpus callosum anomalies (commonly thinning) in several. Dysmorphic features have been reported in almost all, although there has been no specific feature suggested.

The first reports on the phenotype associated with biallelic PIDD1 mutations were made by Harripaul et al (2018 - PMID: 28397838) and Hu et al (2019 - PMID: 29302074) [both studies investigating large cohorts of individuals with ID from consanguineous families].

Sheikh et al (2021 - PMID: 33414379) provided details on the phenotype of 15 individuals from 5 families including those from the previous 2 reports and studied provided evidence on the role of PIDD1 and the effect of variants.

Zaki et al (2021 - PMID: 34163010) reported 11 additional individuals from 6 consanguineous families, summarize the features of all subjects published in the literature and review the neuroradiological features of the disorder.

PIDD1 encodes p53-induced death domain protein 1. The protein is part of the PIDDosome, a multiprotein complex also composed of the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 and induces apoptosis in response to DNA damage.

There are 5 potential PIDD1 mRNA transcript variants with NM_145886.4 corresponding to the longest. Similar to the protein encoded by CRADD, PIDD1 contains a death domain (DD - aa 774-893). Constitutive post-translational processing gives PIDD1-N, PIDD1-C the latter further processed into PIDD1-CC (by auto-cleavage). Serine residues at pos. 446 and 588 are involved in this autoprocessing generating PIDD1-C (aa 446-910) and PIDD1-CC (aa 774-893). The latter is needed for caspase-2 activation.

Most (if not all) individuals belonged to consanguineous families of different origins and harbored pLoF or missense variants.

Variants reported so far include : c.2587C>T; p.Gln863* / c.1909C>T ; p.Arg637* / c.2443C>T / p.Arg815Trp / c.2275-1G>A which upon trap assay was shown to lead to skipping of ex15 with direct splicing form exon14 to the terminal exon 16 (resulting to p.Arg759Glyfs*1 with exlcusion of the entire DD) / c.2584C>T; p.Arg862Trp / c.1340G>A; p.Trp447* / c.2116_2120del; p.Val706His*, c.1564_1565del; p.Gly602fs*26

Evidence so far provided includes:
- Biallelic CRADD variants cause a NDD disorder and a highly similar gyration pattern.
- Confirmation of splicing effect (eg. for c.2275-1G>A premature stop in position 760) or poor expression (NM_145886.3:c.2587C>T; p.Gln863*). Arg815Trp did not affect autoprocessing or protein stability.
- Abnormal localization pattern, loss of interaction with CRADD and failure to activate caspase-2 (MDM2 cleavage assay) [p.Gln863* and Arg815Trp]
- Available expression data from GTEx (PIDD1 having broad expression in multiple tissues, but higher in brain cerebellum) as well as BrainSpan and PsychEncode studies suggesting high coexpression of PIDD1, CRADD and CASP2 in many regions in the developing human brain.
- Variants in other genes encoding proteins interacting with PIDD1 (MADD, FADD, DNAJ, etc) are associated with NDD.

Pidd-1 ko mice (ex3-15 removal) lack however CNS-related phenotypes. These show decreased anxiety but no motor anomalies. This has also been the case with Cradd-/- mice displaying no significant CNS phenotypes without lamination defects.

There is currently no associated phenotype in OMIM, PanelApp Australia. PIDD1 is listed in the DD panel of G2P (PIDD1-relared NDD / biallelic / loss of function / probable) . SysID includes PIDD1 among the current primary ID genes.

Overall the gene appears to be relevant for the epilepsy panel, panels for gyration and/or corpus callosum anomalies etc.
Sources: Literature, Other; to: There is enough evidence to include this gene in the current panel with green rating.

Biallelic PIDD1 pathogenic variants have been reported in 26 individuals (11 families) with DD (all), variable degrees of ID (mild to severe), behavioral (eg. aggression/self-mutilation in several, ADHD) and/or psychiatric abnormalities (ASD, psychosis in 5 belonging to 3 families), well-controlled epilepsy is some (9 subjects from 6 families) and MRI abnormalities notably abnormal gyration pattern (pachygyria with predominant anterior gradient) as well as corpus callosum anomalies (commonly thinning) in several. Dysmorphic features have been reported in almost all, although there has been no specific feature suggested.

The first reports on the phenotype associated with biallelic PIDD1 mutations were made by Harripaul et al (2018 - PMID: 28397838) and Hu et al (2019 - PMID: 29302074) [both studies investigating large cohorts of individuals with ID from consanguineous families].

Sheikh et al (2021 - PMID: 33414379) provided details on the phenotype of 15 individuals from 5 families including those from the previous 2 reports and studied provided evidence on the role of PIDD1 and the effect of variants.

Zaki et al (2021 - PMID: 34163010) reported 11 additional individuals from 6 consanguineous families, summarize the features of all subjects published in the literature and review the neuroradiological features of the disorder.

PIDD1 encodes p53-induced death domain protein 1. The protein is part of the PIDDosome, a multiprotein complex also composed of the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 and induces apoptosis in response to DNA damage.

There are 5 potential PIDD1 mRNA transcript variants with NM_145886.4 corresponding to the longest. Similar to the protein encoded by CRADD, PIDD1 contains a death domain (DD - aa 774-893). Constitutive post-translational processing gives PIDD1-N, PIDD1-C the latter further processed into PIDD1-CC (by auto-cleavage). Serine residues at pos. 446 and 588 are involved in this autoprocessing generating PIDD1-C (aa 446-910) and PIDD1-CC (aa 774-893). The latter is needed for caspase-2 activation.

Most (if not all) individuals belonged to consanguineous families of different origins and harbored pLoF or missense variants.

Variants reported so far include : c.2587C>T; p.Gln863* / c.1909C>T ; p.Arg637* / c.2443C>T / p.Arg815Trp / c.2275-1G>A which upon trap assay was shown to lead to skipping of ex15 with direct splicing form exon14 to the terminal exon 16 (resulting to p.Arg759Glyfs*1 with exlcusion of the entire DD) / c.2584C>T; p.Arg862Trp / c.1340G>A; p.Trp447* / c.2116_2120del; p.Val706His*, c.1564_1565del; p.Gly602fs*26

Evidence so far provided includes:
- Biallelic CRADD variants cause a NDD disorder and a highly similar gyration pattern.
- Confirmation of splicing effect (eg. for c.2275-1G>A premature stop in position 760) or poor expression (NM_145886.3:c.2587C>T; p.Gln863*). Arg815Trp did not affect autoprocessing or protein stability.
- Abnormal localization pattern, loss of interaction with CRADD and failure to activate caspase-2 (MDM2 cleavage assay) [p.Gln863* and Arg815Trp]
- Available expression data from GTEx (PIDD1 having broad expression in multiple tissues, but higher in brain cerebellum) as well as BrainSpan and PsychEncode studies suggesting high coexpression of PIDD1, CRADD and CASP2 in many regions in the developing human brain.
- Variants in other genes encoding proteins interacting with PIDD1 (MADD, FADD, DNAJ, etc) are associated with NDD.

Pidd-1 ko mice (ex3-15 removal) lack however CNS-related phenotypes. These show decreased anxiety but no motor anomalies. This has also been the case with Cradd-/- mice displaying no significant CNS phenotypes without lamination defects.

There is currently no associated phenotype in OMIM, PanelApp Australia. PIDD1 is listed in the DD panel of G2P (PIDD1-related NDD / biallelic / loss of function / probable) . SysID includes PIDD1 among the current primary ID genes.

Overall the gene appears to be relevant for the epilepsy panel, panels for gyration and/or corpus callosum anomalies etc.
Sources: Literature, Other
Early onset or syndromic epilepsy v2.402 PIDD1 Konstantinos Varvagiannis gene: PIDD1 was added
gene: PIDD1 was added to Genetic epilepsy syndromes. Sources: Literature,Other
Mode of inheritance for gene: PIDD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIDD1 were set to 28397838; 29302074; 33414379; 34163010
Phenotypes for gene: PIDD1 were set to Global developmental delay; Intellectual disability; Seizures; Autism; Behavioral abnormality; Psychosis; Pachygyria; Lissencephaly; Abnormality of the corpus callosum
Penetrance for gene: PIDD1 were set to Complete
Review for gene: PIDD1 was set to GREEN
Added comment: There is enough evidence to include this gene in the current panel with green rating.

Biallelic PIDD1 pathogenic variants have been reported in 26 individuals (11 families) with DD (all), variable degrees of ID (mild to severe), behavioral (eg. aggression/self-mutilation in several, ADHD) and/or psychiatric abnormalities (ASD, psychosis in 5 belonging to 3 families), well-controlled epilepsy is some (9 subjects from 6 families) and MRI abnormalities notably abnormal gyration pattern (pachygyria with predominant anterior gradient) as well as corpus callosum anomalies (commonly thinning) in several. Dysmorphic features have been reported in almost all, although there has been no specific feature suggested.

The first reports on the phenotype associated with biallelic PIDD1 mutations were made by Harripaul et al (2018 - PMID: 28397838) and Hu et al (2019 - PMID: 29302074) [both studies investigating large cohorts of individuals with ID from consanguineous families].

Sheikh et al (2021 - PMID: 33414379) provided details on the phenotype of 15 individuals from 5 families including those from the previous 2 reports and studied provided evidence on the role of PIDD1 and the effect of variants.

Zaki et al (2021 - PMID: 34163010) reported 11 additional individuals from 6 consanguineous families, summarize the features of all subjects published in the literature and review the neuroradiological features of the disorder.

PIDD1 encodes p53-induced death domain protein 1. The protein is part of the PIDDosome, a multiprotein complex also composed of the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 and induces apoptosis in response to DNA damage.

There are 5 potential PIDD1 mRNA transcript variants with NM_145886.4 corresponding to the longest. Similar to the protein encoded by CRADD, PIDD1 contains a death domain (DD - aa 774-893). Constitutive post-translational processing gives PIDD1-N, PIDD1-C the latter further processed into PIDD1-CC (by auto-cleavage). Serine residues at pos. 446 and 588 are involved in this autoprocessing generating PIDD1-C (aa 446-910) and PIDD1-CC (aa 774-893). The latter is needed for caspase-2 activation.

Most (if not all) individuals belonged to consanguineous families of different origins and harbored pLoF or missense variants.

Variants reported so far include : c.2587C>T; p.Gln863* / c.1909C>T ; p.Arg637* / c.2443C>T / p.Arg815Trp / c.2275-1G>A which upon trap assay was shown to lead to skipping of ex15 with direct splicing form exon14 to the terminal exon 16 (resulting to p.Arg759Glyfs*1 with exlcusion of the entire DD) / c.2584C>T; p.Arg862Trp / c.1340G>A; p.Trp447* / c.2116_2120del; p.Val706His*, c.1564_1565del; p.Gly602fs*26

Evidence so far provided includes:
- Biallelic CRADD variants cause a NDD disorder and a highly similar gyration pattern.
- Confirmation of splicing effect (eg. for c.2275-1G>A premature stop in position 760) or poor expression (NM_145886.3:c.2587C>T; p.Gln863*). Arg815Trp did not affect autoprocessing or protein stability.
- Abnormal localization pattern, loss of interaction with CRADD and failure to activate caspase-2 (MDM2 cleavage assay) [p.Gln863* and Arg815Trp]
- Available expression data from GTEx (PIDD1 having broad expression in multiple tissues, but higher in brain cerebellum) as well as BrainSpan and PsychEncode studies suggesting high coexpression of PIDD1, CRADD and CASP2 in many regions in the developing human brain.
- Variants in other genes encoding proteins interacting with PIDD1 (MADD, FADD, DNAJ, etc) are associated with NDD.

Pidd-1 ko mice (ex3-15 removal) lack however CNS-related phenotypes. These show decreased anxiety but no motor anomalies. This has also been the case with Cradd-/- mice displaying no significant CNS phenotypes without lamination defects.

There is currently no associated phenotype in OMIM, PanelApp Australia. PIDD1 is listed in the DD panel of G2P (PIDD1-relared NDD / biallelic / loss of function / probable) . SysID includes PIDD1 among the current primary ID genes.

Overall the gene appears to be relevant for the epilepsy panel, panels for gyration and/or corpus callosum anomalies etc.
Sources: Literature, Other
Intellectual disability v3.1217 PIDD1 Konstantinos Varvagiannis gene: PIDD1 was added
gene: PIDD1 was added to Intellectual disability. Sources: Literature,Other
Mode of inheritance for gene: PIDD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIDD1 were set to 28397838; 29302074; 33414379; 34163010
Phenotypes for gene: PIDD1 were set to Global developmental delay; Intellectual disability; Seizures; Autism; Behavioral abnormality; Psychosis; Pachygyria; Lissencephaly; Abnormality of the corpus callosum
Penetrance for gene: PIDD1 were set to Complete
Review for gene: PIDD1 was set to GREEN
Added comment: There is enough evidence to include this gene in the current panel with green rating.

Biallelic PIDD1 pathogenic variants have been reported in 26 individuals (11 families) with DD (all), variable degrees of ID (mild to severe), behavioral (eg. aggression/self-mutilation in several, ADHD) and/or psychiatric abnormalities (ASD, psychosis in 5 belonging to 3 families), well-controlled epilepsy is some (9 subjects from 6 families) and MRI abnormalities notably abnormal gyration pattern (pachygyria with predominant anterior gradient) as well as corpus callosum anomalies (commonly thinning) in several. Dysmorphic features have been reported in almost all, although there has been no specific feature suggested.

The first reports on the phenotype associated with biallelic PIDD1 mutations were made by Harripaul et al (2018 - PMID: 28397838) and Hu et al (2019 - PMID: 29302074) [both studies investigating large cohorts of individuals with ID from consanguineous families].

Sheikh et al (2021 - PMID: 33414379) provided details on the phenotype of 15 individuals from 5 families including those from the previous 2 reports and studied provided evidence on the role of PIDD1 and the effect of variants.

Zaki et al (2021 - PMID: 34163010) reported 11 additional individuals from 6 consanguineous families, summarize the features of all subjects published in the literature and review the neuroradiological features of the disorder.

PIDD1 encodes p53-induced death domain protein 1. The protein is part of the PIDDosome, a multiprotein complex also composed of the bipartite linker protein CRADD (also known as RAIDD) and the proform of caspase-2 and induces apoptosis in response to DNA damage.

There are 5 potential PIDD1 mRNA transcript variants with NM_145886.4 corresponding to the longest. Similar to the protein encoded by CRADD, PIDD1 contains a death domain (DD - aa 774-893). Constitutive post-translational processing gives PIDD1-N, PIDD1-C the latter further processed into PIDD1-CC (by auto-cleavage). Serine residues at pos. 446 and 588 are involved in this autoprocessing generating PIDD1-C (aa 446-910) and PIDD1-CC (aa 774-893). The latter is needed for caspase-2 activation.

Most (if not all) individuals belonged to consanguineous families of different origins and harbored pLoF or missense variants.

Variants reported so far include : c.2587C>T; p.Gln863* / c.1909C>T ; p.Arg637* / c.2443C>T / p.Arg815Trp / c.2275-1G>A which upon trap assay was shown to lead to skipping of ex15 with direct splicing form exon14 to the terminal exon 16 (resulting to p.Arg759Glyfs*1 with exlcusion of the entire DD) / c.2584C>T; p.Arg862Trp / c.1340G>A; p.Trp447* / c.2116_2120del; p.Val706His*, c.1564_1565del; p.Gly602fs*26

Evidence so far provided includes:
- Biallelic CRADD variants cause a NDD disorder and a highly similar gyration pattern.
- Confirmation of splicing effect (eg. for c.2275-1G>A premature stop in position 760) or poor expression (NM_145886.3:c.2587C>T; p.Gln863*). Arg815Trp did not affect autoprocessing or protein stability.
- Abnormal localization pattern, loss of interaction with CRADD and failure to activate caspase-2 (MDM2 cleavage assay) [p.Gln863* and Arg815Trp]
- Available expression data from GTEx (PIDD1 having broad expression in multiple tissues, but higher in brain cerebellum) as well as BrainSpan and PsychEncode studies suggesting high coexpression of PIDD1, CRADD and CASP2 in many regions in the developing human brain.
- Variants in other genes encoding proteins interacting with PIDD1 (MADD, FADD, DNAJ, etc) are associated with NDD.

Pidd-1 ko mice (ex3-15 removal) lack however CNS-related phenotypes. These show decreased anxiety but no motor anomalies. This has also been the case with Cradd-/- mice displaying no significant CNS phenotypes without lamination defects.

There is currently no associated phenotype in OMIM, PanelApp Australia. PIDD1 is listed in the DD panel of G2P (PIDD1-relared NDD / biallelic / loss of function / probable) . SysID includes PIDD1 among the current primary ID genes.

Overall the gene appears to be relevant for the epilepsy panel, panels for gyration and/or corpus callosum anomalies etc.
Sources: Literature, Other
Primary immunodeficiency or monogenic inflammatory bowel disease v2.455 LAMTOR2 Arina Puzriakova Classified gene: LAMTOR2 as Green List (high evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.455 LAMTOR2 Arina Puzriakova Added comment: Comment on list classification: Gene was reassessed following a recent Amber review by Zornitza Stark. Although there has only been one family reported to date, the rating was based on multiple Green GMS expert reviews as the functional support was deemed sufficiently compelling. Therefore, the Green gene rating will be maintained on this panel.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.455 LAMTOR2 Arina Puzriakova Gene: lamtor2 has been classified as Green List (High Evidence).
Ichthyosis and erythrokeratoderma v1.62 ASPRV1 Arina Puzriakova Classified gene: ASPRV1 as Amber List (moderate evidence)
Ichthyosis and erythrokeratoderma v1.62 ASPRV1 Arina Puzriakova Gene: asprv1 has been classified as Amber List (Moderate Evidence).
Ichthyosis and erythrokeratoderma v1.61 ASPRV1 Arina Puzriakova Phenotypes for gene: ASPRV1 were changed from palmoplantar keratoderma; lamellar ichthyosis to Ichthyosis, lamellar, autosomal dominant, OMIM:146750
Primary immunodeficiency or monogenic inflammatory bowel disease v2.454 RGS10 Arina Puzriakova Classified gene: RGS10 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.454 RGS10 Arina Puzriakova Added comment: Comment on list classification: New gene added by Boaz Palterer. Single family with 3 affected sibs reported (PMID:34315806), who presented with short stature and immunodeficiency and harboured compound het variants in RGS10 that segregated with disease. However, the sibs also carried a heterozygous PIK3CD (E525K) variant that has previously been deemed pathogenic in Activated PI3 Kinase Delta Syndrome (APDS), a primary immunodeficiency. The variant was excluded as the father also carried the PIK3CD variant but was mostly healthy and none of the 3 affected sibs displayed the full spectrum of symptoms associated with APDS. Nonetheless, APDS is a clinically heterogeneous condition with variable penetrance among affected individuals and so the contribution of PIK3CD to the patients immune dysregulation cannot be completely ruled out.

There are no further reports of an association between RGS10 variants and immunodeficiency to date, and therefore rating Red until further evidence emerges.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.454 RGS10 Arina Puzriakova Gene: rgs10 has been classified as Red List (Low Evidence).
Neurological ciliopathies v1.16 ARL3 Ivone Leong Phenotypes for gene: ARL3 were changed from Joubert syndrome 35 MIM#61816 to Joubert syndrome 35, OMIM:61816
Paediatric or syndromic cardiomyopathy v1.53 KIF20A Ivone Leong Classified gene: KIF20A as Red List (low evidence)
Paediatric or syndromic cardiomyopathy v1.53 KIF20A Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM but not in Gene2Phenotype. PMID: 29357359 describes 1 family with 2 affect sibs. The authors also made a zebrafish MO model, which had a progressive cardiac phenotype starting at 48 hpf. Currently, there is insufficient evidence to support a gene-disease association. Therefore this gene has been given a Red rating.
Paediatric or syndromic cardiomyopathy v1.53 KIF20A Ivone Leong Gene: kif20a has been classified as Red List (Low Evidence).
Paediatric or syndromic cardiomyopathy v1.52 KIF20A Ivone Leong Phenotypes for gene: KIF20A were changed from Cardiomyopathy, familial restrictive, 6, MIM# 619433 to ?Cardiomyopathy, familial restrictive, 6, OMIM:619433
Cardiac arrhythmias - additional genes v1.12 ANK2 Ivone Leong Tag Q3_21_expert_review tag was added to gene: ANK2.
Cardiac arrhythmias - additional genes v1.12 ANK2 Ivone Leong Publications for gene: ANK2 were set to
Structural eye disease v1.76 SMO Ivone Leong Tag mosaicism tag was added to gene: SMO.
Tag somatic tag was added to gene: SMO.
Congenital muscular dystrophy v2.15 FHL1 Ivone Leong Publications for gene: FHL1 were set to
Primary immunodeficiency or monogenic inflammatory bowel disease v2.453 ARHGAP42 Arina Puzriakova Classified gene: ARHGAP42 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.453 ARHGAP42 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Only a single individual reported to date with a homozygous stop-gain variant in ARHGAP42 associated with immunological findings, among other features (PMID: 34232960). Rating Red, awaiting further evidence.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.453 ARHGAP42 Arina Puzriakova Gene: arhgap42 has been classified as Red List (Low Evidence).
Intellectual disability v3.1217 RFX7 Ivone Leong Phenotypes for gene: RFX7 were changed from ID, ASD, ADHD to Intellectual disability, MONDO:0001071, autism spectrum disorder, MONDO:0005258, attention deficit-hyperactivity disorder, MONDO:0007743
Intellectual disability v3.1216 ZC3H14 Ivone Leong commented on gene: ZC3H14
Hereditary neuropathy or pain disorder v1.37 VCP Zornitza Stark reviewed gene: VCP: Rating: GREEN; Mode of pathogenicity: Other; Publications: 25125609, 25878907, 32165109; Phenotypes: Charcot-Marie-Tooth disease, type 2Y, MIM# 616687; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Monogenic hearing loss v2.179 CLDN9 Zornitza Stark reviewed gene: CLDN9: Rating: GREEN; Mode of pathogenicity: None; Publications: 31175426, 19696885, 34265170; Phenotypes: Deafness, autosomal recessive 116, MIM#619093; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Cerebellar hypoplasia v1.54 SNX14 Ivone Leong Added comment: Comment on mode of inheritance: MOI changed from "BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal" to "BIALLELIC, autosomal or pseudoautosomal". No evidence of monoallelic forms of the disease was found. MOI reported in OMIM and Gene2Phenotype is Biallelic.
Cerebellar hypoplasia v1.54 SNX14 Ivone Leong Mode of inheritance for gene: SNX14 was changed from BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Ataxia and cerebellar anomalies - narrow panel v2.226 SNX14 Ivone Leong Tag Q3_21_MOI tag was added to gene: SNX14.
Ataxia and cerebellar anomalies - narrow panel v2.226 SNX14 Ivone Leong reviewed gene: SNX14: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Clefting v2.46 SF3B2 Zornitza Stark gene: SF3B2 was added
gene: SF3B2 was added to Clefting. Sources: Literature
Mode of inheritance for gene: SF3B2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SF3B2 were set to 34344887
Phenotypes for gene: SF3B2 were set to Craniofacial microsomia
Review for gene: SF3B2 was set to GREEN
gene: SF3B2 was marked as current diagnostic
Added comment: Twenty individuals from seven families reported with de novo or transmitted haploinsufficient variants in SF3B2. Affected individuals had mandibular hypoplasia, microtia, facial and preauricular tags, epibulbar dermoids, lateral oral clefts in addition to skeletal and cardiac abnormalities.

Targeted morpholino knockdown of SF3B2 in Xenopus resulted in disruption of cranial neural crest precursor formation and subsequent craniofacial cartilage defects, supporting a link between spliceosome mutations and impaired neural crest development in congenital craniofacial disease.

The families were ascertained from a cohort and the authors suggest that haploinsufficient variants in SF3B2 are the most prevalent genetic cause of CFM, explaining ~3% of sporadic and ~25% of familial cases.
Sources: Literature
Clefting v2.46 SF3B4 Zornitza Stark Deleted their review
Clefting v2.46 SF3B4 Zornitza Stark reviewed gene: SF3B4: Rating: GREEN; Mode of pathogenicity: None; Publications: 34344887; Phenotypes: Craniofacial microsomia; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 GIMAP5 Zornitza Stark reviewed gene: GIMAP5: Rating: GREEN; Mode of pathogenicity: None; Publications: 33956074; Phenotypes: Portal hypertension, noncirrhotic, 2, MIM# 619463; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1216 AP1G1 Zornitza Stark gene: AP1G1 was added
gene: AP1G1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: AP1G1 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: AP1G1 were set to 34102099
Phenotypes for gene: AP1G1 were set to Neurodevelopmental disorder (NDD); Intellectual Disability; Epilepsy
Review for gene: AP1G1 was set to GREEN
gene: AP1G1 was marked as current diagnostic
Added comment: Two bi-allelic homozygous missense variants were found in two distinct families with Italian and Pakistani origins; homozygous missense variants.

Eight de novo heterozygous variants were identified in nine isolated affected individuals from nine families; including five missense, two frameshift, and one intronic variant that disrupts the canonical splice acceptor site.

Knocking out AP1G1 Zebrafish model resulted in severe developmental abnormalities and increased lethality.

All individuals had neurodevelopmental disorder (NDD) including global developmental delay and ID, which varied in severity from mild to severe.

GREEN for mono-allelic, AMBER for bi-allelic.
Sources: Literature
Congenital myopathy v2.56 SPTBN4 Zornitza Stark reviewed gene: SPTBN4: Rating: GREEN; Mode of pathogenicity: None; Publications: 33772159, 29861105; Phenotypes: Neurodevelopmental disorder with hypotonia, neuropathy, and deafness, MIM# 617519; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1216 TP73 Zornitza Stark edited their review of gene: TP73: Added comment: New publication adds further evidence for gene-disease association, PMID 34077761:

- Seven individuals from five unrelated families homozygous for TP73 variants (includes 1x large deletion, 1x splice variant, 1x frameshift and 2x nonsense variants) and cortical malformations/ID
- In vitro ciliogenesis experiments demonstrated that epithelial cells from TP73 variant carriers had reduced number of ciliated cells and shortened cilia resulting in abnormal ciliary clearance of the airways compared to healthy controls; Changed rating: GREEN; Changed publications to: 31130284, 34077761
Limb disorders v2.49 HMGB1 Zornitza Stark gene: HMGB1 was added
gene: HMGB1 was added to Limb disorders. Sources: Literature
Mode of inheritance for gene: HMGB1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: HMGB1 were set to 34159400
Phenotypes for gene: HMGB1 were set to Mirror image foot polydactyly
Review for gene: HMGB1 was set to RED
Added comment: 1x de novo fs in a proband with severe mirror image foot polydactyly. No functional studies done but cited Itou 2011 - mouse and zebrafish studies demonstrated the role of HMGB1 in regulating digit number during embryonic limb development
Sources: Literature
Limb disorders v2.49 UBA2 Zornitza Stark reviewed gene: UBA2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34159400; Phenotypes: Split hand malformation; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Congenital disorders of glycosylation v2.74 EDEM3 Zornitza Stark gene: EDEM3 was added
gene: EDEM3 was added to Congenital disorders of glycosylation. Sources: Literature
Mode of inheritance for gene: EDEM3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EDEM3 were set to 34143952
Phenotypes for gene: EDEM3 were set to Congenital disorder of glycosylation
Review for gene: EDEM3 was set to GREEN
gene: EDEM3 was marked as current diagnostic
Added comment: PMID: 34143952: 7 families (11 individuals) with 6x PTV and 2x missense variants with neurodevelopmental delay and variable facial dysmorphisms. The unaffected parents were all heterozygous carriers. Functional studies show loss of EDEM3 enzymatic activity.
Sources: Literature
Adult onset neurodegenerative disorder v2.179 VRK1 Zornitza Stark reviewed gene: VRK1: Rating: AMBER; Mode of pathogenicity: None; Publications: 34169149, 26583493, 31837156; Phenotypes: Adult-onset spinal muscular atrophy without pontocerebellar hypoplasia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1216 CLCN3 Zornitza Stark gene: CLCN3 was added
gene: CLCN3 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: CLCN3 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: CLCN3 were set to 34186028
Phenotypes for gene: CLCN3 were set to Neurodevelopmental disorder
Mode of pathogenicity for gene: CLCN3 was set to Other
Review for gene: CLCN3 was set to GREEN
gene: CLCN3 was marked as current diagnostic
Added comment: 11 individuals reported, 9 that carried 8 different rare heterozygous missense variants in CLCN3, and 2 siblings that were homozygous for an NMD-predicted frameshift variant likely abolishing ClC-3 function. All missense variants were confirmed to be de novo in eight individuals for whom parental data was available.

The 11 individuals in the cohort share clinical features of variable severity. All 11 have GDD or ID and dysmorphic features, and a majority has mood or behavioural disorders and structural brain abnormalities:
- Structural brain abnormalities on MRI (9/11) included partial or full agenesis of the corpus callosum (6/9), disorganized cerebellar folia (4/9), delayed myelination (3/9), decreased white matter volume (3/9), pons hypoplasia (3/9), and dysmorphic dentate nuclei (3/9). Six of those with brain abnormalities also presented with seizures.
- Nine have abnormal vision, including strabismus in four and inability to fix or follow in the two with homozygous loss-of-function variants.
- Hypotonia ranging from mild to severe was reported in 7 of the 11 individuals.
- Six have mood or behavioural disorders, particularly anxiety (3/6).
- Consistent dysmorphic facial features included microcephaly, prominent forehead, hypertelorism, down-slanting palpebral fissures, full cheeks, and micrognathia.

The severity of disease in the two siblings with homozygous disruption of ClC-3 is consistent with the drastic phenotype seen in Clcn3 KO mice. The disease was more severe in two siblings carrying homozygous loss-of-function variants with the presence of GDD, absent speech, seizures, and salt and pepper fundal pigmentation in both individuals, with one deceased at 14 months of age. The siblings also had significant neuroanatomical findings including diffusely decreased white matter volume, thin corpora callosa, small hippocampi, and disorganized cerebellar folia. Supporting biallelic inheritance for LoF variants, disruption of mouse Clcn3 results in drastic neurodegeneration with loss of the hippocampus a few months after birth and early retinal degeneration. Clcn3−/− mice display severe neurodegeneration, whereas heterozygous Clcn3+/− mice appear normal.

Patch-clamp studies were used to investigate four of the missense variants. These suggested a gain of function in two variants with increased current in HEK cells, however they also showed reduced rectification of voltage and a loss of transient current, plus decreased current amplitude, glycosylation and surface expression when expressed in oocytes, and were suspected to interfere with channel gating and a negative feedback mechanism. These effects were also shown to vary depending on pH levels. The current of the remaining two variants did not differ from WT. For heterozygous missense variants, the disruption induced may be at least partially conferred to mutant/WT homodimers and mutant/ClC-4 heterodimers.

Both loss and gain of function in this gene resulted in the same phenotype.

Green for mono-allelic variants, Amber/Red for bi-allelic.
Sources: Literature
Intellectual disability v3.1216 TNPO2 Zornitza Stark reviewed gene: TNPO2: Rating: GREEN; Mode of pathogenicity: None; Publications: 34314705; Phenotypes: Intellectual disability, dysmorphic features; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.1216 ANK2 Zornitza Stark gene: ANK2 was added
gene: ANK2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ANK2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ANK2 were set to 22542183; 25363768; 27479843; 28554332; 30564305; 30755392; 31981491; 33004838; 33057194
Phenotypes for gene: ANK2 were set to Complex neurodevelopmental disorder, MONDO:0100038
Review for gene: ANK2 was set to GREEN
gene: ANK2 was marked as current diagnostic
Added comment: Note link with cardiac abnormalities such as LongQT is DISPUTED.

However, more than 10 unrelated individuals reported with neurodevelopmental phenotype, comprising autism/ID and de novo truncating variants, in addition to many other individuals as part of large NDD cohorts. This association has been assessed as DEFINITIVE by ClinGen.
Sources: Literature
Cardiac arrhythmias - additional genes v1.11 ANK2 Zornitza Stark reviewed gene: ANK2: Rating: RED; Mode of pathogenicity: None; Publications: 31983240; Phenotypes: Long QT syndrome 4, MIM# 600919; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Hereditary ataxia with onset in adulthood v2.81 PRDX3 Zornitza Stark gene: PRDX3 was added
gene: PRDX3 was added to Hereditary ataxia - adult onset. Sources: Literature
Mode of inheritance for gene: PRDX3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PRDX3 were set to 33889951
Phenotypes for gene: PRDX3 were set to Cerebellar ataxia (early onset, mild to moderate, progressive)
Review for gene: PRDX3 was set to GREEN
gene: PRDX3 was marked as current diagnostic
Added comment: Biallelic variants in 5 unrelated families with early onset (median 21 years , range 13-22 years) with ataxia with variable additional hyper- and hypokinetic movement disorders, and severe early-onset cerebellar atrophy (seen on MRI), and involvement of the brainstem, medullary olive and parietal cortex.

Evolution of the disease was gait ataxia leading to upper limb ataxia, then dysarthria and then dysphagia, all within a decade. For some of these patients, the phenotype included myoclonus, dystonia and / or tremor. Mild classical mitochondrial features were seen in one of the patients, namely ptosis and COX-negative fibres.

The variants were homozygous nonsense, homozygous frameshift, homozygous missense, and a compound heterozygote with a splice variant and missense, all leading to complete loss of the protein. Oxidative stress and mitochondrial dysfunction was indicated as the disease mechanism.

The families originated from Germany, France, India and two from eastern Turkey. The two families from Turkey were seemingly unrelated to each other but had the same homozygous missense, suggestive of founder effect.

Patient fibroblasts from each of the five probands showed lack of protein (via Western blot) and decreased glutathione peroxidase activity and decreased mitochondrial maximal respiratory capacity.

PRDX3 encodes peroxiredoxin 3, a mitochondrial antioxidant protein, that catalyses the reduction of hydrogen peroxide. It localises in the mitochondria, where most hydrogen peroxide is generated.

Functional studies: PRDX3 knockdown (induced by silencing RNA against PRDX3) in cerebellar medulloblastoma cells showed significantly decreased cell viability, increased hydrogen peroxide levels and increased susceptibility to apoptosis triggered by reactive oxygen species.

In addition, induced knockdown drosophila (in vivo animal model) had aberrant locomotor phenotypes and reduced lifespans, while immunolabelling of the brain showed increased cell death after exposure to oxidative stress.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 ARHGAP42 Zornitza Stark gene: ARHGAP42 was added
gene: ARHGAP42 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: ARHGAP42 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ARHGAP42 were set to 34232960
Phenotypes for gene: ARHGAP42 were set to Interstitial lung disease; systemic hypertension; immunological abnormalities
Review for gene: ARHGAP42 was set to RED
Added comment: Single individual reported with homozygous LoF variant, chILD disorder, systemic hypertension, and immunological findings.
Sources: Literature
Intellectual disability v3.1216 LINGO4 Zornitza Stark gene: LINGO4 was added
gene: LINGO4 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: LINGO4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LINGO4 were set to 33098801
Phenotypes for gene: LINGO4 were set to Intellectual disability; speech disorder
Review for gene: LINGO4 was set to GREEN
gene: LINGO4 was marked as current diagnostic
Added comment: 3 unrelated individuals reported with bi-allelic variants in this gene and neurodevelopmental disorder:
1 x individual compound heterozygous for 2x missense variants:
c.679C>A; c.1262G>A p.Leu227Met; p.Arg421Gln. Phenotype: infancy-onset
generalized dystonia; ID, speech disorder

1 x individual homozygous for missense variant: c.679C>A p.Leu227Met Phenotype: ID, speech disorder

1 x individual homozygous for missense variant: c.1673G>A p.Ser558Asn Phenotype: ID, speech disorder
Sources: Literature
Childhood onset dystonia, chorea or related movement disorder v1.140 ARFGEF3 Zornitza Stark gene: ARFGEF3 was added
gene: ARFGEF3 was added to Childhood onset dystonia or chorea or related movement disorder. Sources: Literature
Mode of inheritance for gene: ARFGEF3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ARFGEF3 were set to 33098801
Phenotypes for gene: ARFGEF3 were set to Dystonia
Review for gene: ARFGEF3 was set to GREEN
gene: ARFGEF3 was marked as current diagnostic
Added comment: 3 unrelated individuals reported with variants in this gene and dystonia:
1 x de novo missense variant: c.6212T>C p.Met2071Thr, phenotype: infancy-onset generalized dystonia (isolated)
1x stop-gain variant c.1773T>G p.Tyr591* inherited from mosaic mother), phenotype: infancy-onset generalized dystonia (isolated)
1 x de novo missense variant (Gene Matcher) c.250A>C p.Met84Leu childhood-onset generalized dystonia (isolated)
Sources: Literature
Intellectual disability v3.1216 IMPDH2 Zornitza Stark gene: IMPDH2 was added
gene: IMPDH2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: IMPDH2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: IMPDH2 were set to 33098801
Phenotypes for gene: IMPDH2 were set to Neurodevelopmental disorder with dystonia
Review for gene: IMPDH2 was set to GREEN
Added comment: 6 unrelated individuals
1x individual in a dystonia cohort index case with infancy-onset dystonia and other neurological manifestations with a de-novo missense variant, c.338G>A (p.Gly113Glu) in IMPDH2, predicted to disrupt an invariant residue within the cystathionine-β-synthase (CBS) domain pair of the encoded protein.
IMPDH2 encodes IMPDH2, a key enzyme in the purine biosynthetic pathway, expressed throughout the brain and not linked previously to any human Mendelian condition.
1x individual with a de-novo substitution, c.337G>A (p.Gly113Arg), was found in in-house whole-exome sequencing data from 500 individuals with neurodevelopmental disorders. Through GeneMatcher, de novo variants identified:
3 x missense: c.729G>C (p.Gln243His), c.619G>C (p.Gly207Arg), and c.619G>A (p.Gly207Arg)
1 x deletion: c.478_480delTCC (p.Ser160del)
The six variants were predicted to be deleterious and none of them seen in control databases. All affected conserved amino acids and resided in and around the cystathionine-β-synthase domain pair.
The described variants are situated in and around the CBS domain pair, a regulatory element in which clustering of pathogenic missense variants has already been shown for the homologue of IMPDH2, IMPDH1.

All individuals shared similar neurodevelopmental phenotypes. Apart from the dystonia cohort index case, one participant had evidence of dystonic posturing.

Modelling of the variants on 3D protein structures revealed spatial clustering near specific functional sites, predicted to result in deregulation of IMPDH2 activity. Additionally, thermal-shift assays showed that the c.619G>A (p.Gly207Arg) variant, identified as within the CBS domain pair, and c.729G>C (p.Gln243His), which is in close vicinity, affected the stability or folding behaviour of IMPDH2.
Sources: Literature
Paediatric or syndromic cardiomyopathy v1.51 KIF20A Zornitza Stark gene: KIF20A was added
gene: KIF20A was added to Cardiomyopathies - including childhood onset. Sources: Literature
Mode of inheritance for gene: KIF20A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: KIF20A were set to 29357359
Phenotypes for gene: KIF20A were set to Cardiomyopathy, familial restrictive, 6, MIM# 619433
Review for gene: KIF20A was set to RED
Added comment: Single family reported, two affected sibs, perinatal lethal cardiomyopathy, compound het variants in this gene.
Sources: Literature
Ataxia and cerebellar anomalies - narrow panel v2.226 ATG7 Zornitza Stark gene: ATG7 was added
gene: ATG7 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature
Mode of inheritance for gene: ATG7 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ATG7 were set to 34161705
Phenotypes for gene: ATG7 were set to Spinocerebellar ataxia, SCAR31, MIM#619422
Review for gene: ATG7 was set to GREEN
Added comment: 12 individuals from 5 unrelated families reported with a complex neurodevelopmental disorder and bi-allelic variants in this gene. Age range from 21 months to 71 years of age. Main clinical features included axial hypotonia, variably impaired intellectual development with poor or absent speech, and delayed walking (up to 7 years of age) or inability to walk. All had ataxia, often with tremor or dyskinesia, as well as dysarthria associated with cerebellar hypoplasia on brain imaging. Most had optic atrophy, and some had ptosis, chronic progressive external ophthalmoplegia, retinopathy, and strabismus; 1 had early-onset cataracts. The more severely affected individuals had spastic paraplegia and inability to walk.

Functional data including mouse model.
Sources: Literature
Mitochondrial disorders v2.48 C2orf69 Zornitza Stark gene: C2orf69 was added
gene: C2orf69 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: C2orf69 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: C2orf69 were set to 34038740; 33945503
Phenotypes for gene: C2orf69 were set to Combined oxidative phosphorylation deficiency-53 (COXPD53), MIM#619423
Review for gene: C2orf69 was set to GREEN
gene: C2orf69 was marked as current diagnostic
Added comment: PMID 34038740: 20 affected children from 8 unrelated families reported, presenting with fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. Endogenous C2ORF69 was found to be (1) loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. Zebrafish model.

PMID 33945503: 8 individuals from 5 families reported with muscle hypotonia, developmental delay, progressive microcephaly, and brain MRI abnormalities. Age at onset ranged from birth to 6 months of age. Six patients had vision impairment, liver abnormalities, inflammation/inflammatory arthritis, and 5 patients had seizures.
Sources: Literature
Childhood solid tumours v2.22 NYNRIN Zornitza Stark gene: NYNRIN was added
gene: NYNRIN was added to Tumour predisposition - childhood onset. Sources: Literature
Mode of inheritance for gene: NYNRIN was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NYNRIN were set to 30885698
Phenotypes for gene: NYNRIN were set to Wilms tumour
Review for gene: NYNRIN was set to AMBER
Added comment: 3 individuals with Wilms Tumour reported from two families and bi-allelic truncating variants.

One of the affected children had an inguinal hernia and another had epilepsy, hypothyroidism, and intellectual disability.
Sources: Literature
Retinal disorders v2.202 IMPG1 Arina Puzriakova Classified gene: IMPG1 as Green List (high evidence)
Retinal disorders v2.202 IMPG1 Arina Puzriakova Gene: impg1 has been classified as Green List (High Evidence).
Retinal disorders v2.201 IMPG1 Arina Puzriakova Classified gene: IMPG1 as Amber List (moderate evidence)
Retinal disorders v2.201 IMPG1 Arina Puzriakova Gene: impg1 has been classified as Amber List (Moderate Evidence).
Retinal disorders v2.200 IMPG1 Arina Puzriakova Added comment: Comment on mode of inheritance: There is sufficient evidence to support the pathogenicity of both mono- and biallelic variant in the context of retinal disorders - and therefore, the MOI should be changed from 'monoallelic' to 'both mono- and biallelic' at the next GMS panel update.
Retinal disorders v2.200 IMPG1 Arina Puzriakova Mode of inheritance for gene: IMPG1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Retinal disorders v2.199 IMPG1 Arina Puzriakova commented on gene: IMPG1: Penetrance for gene IMPG1 was set to 'Incomplete' - asymptomatic heterozygous carriers of IMPG1 variants with normal clinical examinations have been observed (PMIDs: 23993198 and 32817297) indicating incomplete penetrance
Retinal disorders v2.199 IMPG1 Arina Puzriakova Penetrance for gene IMPG1 was set from to Complete
Tag Q3_21_MOI tag was added to IMPG1.
Retinal disorders v2.198 IMPG1 Arina Puzriakova Phenotypes for gene: IMPG1 were changed from Macular dystrophy, vitelliform, 4 to Macular dystrophy, vitelliform, 4, OMIM:616151; Retinitis pigmentosa, MONDO:0019200
Retinal disorders v2.197 IMPG1 Arina Puzriakova Publications for gene: IMPG1 were set to
Retinal disorders v2.196 IMPG1 Arina Puzriakova edited their review of gene: IMPG1: Changed phenotypes to: Macular dystrophy, vitelliform, 4, OMIM:616151, Retinitis pigmentosa, MONDO:0019200
Retinal disorders v2.196 IMPG1 Arina Puzriakova reviewed gene: IMPG1: Rating: GREEN; Mode of pathogenicity: None; Publications: 23993198, 28644393, 30589393, 30688845, 32817297; Phenotypes: Macular dystrophy, vitelliform, 4, OMIM:616151, Retinitis pigmentosa; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Fetal anomalies v1.703 COL4A2 Arina Puzriakova Publications for gene: COL4A2 were set to
Fetal anomalies v1.702 COL4A2 Arina Puzriakova reviewed gene: COL4A2: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Fetal anomalies v1.702 COL4A1 Arina Puzriakova reviewed gene: COL4A1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Fetal anomalies v1.702 COL4A1 Arina Puzriakova Publications for gene: COL4A1 were set to
Likely inborn error of metabolism v2.171 APOA5 Sarah Leigh commented on gene: APOA5: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.
Undiagnosed metabolic disorders v1.477 APOA5 Sarah Leigh commented on gene: APOA5: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.
Familial chylomicronaemia syndrome (FCS) v1.19 APOA5 Sarah Leigh commented on gene: APOA5: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.
Severe hypertriglyceridaemia v1.16 APOA5 Sarah Leigh commented on gene: APOA5: The Q3_21_MOI tag has been added to this gene as the MOI should be changed to - BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal.
Likely inborn error of metabolism v2.171 APOA5 Sarah Leigh Tag Q3_21_MOI tag was added to gene: APOA5.
Undiagnosed metabolic disorders v1.477 APOA5 Sarah Leigh Tag Q3_21_MOI tag was added to gene: APOA5.
Familial chylomicronaemia syndrome (FCS) v1.19 APOA5 Sarah Leigh Tag Q3_21_MOI tag was added to gene: APOA5.
Severe hypertriglyceridaemia v1.16 APOA5 Sarah Leigh Tag Q3_21_MOI tag was added to gene: APOA5.
Likely inborn error of metabolism v2.171 APOA5 Sarah Leigh edited their review of gene: APOA5: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for familial hypertriglycidaemia. Both risk polymorphisms (PMID 12417525; 12915450) and rarer APOA5 variants have been identified in hyperchylomicronemia, late-onset (OMIM:144650) and susceptibility to hypertriglyceridemia (OMIM:145750)(PMID: 23307945; 27678447; 16200213). In general, cases carrying biallelic variants (both polymorphisms and rarer variants) have a severer phenotype than monoallelic carriers (PMID: 12417525; 23307945; 27678447; 16200213).; Changed mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Undiagnosed metabolic disorders v1.477 APOA5 Sarah Leigh edited their review of gene: APOA5: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for familial hypertriglycidaemia. Both risk polymorphisms (PMID 12417525; 12915450) and rarer APOA5 variants have been identified in hyperchylomicronemia, late-onset (OMIM:144650) and susceptibility to hypertriglyceridemia (OMIM:145750)(PMID: 23307945; 27678447; 16200213). In general, cases carrying biallelic variants (both polymorphisms and rarer variants) have a severer phenotype than monoallelic carriers (PMID: 12417525; 23307945; 27678447; 16200213).; Changed mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder v1.140 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Dystonia; spastic paraplegia; intellectual disability to NESCAV syndrome, OMIM:614255
Childhood onset dystonia, chorea or related movement disorder v1.139 KIF1A Arina Puzriakova Classified gene: KIF1A as Amber List (moderate evidence)
Childhood onset dystonia, chorea or related movement disorder v1.139 KIF1A Arina Puzriakova Added comment: Comment on list classification: Dystonia can be feature of NESCAV syndrome (MIM# 614255) caused by heterozygous variants in this gene. However, KIF1A is associated with multiple phenotypes that do not include dystonia, and even NESCAV syndrome is more likely to be investigated in the context of other more prominent features such as spasticity and intellectual disability, for which this gene is already Green. For this reason, classifying as Amber on this panel.
Childhood onset dystonia, chorea or related movement disorder v1.139 KIF1A Arina Puzriakova Gene: kif1a has been classified as Amber List (Moderate Evidence).
Familial chylomicronaemia syndrome (FCS) v1.19 APOA5 Sarah Leigh reviewed gene: APOA5: 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 hypertriglyceridaemia v1.16 APOA5 Sarah Leigh edited their review of gene: APOA5: Added comment: Associated with relevant phenotype in OMIM and as confirmed Gen2Phen gene for familial hypertriglycidaemia. Both risk polymorphisms (PMID 12417525; 12915450) and rarer APOA5 variants have been identified in hyperchylomicronemia, late-onset (OMIM:144650) and susceptibility to hypertriglyceridemia (OMIM:145750)(PMID: 23307945; 27678447; 16200213). In general, cases carrying biallelic variants (both polymorphisms and rarer variants) have a severer phenotype than monoallelic carriers (PMID: 12417525; 23307945; 27678447; 16200213).; Changed rating: GREEN; Changed mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Ataxia and cerebellar anomalies - narrow panel v2.226 KIF1A Arina Puzriakova Classified gene: KIF1A as Amber List (moderate evidence)
Ataxia and cerebellar anomalies - narrow panel v2.226 KIF1A Arina Puzriakova Added comment: Comment on list classification: There are sufficient cases (>3) with monoallelic KIF1A variants and cerebellar atrophy and/or ataxia to rate as Green on this panel.
Ataxia and cerebellar anomalies - narrow panel v2.226 KIF1A Arina Puzriakova Gene: kif1a has been classified as Amber List (Moderate Evidence).
Ataxia and cerebellar anomalies - narrow panel v2.225 KIF1A Arina Puzriakova Added comment: Comment on mode of inheritance: Cerebellar anomalies associated with recessive KIF1A-related HSP are significantly milder than those observed in individuals with dominant HSP or NESCAV syndrome. There are also only 2 families with biallelic variants who presented with the relevant features, which does not reach the threshold for inclusion under this MOI at this time.

For this reason, the MOI has been set to 'monoallelic' only with the 'watchlist_MOI' tag to monitor future evidence linking biallelic variants with cerebellar ataxia.
Ataxia and cerebellar anomalies - narrow panel v2.225 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Ataxia and cerebellar anomalies - narrow panel v2.224 KIF1A Arina Puzriakova gene: KIF1A was added
gene: KIF1A was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature
Q3_21_rating, watchlist_moi tags were added to gene: KIF1A.
Mode of inheritance for gene: KIF1A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: KIF1A were set to 22258533; 28332297; 25265257; 26125038; 26354034; 31805580; 32096284; 32737135; 32746806; 34121983; https://doi.org/10.1016/j.ejpn.2017.04.926
Phenotypes for gene: KIF1A were set to Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Review for gene: KIF1A was set to GREEN
Added comment: KIF1A is associated HSP type 30 (MIM# 610357) which can be inherited recessively or dominantly, as well as NESCAV syndrome (MIM# 614255) caused by heterozygous variants in this gene.

Cerebellar signs including: ataxia; dysmetria; and saccadic ocular pursuit, associated with mild cerebellar atrophy, were reported in 2/4 families with recessive HSP (PMID: 21487076; 22258533; 28332297).

Variable ataxic features, cerebellar signs and cerebellar atrophy have been described in multiple cases with the complex forms of dominant KIF1A-related HSP (PMID: 31805580; 32737135), but these features are even more prominent in individuals with NESCAV syndrome (PMID: 25265257; 26125038; 26354034; 32096284; 34121983).

Of note, at least 11 heterozygous cases have been described in which congenital or early onset ataxia with cerebellar signs was the presenting clinical feature (PMID: 26354034; 32737135; 32746806; https://doi.org/10.1016/j.ejpn.2017.04.926)
Sources: Literature
Likely inborn error of metabolism v2.171 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 27678447; 16200213; 12417525; 23307945
Likely inborn error of metabolism v2.171 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 27678447; 16200213; 12417525
Undiagnosed metabolic disorders v1.477 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 12417525; 27678447; 16200213
Familial chylomicronaemia syndrome (FCS) v1.19 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 12417525; 27678447; 16200213
Severe hypertriglyceridaemia v1.16 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 12417525; 27678447; 16200213
Likely inborn error of metabolism v2.170 APOA5 Sarah Leigh Phenotypes for gene: APOA5 were changed from Hyperchylomicronemia, late-onset 144650; Familial hypertriglyceridaemia (Inherited hypertriglyceridaemias); {Hypertriglyceridemia, susceptibility to} 145750 to Hyperchylomicronemia, late-onset OMIM:144650; hyperlipoproteinemia type V MONDO:0007762; {Hypertriglyceridemia, susceptibility to} OMIM:145750; hypertriglyceridemia, familial MONDO:0007788
Undiagnosed metabolic disorders v1.476 APOA5 Sarah Leigh Phenotypes for gene: APOA5 were changed from Familial hypertriglyceridaemia (Inherited hypertriglyceridaemias); Hyperchylomicronemia, late-onset 144650; {Hypertriglyceridemia, susceptibility to} 145750 to Hyperchylomicronemia, late-onset OMIM:144650; hyperlipoproteinemia type V MONDO:0007762; {Hypertriglyceridemia, susceptibility to} OMIM:145750; hypertriglyceridemia, familial MONDO:0007788
Familial chylomicronaemia syndrome (FCS) v1.18 APOA5 Sarah Leigh Phenotypes for gene: APOA5 were changed from Hyperchylomicronemia, late-onset OMIM:144650; hyperlipoproteinemia type V MONDO:0007762 to Hyperchylomicronemia, late-onset OMIM:144650; hyperlipoproteinemia type V MONDO:0007762; {Hypertriglyceridemia, susceptibility to} OMIM:145750; hypertriglyceridemia, familial MONDO:0007788
Hereditary neuropathy or pain disorder v1.37 Ivone Leong List of related panels changed from R78 to R78; Hereditary neuropathy or pain disorder – NOT PMP22 copy number
Panel version 1.36 has been signed off on 2021-08-05
Adult onset leukodystrophy v1.26 Ivone Leong List of related panels changed from R62 to R62; Adult onset leukodystrophy
Panel version 1.25 has been signed off on 2021-08-05
Adult onset hereditary spastic paraplegia v1.28 Ivone Leong List of related panels changed from R60 to R60; Adult onset hereditary spastic paraplegia
Panel version 1.27 has been signed off on 2021-08-05
Adult onset neurodegenerative disorder v2.179 Ivone Leong List of related panels changed from R58 to R58; Adult onset neurodegenerative disorder
Panel version 2.178 has been signed off on 2021-08-05
Childhood onset dystonia, chorea or related movement disorder v1.138 Ivone Leong List of related panels changed from R57 to R57; Childhood onset dystonia; chorea or related movement disorder
Panel version 1.137 has been signed off on 2021-08-05
Adult onset dystonia, chorea or related movement disorder v1.122 Ivone Leong List of related panels changed from R56 to R56; Adult onset dystonia; chorea or related movement disorder
Panel version 1.121 has been signed off on 2021-08-05
Retinal disorders v2.196 Ivone Leong List of related panels changed from Posterior segment abnormalities; Cone Dysfunction Syndrome; Developmental macular and foveal dystrophy; Inherited macular dystrophy; Leber Congenital Amaurosis Early-Onset Severe Retinal Dystrophy; Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy; Leber Congenital Amaurosis or Early-Onset Severe Retinal Dystrophy; Rod Dysfunction Syndrome; Rod-cone dystrophy; Familial exudative vitreoretinopathy; Familial exudative retinopathy; R32; R33; R34; R35 to Posterior segment abnormalities; Cone Dysfunction Syndrome; Developmental macular and foveal dystrophy; Inherited macular dystrophy; Leber Congenital Amaurosis Early-Onset Severe Retinal Dystrophy; Leber Congenital Amaurosis / Early-Onset Severe Retinal Dystrophy; Leber Congenital Amaurosis or Early-Onset Severe Retinal Dystrophy; Rod Dysfunction Syndrome; Rod-cone dystrophy; Familial exudative vitreoretinopathy; Familial exudative retinopathy; R32; R33; R34; R35; Possible X-linked retinitis pigmentosa; Sorsby retinal dystrophy; Doyne retinal dystrophy
Panel version 2.195 has been signed off on 2021-08-05
Bilateral congenital or childhood onset cataracts v2.77 Ivone Leong List of related panels changed from R31 to R31; Bilateral congenital or childhood onset cataracts
Panel version 2.76 has been signed off on 2021-08-05
Familial dysautonomia v1.13 KIF1A Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'biallelic' to 'both mono- and biallelic' - features of dysautonomia are observed in multiple KIF1A-related phenotypes, including an autonomic-sensory neuropathy (MIM# 614213) associated with biallelic inheritance and NESCAV syndrome (MIM# 614255) caused by monoallelic variants in this gene. Therefore, both MOIs are pertinent to this panel.
Familial dysautonomia v1.13 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Familial dysautonomia v1.12 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Neuropathy, hereditary sensory, type IIC, OMIM:614213 to Neuropathy, hereditary sensory, type IIC, OMIM:614213; NESCAV syndrome, OMIM:614255
Familial dysautonomia v1.11 KIF1A Arina Puzriakova Publications for gene: KIF1A were set to 21820098; 21089229
Hereditary neuropathy v1.391 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Neuropathy, hereditary sensory, type IIC, 614213; Hereditary Sensory and Autonomic Neuropathy, Type II to Neuropathy, hereditary sensory, type IIC, OMIM:614213; Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Hereditary neuropathy or pain disorder v1.36 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Hereditary Sensory and Autonomic Neuropathy, Type II; Neuropathy, hereditary sensory, type IIC, 614213 to Neuropathy, hereditary sensory, type IIC, OMIM:614213; Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Hereditary neuropathy or pain disorder v1.35 KIF1A Arina Puzriakova Tag Q3_21_MOI tag was added to gene: KIF1A.
Tag Q3_21_expert_review tag was added to gene: KIF1A.
Hereditary neuropathy or pain disorder v1.35 KIF1A Arina Puzriakova Added comment: Comment on mode of inheritance: Biallelic variants are associated with autonomic-sensory neuropathy (MIM# 614213). KIF1A is also associated HSP type 30 (MIM# 610357) which can be inherited recessively or dominantly, as well as NESCAV syndrome (MIM# 614255) caused by heterozygous variants in this gene - both monoallelic conditions have been shown to include peripheral sensorimotor neuropathy.

For this reason, the MOI could be changed from 'biallelic' to 'both mono- and biallelic' if it is decided to include genes on this panel that cause neuropathy as part of a more complex phenotype (tagged for GMS review)
Hereditary neuropathy or pain disorder v1.35 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Severe hypertriglyceridaemia v1.15 APOA5 Sarah Leigh Phenotypes for gene: APOA5 were changed from Hyperchylomicronemia, late-onset 144650; {Hypertriglyceridemia, susceptibility to} 145750 to Hyperchylomicronemia, late-onset OMIM:144650; hyperlipoproteinemia type V MONDO:0007762; {Hypertriglyceridemia, susceptibility to} OMIM:145750; hypertriglyceridemia, familial MONDO:0007788
Hereditary neuropathy v1.390 KIF1A Arina Puzriakova Added comment: Comment on mode of inheritance: Biallelic variants are associated with autonomic-sensory neuropathy (MIM# 614213). KIF1A is also associated HSP type 30 (MIM# 610357) which can be inherited recessively or dominantly, as well as NESCAV syndrome (MIM# 614255) caused by heterozygous variants in this gene - both monoallelic conditions have been shown to include peripheral sensorimotor neuropathy.

For this reason, the MOI has been changed from 'biallelic' to 'both mono- and biallelic'
Hereditary neuropathy v1.390 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Severe hypertriglyceridaemia v1.14 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 16200213
Familial chylomicronaemia syndrome (FCS) v1.17 APOA5 Sarah Leigh Publications for gene: APOA5 were set to
Undiagnosed metabolic disorders v1.475 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 27678447; 16200213
Likely inborn error of metabolism v2.169 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 27678447; 16200213
Likely inborn error of metabolism v2.168 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 27678447; 16200213
Likely inborn error of metabolism v2.168 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308; 27678447; 16200213
Likely inborn error of metabolism v2.167 PIGS Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.167 PIGS Arina Puzriakova gene: PIGS was added
gene: PIGS was added to Inborn errors of metabolism. Sources: Expert Review Amber,Expert list
for-review tags were added to gene: PIGS.
Mode of inheritance for gene: PIGS was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PIGS were set to 30269814
Phenotypes for gene: PIGS were set to Glycosylphosphatidylinositol biosynthesis defect 18 618143
Likely inborn error of metabolism v2.166 GMPPA Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.166 GMPPA Arina Puzriakova gene: GMPPA was added
gene: GMPPA was added to Inborn errors of metabolism. Sources: Expert Review Amber,Expert list
for-review tags were added to gene: GMPPA.
Mode of inheritance for gene: GMPPA was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GMPPA were set to 24035193; 28574218
Phenotypes for gene: GMPPA were set to Alacrima, achalasia, and mental retardation syndrome (MIM# 615510)
Likely inborn error of metabolism v2.165 GALNT2 Arina Puzriakova Tag for-review was removed from gene: GALNT2.
Tag Q2_21_rating tag was added to gene: GALNT2.
Likely inborn error of metabolism v2.165 GALNT2 Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.165 GALNT2 Arina Puzriakova gene: GALNT2 was added
gene: GALNT2 was added to Inborn errors of metabolism. Sources: Expert Review Amber,Literature
for-review tags were added to gene: GALNT2.
Mode of inheritance for gene: GALNT2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GALNT2 were set to 27508872; 32293671
Phenotypes for gene: GALNT2 were set to Congenital disorder of glycosylation, type IIt 618885
Likely inborn error of metabolism v2.164 FUK Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.164 FUK Arina Puzriakova gene: FUK was added
gene: FUK was added to Inborn errors of metabolism. Sources: Expert Review Amber,Expert list
watchlist, new-gene-name tags were added to gene: FUK.
Mode of inheritance for gene: FUK was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FUK were set to 30503518
Phenotypes for gene: FUK were set to Congenital disorder of glycosylation with defective fucosylation 2 OMIM:618324; congenital disorder of glycosylation with defective fucosylation 2 MONDO:0020777
Likely inborn error of metabolism v2.163 EOGT Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.163 EOGT Arina Puzriakova gene: EOGT was added
gene: EOGT was added to Inborn errors of metabolism. Sources: Expert Review Amber,Expert list
Q2_21_rating tags were added to gene: EOGT.
Mode of inheritance for gene: EOGT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EOGT were set to 23522784; 31368252; 29924900
Phenotypes for gene: EOGT were set to Adams-Oliver syndrome 4 OMIM:615297; Adams-Oliver syndrome 4 MONDO:0014124
Likely inborn error of metabolism v2.162 SSR3 Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.162 SSR3 Arina Puzriakova gene: SSR3 was added
gene: SSR3 was added to Inborn errors of metabolism. Sources: Expert Review Amber,Literature
Mode of inheritance for gene: SSR3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SSR3 were set to 30945312
Phenotypes for gene: SSR3 were set to Congenital disorder of glycosylation
Likely inborn error of metabolism v2.161 CSGALNACT1 Arina Puzriakova Tag for-review was removed from gene: CSGALNACT1.
Tag Q2_21_rating tag was added to gene: CSGALNACT1.
Likely inborn error of metabolism v2.161 CSGALNACT1 Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.161 CSGALNACT1 Arina Puzriakova gene: CSGALNACT1 was added
gene: CSGALNACT1 was added to Inborn errors of metabolism. Sources: Expert list,Expert Review Amber
for-review tags were added to gene: CSGALNACT1.
Mode of inheritance for gene: CSGALNACT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CSGALNACT1 were set to 31705726; 31325655; 31705726
Phenotypes for gene: CSGALNACT1 were set to Congenital disorder of glycosylation; Skeletal dysplasia, mild, with joint laxity and advanced bone age OMIM:618870; skeletal dysplasia, mild, with joint laxity and advanced bone age MONDO:0030029
Likely inborn error of metabolism v2.160 B4GALNT1 Arina Puzriakova Entity copied from Congenital disorders of glycosylation v2.74
Likely inborn error of metabolism v2.160 B4GALNT1 Arina Puzriakova gene: B4GALNT1 was added
gene: B4GALNT1 was added to Inborn errors of metabolism. Sources: Expert Review Amber,Expert list
Q2_21_rating tags were added to gene: B4GALNT1.
Mode of inheritance for gene: B4GALNT1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: B4GALNT1 were set to 23746551; 24103911
Phenotypes for gene: B4GALNT1 were set to Spastic paraplegia 26, autosomal recessive, OMIM:609195; Hereditary spastic paraplegia 26, MONDO:0012213
Congenital disorders of glycosylation v2.74 B4GALNT1 Arina Puzriakova Phenotypes for gene: B4GALNT1 were changed from Spastic paraplegia 26, autosomal recessive OMIM:609195; hereditary spastic paraplegia 26 MONDO:0012213 to Spastic paraplegia 26, autosomal recessive, OMIM:609195; Hereditary spastic paraplegia 26, MONDO:0012213
Congenital disorders of glycosylation v2.73 SSR3 Arina Puzriakova Classified gene: SSR3 as Amber List (moderate evidence)
Congenital disorders of glycosylation v2.73 SSR3 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. SSR3 is currently not associated with any phenotype in OMIM or G2P. Only a single case reported to date (PMID: 30945312); however, supported by functional data. Variants in other TRAP complex subunits (e.g. SSR4) have been shown to cause a CDG.

Rating Amber, awaiting further cases prior to inclusion as diagnostic-grade.
Congenital disorders of glycosylation v2.73 SSR3 Arina Puzriakova Gene: ssr3 has been classified as Amber List (Moderate Evidence).
Congenital disorders of glycosylation v2.72 SSR3 Arina Puzriakova Phenotypes for gene: SSR3 were changed from Congenital disorder of glycosylation, type Iu, MIM#615042 to Congenital disorder of glycosylation
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 MCM4 Zornitza Stark reviewed gene: MCM4: Rating: AMBER; Mode of pathogenicity: None; Publications: 22354167, 22354170, 22499342; Phenotypes: Immunodeficiency 54, MIM# 609981; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies v1.701 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from MENTAL RETARDATION, AUTOSOMAL DOMINANT 9; NEUROPATHY, HEREDITARY SENSORY, TYPE IIC to NEUROPATHY, HEREDITARY SENSORY, TYPE IIC, 614213; NESCAV SYNDROME, 614255
DDG2P v2.41 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from NEUROPATHY, HEREDITARY SENSORY, TYPE IIC 614213; MENTAL RETARDATION, AUTOSOMAL DOMINANT 9 614255 to NEUROPATHY, HEREDITARY SENSORY, TYPE IIC, 614213; NESCAV SYNDROME, 614255
Adult onset neurodegenerative disorder v2.178 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Spastic paraplegia 30, autosomal recessive to Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Adult onset neurodegenerative disorder v2.177 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Adult onset neurodegenerative disorder v2.176 KIF1A Arina Puzriakova Tag watchlist was removed from gene: KIF1A.
Hereditary spastic paraplegia v1.232 KIF1A Arina Puzriakova Publications for gene: KIF1A were set to Erlich et al. (2011)
Childhood onset hereditary spastic paraplegia v2.49 KIF1A Arina Puzriakova Publications for gene: KIF1A were set to 21487076; 22258533; 28362824
Adult onset hereditary spastic paraplegia v1.27 KIF1A Arina Puzriakova Publications for gene: KIF1A were set to 21487076; 22258533; 28362824
Hereditary spastic paraplegia v1.231 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Spastic paraplegia 30, autosomal recessive to Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Adult onset hereditary spastic paraplegia v1.26 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Spastic paraplegia 30, autosomal recessive, 610357; Neuropathy, hereditary sensory, type IIC, 614213, AR; Mental retardation, autosomal dominant 9, 614255, AD to Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Childhood onset hereditary spastic paraplegia v2.48 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Spastic paraplegia 30, autosomal recessive, 610357; Mental retardation, autosomal dominant 9, 614255, AD; Neuropathy, hereditary sensory, type IIC, 614213 to Spastic paraplegia 30, autosomal dominant, OMIM:610357; Spastic paraplegia 30, autosomal recessive, OMIM:610357; NESCAV syndrome, OMIM:614255
Hereditary spastic paraplegia v1.230 KIF1A Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'biallelic' only to 'both mono- and biallelic'

De novo and inherited heterozygous variants in the motor domain have been identified in patients with pure and complex HSP. Variants outside motor domain reported to be biallelic. Both adult and childhood onset. Null alleles show biallelic inheritance.
Hereditary spastic paraplegia v1.230 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.402 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Mental retardation, autosomal dominant 9 614255 to NESCAV syndrome, OMIM:614255
Intellectual disability v3.1216 KIF1A Arina Puzriakova Added comment: Comment on mode of inheritance: ID is most prominent in patients with NESCAV syndrome (MIM# 614255) caused by monoallelic variants in this gene. KIF1A is also associated HSP type 30 (MIM# 610357) which can be inherited recessively or dominantly - however, mostly only the dominant form has been shown to involve some variable cognitive impairment. Of the 4 families reported to date with recessive HSP (PMID: 21487076; 22258533; 28332297), only 1 presented with ID (PMID: 28332297).

Therefore, MOI should remain at 'monoallelic' only on this panel.
Intellectual disability v3.1216 KIF1A Arina Puzriakova Mode of inheritance for gene: KIF1A was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability v3.1215 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Mental Retardation, Dominant; Spastic paraplegia 30, autosomal recessive, 610357Neuropathy, hereditary sensory, type IIC, 614213Mental retardation, autosomal dominant 9, 614255; MENTAL RETARDATION, AUTOSOMAL DOMINANT 9 to NESCAV syndrome, OMIM:614255; Spastic paraplegia 30, autosomal dominant, OMIM:610357
Paroxysmal central nervous system disorders v1.17 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Hereditary Sensory and Autonomic Neuropathy, Type II; Neuropathy, hereditary sensory, type IIC, 614213 to Neuropathy, hereditary sensory, type IIC, OMIM:614213
Pain syndromes v1.10 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Neuropathy, hereditary sensory, type IIC, 614213; Hereditary Sensory and Autonomic Neuropathy, Type II to Neuropathy, hereditary sensory, type IIC, OMIM:614213
Familial dysautonomia v1.10 KIF1A Arina Puzriakova Phenotypes for gene: KIF1A were changed from Neuropathy, hereditary sensory, type IIC 614213 to Neuropathy, hereditary sensory, type IIC, OMIM:614213
Undiagnosed metabolic disorders v1.474 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308
Likely inborn error of metabolism v2.159 APOA5 Sarah Leigh Publications for gene: APOA5 were set to 27604308
Likely inborn error of metabolism v2.158 APOA1 Sarah Leigh commented on gene: APOA1: Both biallelic and monoallelic APOA1 variants are associated with OMIM:618463, however, heterozygous cases have either a milder phenotype or are unaffected. Certain heterozygous APOA1 variants are regarded as Amyloidogenic and are associated with OMIM:105200 (PMID 32022753, 24 variants listed in table 1).
Undiagnosed metabolic disorders v1.473 APOA1 Sarah Leigh commented on gene: APOA1: Both biallelic and monoallelic APOA1 variants are associated with OMIM:618463, however, heterozygous cases have either a milder phenotype or are unaffected. Certain heterozygous APOA1 variants are regarded as Amyloidogenic and are associated with OMIM:105200 (PMID 32022753, 24 variants listed in table 1).
Likely inborn error of metabolism v2.158 APOA1 Sarah Leigh Phenotypes for gene: APOA1 were changed from Corneal clouding, autosomal recessive; Apolipoprotein A-I deficiency (Disorders of high density lipoprotein metabolism); ApoA-I and apoC-III deficiency, combined; Amyloidosis, 3 or more types 105200; Hypoalphalipoproteinemia 604091 to Amyloidosis, 3 or more types OMIM:105200; familial visceral amyloidosis MONDO:0007099; ApoA-I and apoC-III deficiency, combined OMIM:618463; Hypoalphalipoproteinemia, primary, 2, with or without corneal clouding OMIM:618463; hypoalphalipoproteinemia, primary, 2 MONDO:0032766
Undiagnosed metabolic disorders v1.473 APOA1 Sarah Leigh Phenotypes for gene: APOA1 were changed from Apolipoprotein A-I deficiency (Disorders of high density lipoprotein metabolism); Amyloidosis, 3 or more types 105200; ApoA-I and apoC-III deficiency, combined; Corneal clouding, autosomal recessive; Hypoalphalipoproteinemia 604091 to Amyloidosis, 3 or more types OMIM:105200; familial visceral amyloidosis MONDO:0007099; ApoA-I and apoC-III deficiency, combined OMIM:618463; Hypoalphalipoproteinemia, primary, 2, with or without corneal clouding OMIM:618463; hypoalphalipoproteinemia, primary, 2 MONDO:0032766
Undiagnosed metabolic disorders v1.472 APOA1 Sarah Leigh Publications for gene: APOA1 were set to 27604308
Likely inborn error of metabolism v2.157 APOA1 Sarah Leigh Publications for gene: APOA1 were set to 27604308
Periodic fever syndromes v1.15 APOA1 Sarah Leigh Added comment: Comment on mode of inheritance: Both biallelic and monoallelic variants have been associated with ApoA-I and apoC-III deficiency, combined OMIM:618463;
Hypoalphalipoproteinemia, primary, 2, with or without corneal clouding OMIM:618463;hypoalphalipoproteinemia, primary, 2 MONDO:0032766
Periodic fever syndromes v1.15 APOA1 Sarah Leigh Mode of inheritance for gene: APOA1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Periodic fever syndromes v1.14 APOA1 Sarah Leigh reviewed gene: APOA1: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Periodic fever syndromes v1.14 APOA1 Sarah Leigh Publications for gene: APOA1 were set to PMID: 26515634; 12050338; 27240838
Hereditary systemic amyloidosis v1.11 APOA1 Sarah Leigh changed review comment from: It would appear that certain heterozygous APOA1 variants are associated with Amyloidosis, 3 or more types OMIM:105200 (PMID 32022753, table 1).; to: It would appear that certain heterozygous APOA1 variants are associated with Amyloidosis, 3 or more types OMIM:105200 (PMID 32022753, 24 variants listed in table 1).
Hereditary systemic amyloidosis v1.11 APOA1 Sarah Leigh edited their review of gene: APOA1: Added comment: It would appear that certain heterozygous APOA1 variants are associated with Amyloidosis, 3 or more types OMIM:105200 (PMID 32022753, table 1).; Changed rating: GREEN; Changed publications to: 32022753
Hereditary systemic amyloidosis v1.11 APOA1 Sarah Leigh Publications for gene: APOA1 were set to 27240838; 21820994; 16925563
Hereditary systemic amyloidosis v1.10 APOA1 Sarah Leigh Added comment: Comment on mode of inheritance: Both biallelic and monoallelic variants have been associated with ApoA-I and apoC-III deficiency, combined OMIM:618463;
Hypoalphalipoproteinemia, primary, 2, with or without corneal clouding OMIM:618463;hypoalphalipoproteinemia, primary, 2 MONDO:0032766
Hereditary systemic amyloidosis v1.10 APOA1 Sarah Leigh Mode of inheritance for gene: APOA1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Hereditary systemic amyloidosis v1.9 APOA1 Sarah Leigh Phenotypes for gene: APOA1 were changed from Amyloidosis, 3 or more types 105200 to Amyloidosis, 3 or more types OMIM:105200; familial visceral amyloidosis MONDO:0007099
Retinal disorders v2.195 CRB1 Ivone Leong Added comment: Comment on phenotypes: Previously:
Leber Congenital Amaurosis;Retinitis pigmentosa-12, autosomal recessive, 600105Leber congenital amaurosis 8, 613835Pigmented paravenous chorioretinal atrophy, 172870;Eye Disorders;Retinitis pigmentosa;Retinitis Pigmentosa, Recessive;Retinitis pigmentosa-12, autosomal recessive, 600105
Retinal disorders v2.195 CRB1 Ivone Leong Phenotypes for gene: CRB1 were changed from Leber Congenital Amaurosis; Retinitis pigmentosa-12, autosomal recessive, 600105Leber congenital amaurosis 8, 613835Pigmented paravenous chorioretinal atrophy, 172870; Eye Disorders; Retinitis pigmentosa; Retinitis Pigmentosa, Recessive; Retinitis pigmentosa-12, autosomal recessive, 600105 to Leber Congenital Amaurosis, OMIM:613835; Retinitis pigmentosa-12, OMIM:600105
White matter disorders and cerebral calcification - narrow panel v1.190 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from General Leukodystrophy & Mitochondrial Leukoencephalopathy; Mitochondrial Leukoencephalopathy; Coenzyme Q10 deficiency, primary, 1 to General Leukodystrophy & Mitochondrial Leukoencephalopathy; Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Unexplained young onset end-stage renal disease v1.20 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Coenzyme Q10 deficiency, primary, 1 301050 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Likely inborn error of metabolism v2.156 COQ2 Ivone Leong Added comment: Comment on phenotypes: Previously:
{Multiple system atrophy, susceptibility to}, 146500;Coenzyme Q10 deficiency;Disorders of CoQ10 biosynthesis (Mitochondrial respiratory chain disorders (caused by nuclear variants only));Disorders of ubiquinone metabolism and biosynthesis;Coenzyme Q10 deficiency, primary, 1, 607426
Likely inborn error of metabolism v2.156 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from {Multiple system atrophy, susceptibility to}, 146500; Coenzyme Q10 deficiency; Disorders of CoQ10 biosynthesis (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Disorders of ubiquinone metabolism and biosynthesis; Coenzyme Q10 deficiency, primary, 1, 607426 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Undiagnosed metabolic disorders v1.471 COQ2 Ivone Leong Added comment: Comment on phenotypes: Previously:
Disorders of CoQ10 biosynthesis (Mitochondrial respiratory chain disorders (caused by nuclear variants only));Disorders of ubiquinone metabolism and biosynthesis;Coenzyme Q10 deficiency, primary, 1, 607426;Coenzyme Q10 deficiency;{Multiple system atrophy, susceptibility to}, 146500
Undiagnosed metabolic disorders v1.471 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Disorders of CoQ10 biosynthesis (Mitochondrial respiratory chain disorders (caused by nuclear variants only)); Disorders of ubiquinone metabolism and biosynthesis; Coenzyme Q10 deficiency, primary, 1, 607426; Coenzyme Q10 deficiency; {Multiple system atrophy, susceptibility to}, 146500 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Inherited white matter disorders v1.130 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Coenzyme Q10 deficiency, primary, 1; Mitochondrial Leukoencephalopathy; General Leukodystrophy & Mitochondrial Leukoencephalopathy to Coenzyme Q10 deficiency, primary, 1, OMIM:607426; General Leukodystrophy & Mitochondrial Leukoencephalopathy
Unexplained kidney failure in young people v1.93 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Coenzyme Q10 deficiency, primary, 1 607426 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Possible mitochondrial disorder - nuclear genes v1.50 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Coenzyme Q10 deficiency, primary, 1, 607426 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Early onset or syndromic epilepsy v2.401 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Coenzyme Q10 deficiency, primary, 1 607426 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Mitochondrial disorders v2.48 COQ2 Ivone Leong Added comment: Comment on phenotypes: Previously:
Disorders of ubiquinone metabolism and biosynthesis;Coenzyme Q10 deficiency, primary, 1, 607426;Coenzyme Q10 deficiency;{Multiple system atrophy, susceptibility to}, 146500
Mitochondrial disorders v2.48 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Disorders of ubiquinone metabolism and biosynthesis; Coenzyme Q10 deficiency, primary, 1, 607426; Coenzyme Q10 deficiency; {Multiple system atrophy, susceptibility to}, 146500 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Proteinuric renal disease v2.52 COQ2 Ivone Leong Phenotypes for gene: COQ2 were changed from Coenzyme Q10 deficiency, primary, 1 #607426 to Coenzyme Q10 deficiency, primary, 1, OMIM:607426
Intellectual disability v3.1214 COG5 Ivone Leong Tag Q3_21_MOI tag was added to gene: COG5.
Intellectual disability v3.1214 COG5 Ivone Leong changed review comment from: MOI should be changed from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BIALLELIC, autosomal or pseudoautosomal".; to: MOI should be changed from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BIALLELIC, autosomal or pseudoautosomal".
Intellectual disability v3.1214 COG5 Ivone Leong reviewed gene: COG5: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Congenital muscular dystrophy v2.14 CAVIN1 Ivone Leong Tag Q3_21_rating tag was added to gene: CAVIN1.
Congenital muscular dystrophy v2.14 CAVIN1 Ivone Leong Classified gene: CAVIN1 as Amber List (moderate evidence)
Congenital muscular dystrophy v2.14 CAVIN1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM but not Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Congenital muscular dystrophy v2.14 CAVIN1 Ivone Leong Gene: cavin1 has been classified as Amber List (Moderate Evidence).
Congenital muscular dystrophy v2.13 CAVIN1 Ivone Leong Phenotypes for gene: CAVIN1 were changed from Lipodystrophy, congenital generalized, type 4 (MIM#613327) to Lipodystrophy, congenital generalized, type 4, OMIM:613327
Congenital myaesthenic syndrome v2.37 SYT2 Ivone Leong edited their review of gene: SYT2: Added comment: Based on the expert review by Zornitza Stark (Australian Genomics), the MOI should be changed from Monoallelic to Both monoallelic and biallelic. It should be noted that in OMIM, this gene has been given an AD MOI and in Gene2Phenotype, it has been given a biallelic MOI.; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Congenital myaesthenic syndrome v2.37 SYT2 Ivone Leong Tag Q3_21_MOI tag was added to gene: SYT2.
Congenital myaesthenic syndrome v2.37 SYT2 Ivone Leong Publications for gene: SYT2 were set to 26519543; 25192047; 27472506; 30533528
Cerebral vascular malformations v2.57 CBL Ivone Leong Tag Q3_21_rating tag was added to gene: CBL.
Cerebral vascular malformations v2.57 CBL Ivone Leong reviewed gene: CBL: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Cerebral vascular malformations v2.57 CBL Ivone Leong Phenotypes for gene: CBL were changed from early-onset moyamoya angiopathy; Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia, OMIM:613563 to early-onset moyamoya angiopathy; moyamoya disease, MONDO:0016820; Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia, OMIM:613563
Cerebral vascular malformations v2.56 CBL Ivone Leong Publications for gene: CBL were set to 28343148; 25283271
Infantile enterocolitis & monogenic inflammatory bowel disease v1.22 ADAM17 Ivone Leong Classified gene: ADAM17 as Green List (high evidence)
Infantile enterocolitis & monogenic inflammatory bowel disease v1.22 ADAM17 Ivone Leong Added comment: Comment on list classification: Promoted from Amber to Green. This gene is associated with a phenotype in OMIM but not Gene2Phenotype. There is enough evidence to support a gene-disease association, therefore this gene has been promoted to Green.
Infantile enterocolitis & monogenic inflammatory bowel disease v1.22 ADAM17 Ivone Leong Gene: adam17 has been classified as Green List (High Evidence).
Infantile enterocolitis & monogenic inflammatory bowel disease v1.21 ADAM17 Ivone Leong Phenotypes for gene: ADAM17 were changed from ADAM-17 deficiency; Inflammatory skin and bowel disease, neonatal, 1 614328 to ADAM-17 deficiency; ?Inflammatory skin and bowel disease, neonatal, 1, OMIM:614328
Infantile enterocolitis & monogenic inflammatory bowel disease v1.20 ADAM17 Ivone Leong Added comment: Comment on publications: Previously:
functional/mouse model evidence that ADAM17 deficiency leads to colitis - 22236242, 27077118, 21041656, 20603312,19299578
Infantile enterocolitis & monogenic inflammatory bowel disease v1.20 ADAM17 Ivone Leong Publications for gene: ADAM17 were set to 22010916; functional/mouse model evidence that ADAM17 deficiency leads to colitis - 22236242, 27077118, 21041656, 20603312,19299578
Limb disorders v2.49 TBX4 Ivone Leong Phenotypes for gene: TBX4 were changed from Ischiocoxopodopatellar syndrome 147891 to Ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension, OMIM:147891
Pulmonary arterial hypertension v2.16 TBX4 Ivone Leong Phenotypes for gene: TBX4 were changed from Ischiocoxopodopatellar syndrome, 147891; Small patella syndrome; SPS; Idiopathic pulmonary arterial hypertension; IPAH; Heritable pulmonary arterial hypertension; HPAH; Pulmonary arterial hypertension to Ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension, OMIM:147891
Fetal anomalies v1.700 TBX4 Ivone Leong Phenotypes for gene: TBX4 were changed from SMALL PATELLA SYNDROME to Ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension, OMIM:147891
Skeletal dysplasia v2.113 TBX4 Ivone Leong Phenotypes for gene: TBX4 were changed from Ischiocoxopodopatellar syndrome 147891; Ischiocoxopodopatellar syndrome 147891 to Ischiocoxopodopatellar syndrome with or without pulmonary arterial hypertension, OMIM:147891
Retinal disorders v2.194 TSPAN12 Ivone Leong Phenotypes for gene: TSPAN12 were changed from Eye Disorders to Eye Disorders; Exudative vitreoretinopathy 5, OMIM:613310
Familial chylomicronaemia syndrome (FCS) v1.16 APOB Ivone Leong Tag Q3_21_NHS_review was removed from gene: APOB.
Familial chylomicronaemia syndrome (FCS) v1.16 APOB Ivone Leong Tag Q3_21_NHS_review tag was added to gene: APOB.
Primary lymphoedema v2.15 TIE1 Ivone Leong Tag watchlist tag was added to gene: TIE1.
Primary lymphoedema v2.15 TIE1 Ivone Leong Classified gene: TIE1 as Amber List (moderate evidence)
Primary lymphoedema v2.15 TIE1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. Based on the expert review this gene has been given an Amber rating until more evidence is available.
Primary lymphoedema v2.15 TIE1 Ivone Leong Gene: tie1 has been classified as Amber List (Moderate Evidence).
Primary lymphoedema v2.14 TIE1 Ivone Leong Phenotypes for gene: TIE1 were changed from Lymphatic malformation 11, MIM# 619401 to Lymphatic malformation 11, OMIM:619401
Fetal anomalies v1.699 TWIST2 Ivone Leong Added comment: Comment on phenotypes: Also associated with Focal facial dermal dysplasia 3, Setleis type, OMIM:227260
Fetal anomalies v1.699 TWIST2 Ivone Leong Phenotypes for gene: TWIST2 were changed from ABLEPHARON MACROSTOMIA SYNDROME; SETLEIS SYNDROME; Ablepharon-macrostomia syndrome, 200110; Barber-Say syndrome, 209885 to Ablepharon-macrostomia syndrome, 200110; Barber-Say syndrome, 209885
DDG2P v2.40 TWIST2 Ivone Leong Phenotypes for gene: TWIST2 were changed from ABLEPHARON MACROSTOMIA SYNDROME 200110; SETLEIS SYNDROME 227260 to ABLEPHARON MACROSTOMIA SYNDROME, OMIM:200110; Focal facial dermal dysplasia 3, Setleis type, OMIM:227260
Familial Tumours Syndromes of the central & peripheral Nervous system v1.10 VHL Ivone Leong Phenotypes for gene: VHL were changed from Von Hippel-Lindau Syndrome; von Hippel-Lindau syndrome, 193300; Renal cell carcinoma, somatic, 144700; Pheochromocytoma, 171300; Hemangioblastoma, cerebellar, somatic; Erythrocytosis, familial, 2, 263400 to von Hippel-Lindau syndrome, OMIM:193300; Pheochromocytoma, OMIM:171300; Hemangioblastoma, cerebellar, somatic
Multiple endocrine tumours v1.13 VHL Ivone Leong Phenotypes for gene: VHL were changed from Endocrine Cancer; Pheochromocytoma, OMIM:171300; von Hippel-Lindau syndrome, OMIM:193300 to Endocrine Cancer; Pheochromocytoma, OMIM:171300; von Hippel-Lindau syndrome, OMIM:193300; Paragangliomas, MONDO:0000448
Multiple endocrine tumours v1.12 VHL Ivone Leong Added comment: Comment on phenotypes: Previously:
Endocrine Cancer; Paragangliomas 1, with or without deafness, 168000; Pheochromocytoma, 171300; Carcinoid tumors, intestinal, 114900; Merkel cell carcinoma, somatic; Paraganglioma and gastric stromal sarcoma, 606864; Cowden syndrome 3, 615106
Multiple endocrine tumours v1.12 VHL Ivone Leong Phenotypes for gene: VHL were changed from Endocrine Cancer; Paragangliomas 1, with or without deafness, 168000; Pheochromocytoma, 171300; Carcinoid tumors, intestinal, 114900; Merkel cell carcinoma, somatic; Paraganglioma and gastric stromal sarcoma, 606864; Cowden syndrome 3, 615106 to Endocrine Cancer; Pheochromocytoma, OMIM:171300; von Hippel-Lindau syndrome, OMIM:193300
Inherited phaeochromocytoma and paraganglioma v1.9 VHL Ivone Leong Phenotypes for gene: VHL were changed from Pheochromocytoma, OMIM:171300 to Pheochromocytoma, OMIM:171300; von Hippel-Lindau syndrome, OMIM:193300
Inherited phaeochromocytoma and paraganglioma excluding NF1 v1.19 VHL Ivone Leong Phenotypes for gene: VHL were changed from Pheochromocytoma, OMIM:171300 to Pheochromocytoma, OMIM:171300; von Hippel-Lindau syndrome, OMIM:193300
Inherited phaeochromocytoma and paraganglioma v1.8 VHL Ivone Leong Publications for gene: VHL were set to
Inherited phaeochromocytoma and paraganglioma v1.7 VHL Ivone Leong Phenotypes for gene: VHL were changed from von Hippel-Lindau syndrome, 193300Renal cell carcinoma, somatic, 144700Pheochromocytoma, 171300Hemangioblastoma, cerebellar, somaticErythrocytosis, familial, 2, 263400 to Pheochromocytoma, OMIM:171300
Inherited phaeochromocytoma and paraganglioma excluding NF1 v1.18 VHL Ivone Leong Phenotypes for gene: VHL were changed from von Hippel-Lindau syndrome, 193300Renal cell carcinoma, somatic, 144700Pheochromocytoma, 171300Hemangioblastoma, cerebellar, somaticErythrocytosis, familial, 2, 263400 to Pheochromocytoma, OMIM:171300
Inherited phaeochromocytoma and paraganglioma excluding NF1 v1.17 VHL Ivone Leong Publications for gene: VHL were set to
Likely inborn error of metabolism v2.155 VKORC1 Ivone Leong Phenotypes for gene: VKORC1 were changed from Vitamin K epoxide reductase deficiency (Other disorders of vitamins and cofactors); Inherited bleeding disorders to Vitamin K-dependent clotting factors, combined deficiency of, 2, OMIM:607473
Undiagnosed metabolic disorders v1.470 VKORC1 Ivone Leong Phenotypes for gene: VKORC1 were changed from Vitamin K epoxide reductase deficiency (Other disorders of vitamins and cofactors); Inherited bleeding disorders to Vitamin K-dependent clotting factors, combined deficiency of, 2, OMIM:607473
Inherited bleeding disorders v1.164 VKORC1 Ivone Leong Phenotypes for gene: VKORC1 were changed from Multiple coagulation factor deficiency type 2 to Vitamin K-dependent clotting factors, combined deficiency of, 2, OMIM:607473
Bleeding and platelet disorders v1.31 VKORC1 Ivone Leong Phenotypes for gene: VKORC1 were changed from 607473 Vitamin K-dependent clotting factors, combined deficiency of, 2; 122700 Warfarin resistance to Vitamin K-dependent clotting factors, combined deficiency of, 2, OMIM:607473; Warfarin resistance, OMIM:122700
Hereditary spastic paraplegia v1.229 WASHC5 Ivone Leong Publications for gene: WASHC5 were set to Valdmanis et al. (2007)
Hereditary spastic paraplegia v1.228 WASHC5 Ivone Leong Phenotypes for gene: WASHC5 were changed from Spastic paraplegia 8, autosomal dominant to Spastic paraplegia 8, autosomal dominant, OMIM:603563
Childhood onset hereditary spastic paraplegia v2.47 WASHC5 Ivone Leong Phenotypes for gene: WASHC5 were changed from Spastic paraplegia 8, autosomal dominant, 603563 to Spastic paraplegia 8, autosomal dominant, OMIM:603563
Adult onset hereditary spastic paraplegia v1.25 WASHC5 Ivone Leong Phenotypes for gene: WASHC5 were changed from Spastic paraplegia 8, autosomal dominant, 603563 to Spastic paraplegia 8, autosomal dominant, OMIM:603563
Gastrointestinal neuromuscular disorders v1.15 RAD21 Zornitza Stark gene: RAD21 was added
gene: RAD21 was added to Gastrointestinal neuromuscular disorders. Sources: Expert Review
Mode of inheritance for gene: RAD21 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RAD21 were set to 14638363; 32193685; 25575569
Phenotypes for gene: RAD21 were set to Mungan syndrome, MIM# 611376
Review for gene: RAD21 was set to GREEN
Added comment: Mono-allelic variants are associated with CdL but bi-allelic variants are associated with Mungan syndrome, which includes pseudo-obstruction.
Sources: Expert Review
Gastrointestinal neuromuscular disorders v1.15 L1CAM Zornitza Stark reviewed gene: L1CAM: Rating: GREEN; Mode of pathogenicity: None; Publications: 9279760, 11857550, 15148591, 15368500, 22354677; Phenotypes: Hydrocephalus with Hirschsprung disease or congenital idiopathic intestinal pseudoobstruction MIM#307000; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 RGS10 Boaz Palterer gene: RGS10 was added
gene: RGS10 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: RGS10 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RGS10 were set to 34315806
Phenotypes for gene: RGS10 were set to short stature; GH deficiency; immunodeficiency; hypergammaglobulinemia; reduced lymphocyte chemotaxis
Penetrance for gene: RGS10 were set to unknown
Review for gene: RGS10 was set to AMBER
Added comment: Chinn et al. a kindred with three affected siblings presenting with short stature and immunodeficiency and segregating with biallelic variants in RGS10 (c.489_491del:p.E163del and c.G511T:p.A171S). The affected individuals exhibited systemic abnormalities directly related to the RGS10 mutations, including recurrent infections, hypergammaglobulinemia, profoundly reduced lymphocyte chemotaxis, abnormal lymph node architecture, and short stature due to growth hormone deficiency. Some functional data is presented.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 ELF4 Boaz Palterer reviewed gene: ELF4: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Inflammatory bowel disease, IBD, mucosal inflammation, fever, ulcers, Behcet-like disease; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Malformations of cortical development v2.46 DPYSL5 Ivone Leong Entity copied from Intellectual disability v3.1214
Malformations of cortical development v2.46 DPYSL5 Ivone Leong gene: DPYSL5 was added
gene: DPYSL5 was added to Malformations of cortical development. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: DPYSL5.
Mode of inheritance for gene: DPYSL5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: DPYSL5 were set to 33894126
Phenotypes for gene: DPYSL5 were set to Neurodevelopmental disorder with corpus callosum agenesis and cerebellar abnormalities
Ataxia and cerebellar anomalies - narrow panel v2.223 DPYSL5 Ivone Leong Entity copied from Intellectual disability v3.1214
Ataxia and cerebellar anomalies - narrow panel v2.223 DPYSL5 Ivone Leong gene: DPYSL5 was added
gene: DPYSL5 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: DPYSL5.
Mode of inheritance for gene: DPYSL5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: DPYSL5 were set to 33894126
Phenotypes for gene: DPYSL5 were set to Neurodevelopmental disorder with corpus callosum agenesis and cerebellar abnormalities
Gastrointestinal neuromuscular disorders v1.15 ACTA2 Zornitza Stark gene: ACTA2 was added
gene: ACTA2 was added to Gastrointestinal neuromuscular disorders. Sources: Expert Review
Mode of inheritance for gene: ACTA2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: ACTA2 were set to 20734336; 29300374
Phenotypes for gene: ACTA2 were set to Multisystemic smooth muscle dysfunction syndrome, MIM# 613834
Review for gene: ACTA2 was set to GREEN
gene: ACTA2 was marked as current diagnostic
Added comment: Multisystemic smooth muscle dysfunction syndrome (MSMDS) presents with a recognizable pattern of complications, including congenital mydriasis, patent ductus arteriosus (PDA), pulmonary artery hypertension, aortic and other arterial aneurysms, moyamoya-like cerebrovascular disease, intestinal hypoperistalsis and malrotation, and hypotonic bladder.

More than 40 unrelated individuals reported, missense at p.Arg179 position.
Sources: Expert Review
Intellectual disability v3.1214 COG4 Arina Puzriakova Publications for gene: COG4 were set to 25529582
Intellectual disability v3.1213 COG4 Arina Puzriakova Added comment: Comment on mode of inheritance: Early developmental delay (speech and motor) can be a feature of Saul-Wilson syndrome (monoallelic inheritance), however cognition is normal. Therefore, the monoallelic form is not pertinent to this panel and the MOI should remain as biallelic only which is associated with CDG-IIj, including psychomotor retardation.
Intellectual disability v3.1213 COG4 Arina Puzriakova Mode of inheritance for gene: COG4 was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1212 COG4 Arina Puzriakova Tag for-review was removed from gene: COG4.
Early onset or syndromic epilepsy v2.400 COG4 Arina Puzriakova Phenotypes for gene: COG4 were changed from to Congenital disorder of glycosylation, type IIj, OMIM:613489
Early onset or syndromic epilepsy v2.399 COG4 Arina Puzriakova Mode of inheritance for gene: COG4 was changed from to BIALLELIC, autosomal or pseudoautosomal
Skeletal dysplasia v2.112 WNT1 Ivone Leong Phenotypes for gene: WNT1 were changed from {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221; Osteogenesis imperfecta, type XV, 615220 to {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221; Osteogenesis imperfecta, type XV, OMIM:615220
Osteogenesis imperfecta v2.18 WNT1 Ivone Leong Phenotypes for gene: WNT1 were changed from Osteogenesis imperfecta, type XV, 615220; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221 to Osteogenesis imperfecta, type XV, OMIM:615220; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221
Osteogenesis imperfecta v2.17 WNT1 Ivone Leong Publications for gene: WNT1 were set to 23434763; 2349931
Osteogenesis imperfecta v2.16 WNT1 Ivone Leong Phenotypes for gene: WNT1 were changed from Osteogenesis imperfecta, type XV, 615220; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221; osteogenesis imperfecta to Osteogenesis imperfecta, type XV, 615220; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221
Osteogenesis imperfecta v2.15 WNT1 Ivone Leong Publications for gene: WNT1 were set to PMID: 23434763; 2349931
Skeletal dysplasia v2.111 WNT1 Ivone Leong Phenotypes for gene: WNT1 were changed from osteogenesis imperfecta; OI/osteoporosis; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221; Osteogenesis imperfecta, type XV, 615220 to {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, OMIM:615221; Osteogenesis imperfecta, type XV, 615220
Fetal anomalies v1.698 WNT1 Ivone Leong Phenotypes for gene: WNT1 were changed from OSTEOGENESIS IMPERFECTA to Osteogenesis imperfecta, type XV, OMIM:615220
Intellectual disability v3.1212 MYCN Ivone Leong Publications for gene: MYCN were set to 21224895; 8470948
Intellectual disability v3.1211 MYCN Ivone Leong Phenotypes for gene: MYCN were changed from Feingold syndrome, 164280; FEINGOLD SYNDROME TYPE 1 to Feingold syndrome 1, OMIM:164280
Intellectual disability v3.1210 MYCN Ivone Leong Publications for gene: MYCN were set to
Intellectual disability v3.1209 PTPN4 Ivone Leong Classified gene: PTPN4 as Amber List (moderate evidence)
Intellectual disability v3.1209 PTPN4 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. Based on the expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1209 PTPN4 Ivone Leong Gene: ptpn4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1209 PTPN4 Ivone Leong Classified gene: PTPN4 as Amber List (moderate evidence)
Intellectual disability v3.1209 PTPN4 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. Based on the expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1209 PTPN4 Ivone Leong Gene: ptpn4 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1208 PTPN4 Ivone Leong Tag Q3_21_rating tag was added to gene: PTPN4.
Ectodermal dysplasia v1.26 CDSN Arina Puzriakova Phenotypes for gene: CDSN were changed from hypotrichosis simplex of the scalp; HYPT2; Hypotrichosis 2, 146520 to Hypotrichosis 2, OMIM:146520
Non-syndromic hypotrichosis v1.9 CDSN Arina Puzriakova Phenotypes for gene: CDSN were changed from hypotrichosis simplex of the scalp; Hypotrichosis 2, 146520; HYPT2 to Hypotrichosis 2, OMIM:146520
Adult solid tumours cancer susceptibility v2.14 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Thyroid cancer; Pituitary adenoma to Multiple endocrine neoplasia, type IV, OMIM:610755; Thyroid cancer; Pituitary adenoma
Endocrine neoplasia v1.23 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Endocrine Cancer; Multiple Endocrine Neoplasia; Multiple endocrine neoplasia, type IV, 610755 to Multiple endocrine neoplasia, type IV, OMIM:610755
Multiple endocrine tumours v1.11 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Multiple endocrine neoplasia, type IV, 610755; Multiple Endocrine Neoplasia; Endocrine Cancer to Multiple endocrine neoplasia, type IV, OMIM:610755
Familial hyperparathyroidism or hypocalciuric hypercalcaemia v2.14 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Multiple endocrine neoplasia, type IV (610755) to Multiple endocrine neoplasia, type IV, OMIM:610755
Adult solid tumours for rare disease v1.25 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Thyroid cancer; Pituitary adenoma to Multiple endocrine neoplasia, type IV, OMIM:610755; Thyroid cancer; Pituitary adenoma
Neuroendocrine cancer pertinent cancer susceptibility v1.2 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Neuroendocrine cancer to Multiple endocrine neoplasia, type IV, OMIM:610755
Parathyroid Cancer v1.4 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Pituitary Cancer, Parathyroid and Hypercalcemia to Multiple endocrine neoplasia, type IV, OMIM:610755; Pituitary Cancer, Parathyroid and Hypercalcemia
Thyroid cancer pertinent cancer susceptibility v1.2 CDKN1B Arina Puzriakova Phenotypes for gene: CDKN1B were changed from Thyroid cancer; Pituitary adenoma to Multiple endocrine neoplasia, type IV, OMIM:610755; Thyroid cancer; Pituitary adenoma
Thyroid cancer pertinent cancer susceptibility v1.1 CDKN1B Arina Puzriakova Mode of inheritance for gene: CDKN1B was changed from BIALLELIC, autosomal or pseudoautosomal to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Hereditary neuropathy or pain disorder v1.34 GSN Ivone Leong Tag Q3_21_rating tag was added to gene: GSN.
Hereditary neuropathy or pain disorder v1.34 GSN Ivone Leong Classified gene: GSN as Amber List (moderate evidence)
Hereditary neuropathy or pain disorder v1.34 GSN Ivone Leong Added comment: Comment on list classification: New gene added by Dmitrijs Rots (RadboudUMC). This gene is associated with a phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Hereditary neuropathy or pain disorder v1.34 GSN Ivone Leong Gene: gsn has been classified as Amber List (Moderate Evidence).
Hereditary neuropathy or pain disorder v1.33 GSN Ivone Leong Phenotypes for gene: GSN were changed from Amyloidosis; cranial neuropathy; peripheral neuropathy; cutis laxa; cardiomyopathy; arrhytmia to Amyloidosis, Finnish type, OMIM:105120; cranial neuropathy; peripheral neuropathy; cutis laxa; cardiomyopathy, MONDO:0004994; arrhythmia
Hereditary neuropathy or pain disorder v1.32 GSN Ivone Leong Publications for gene: GSN were set to PMID: 33499149; 26339870
Hereditary neuropathy or pain disorder v1.31 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Lipodystrophy, congenital generalized, type 2 269700; Neuropathy, distal hereditary motor, type VA 600794; Encephalopathy, progressive, with or without lipodystrophy, 615924; Silver spastic paraplegia syndrome 270685 to Neuropathy, distal hereditary motor, type VC, OMIM:619112
Hereditary neuropathy v1.389 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Neuropathy, distal hereditary motor, type VA 600794; Encephalopathy, progressive, with or without lipodystrophy, 615924; Lipodystrophy, congenital generalized, type 2 269700; Silver spastic paraplegia syndrome 270685 to Neuropathy, distal hereditary motor, type VC, OMIM:619112
Adult onset hereditary spastic paraplegia v1.24 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Silver spastic paraplegia syndrome, 270685 to Silver spastic paraplegia syndrome, OMIM:270685
Childhood onset hereditary spastic paraplegia v2.46 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Silver spastic paraplegia syndrome, 270685 to Silver spastic paraplegia syndrome, OMIM:270685
Hereditary spastic paraplegia v1.227 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Silver spastic paraplegia syndrome, to Silver spastic paraplegia syndrome, OMIM:270685
Intellectual disability v3.1208 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Encephalopathy, progressive, with or without lipodystrophy 615924; Lipodystrophy, congenital generalized, type 2 269700; Neuropathy, distal hereditary motor, type VA 600794; Silver spastic paraplegia syndrome 270685 to Encephalopathy, progressive, with or without lipodystrophy, OMIM:615924; Lipodystrophy, congenital generalized, type 2, OMIM:269700
Intellectual disability v3.1207 BSCL2 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: BSCL2.
Intellectual disability v3.1207 BSCL2 Arina Puzriakova Added comment: Comment on mode of inheritance: Monoallelic variants lead to a motor neuropathy (MIM# 619112) or spastic paraplegia (MIM# 270685) presentation, both characterised by motor symptoms, but neither are associated with any cognitive deficits. On the other hand, biallelic variants cause encephalopathy (MIM# 615924) or generalised lipodystrophy (MIM# 269700) which do include cognitive decline and intellectual impairment, respectively.

Therefore, the MOI should be changed from 'Both mono- and biallelic' to 'Biallelic' only at the next GMS panel review.
Intellectual disability v3.1207 BSCL2 Arina Puzriakova Mode of inheritance for gene: BSCL2 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.50 RNU12 Eleanor Williams Classified gene: RNU12 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.50 RNU12 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from grey to amber. It could be promoted to green after GMS review as there are 3 unrelated cases with a craniosynostosis phenotype. However, variants in this gene would not currently be reported as it is not a protein coding gene. An Ensembl ID also needs to be added before it is promoted to green.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.50 RNU12 Eleanor Williams Gene: rnu12 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.49 RNU12 Eleanor Williams Tag Q3_21_rating tag was added to gene: RNU12.
Tag Q3_21_expert_review tag was added to gene: RNU12.
Early onset or syndromic epilepsy v2.398 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Intractable epilepsy and neurological regression; Encephalopathy, progressive, with or without lipodystrophy 615924; Lipodystrophy, congenital generalized, type 2 269700; Neuropathy, distal hereditary motor, type VA 600794; Silver spastic paraplegia syndrome 270685 to Encephalopathy, progressive, with or without lipodystrophy, OMIM:615924
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.49 RNU12 Eleanor Williams Tag currently-ngs-unreportable tag was added to gene: RNU12.
Monogenic diabetes v2.43 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Berardinelli-Seip congenital lipodystrophy; Lipodystrophy, congenital generalized, type 2, 269700 to Lipodystrophy, congenital generalized, type 2, OMIM:269700
Lipodystrophy - childhood onset v2.16 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Lipodystrophy, congenital generalized, type 2, 269700 to Lipodystrophy, congenital generalized, type 2, OMIM:269700; Encephalopathy, progressive, with or without lipodystrophy, OMIM:615924
Insulin resistance (including lipodystrophy) v1.13 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Lipodystrophy, congenital generalized, type 2, 269700 to Lipodystrophy, congenital generalized, type 2, OMIM:269700; Encephalopathy, progressive, with or without lipodystrophy, OMIM:615924
Familial diabetes v1.62 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Berardinelli-Seip congenital lipodystrophy to Lipodystrophy, congenital generalized, type 2, OMIM:269700
Diabetes with additional phenotypes suggestive of a monogenic aetiology v1.63 BSCL2 Arina Puzriakova Phenotypes for gene: BSCL2 were changed from Berardinelli-Seip congenital lipodystrophy to Lipodystrophy, congenital generalized, type 2, OMIM:269700
Early onset or syndromic epilepsy v2.397 DLL1 Arina Puzriakova Tag Q3_21_rating was removed from gene: DLL1.
Tag for-review tag was added to gene: DLL1.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 LAMTOR2 Zornitza Stark reviewed gene: LAMTOR2: Rating: AMBER; Mode of pathogenicity: None; Publications: 17195838, 24092934; Phenotypes: Immunodeficiency due to defect in MAPBP-interacting protein, MIM# 610798; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.49 RNU12 Eleanor Williams Phenotypes for gene: RNU12 were changed from CDAGS syndrome MIM#603116; Craniosynostosis, Delayed closure of the fontanelles, cranial defects, clavicular hypoplasia, Anal and Genitourinary malformations, and Skin manifestations to CDAGS syndrome, OMIM:603116; craniosynostosis-anal anomalies-porokeratosis syndrome, MONDO:001128
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.48 RNU12 Eleanor Williams edited their review of gene: RNU12: Changed phenotypes to: CDAGS syndrome, OMIM:603116, craniosynostosis-anal anomalies-porokeratosis syndrome, MONDO:0011287
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.48 RNU12 Eleanor Williams reviewed gene: RNU12: Rating: ; Mode of pathogenicity: None; Publications: 34085356; Phenotypes: CDAGS syndrome, OMIM:603116; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Limb disorders v2.48 LTBP1 Eleanor Williams Tag Q3_21_rating tag was added to gene: LTBP1.
Limb disorders v2.48 LTBP1 Eleanor Williams Classified gene: LTBP1 as Amber List (moderate evidence)
Limb disorders v2.48 LTBP1 Eleanor Williams Added comment: Comment on list classification: Promoting from red to amber but with a recommendation for green rating following GMS review. Individuals from 3 unrelated families reported with brachydactyly as part of a broader phenotype.
Limb disorders v2.48 LTBP1 Eleanor Williams Gene: ltbp1 has been classified as Amber List (Moderate Evidence).
Limb disorders v2.47 LTBP1 Eleanor Williams gene: LTBP1 was added
gene: LTBP1 was added to Limb disorders. Sources: Literature
Mode of inheritance for gene: LTBP1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: LTBP1 were set to 33991472
Phenotypes for gene: LTBP1 were set to Cutis laxa, autosomal recessive, type IIE, OMIM:619451; Brachydactyly, HP:0001156; Clinodactyly, HP:0030084; Syndactyly, HP:0001159
Review for gene: LTBP1 was set to GREEN
Added comment: Associated with Cutis laxa, autosomal recessive, type IIE #619451 (AR) in OMIM.

PMID: 33991472 - Pottie et al 2021 - report 8 individuals from 4 unrelated consanguineous families with 4 different homozygous premature truncating LTBP1 variants. Core clinical features include cutis laxa, craniosynostosis, a copper beaten calvarium, short stature, and discernible craniofacial characteristics. Brachydactyly was noted in 7/8 individuals, Clinodactyly in 7/8 individuals and Syndactyly in 5/8 individuals.
Sources: Literature
Skeletal dysplasia v2.110 LTBP1 Eleanor Williams changed review comment from: Short stature was noted in 8/8 (100%) of the patients reported in PMID:33991472; to: Short stature was noted in 8/8 (100%) and Genua vara (bow-leggedness) in 3/8 (37.5) of the patients reported in PMID:33991472
Ehlers Danlos syndrome with a likely monogenic cause v2.63 LTBP1 Eleanor Williams Classified gene: LTBP1 as Amber List (moderate evidence)
Ehlers Danlos syndrome with a likely monogenic cause v2.63 LTBP1 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber with a recommendation for green rating following GMS review. 3 families reported where joint hyperlaxity is noted.
Ehlers Danlos syndrome with a likely monogenic cause v2.63 LTBP1 Eleanor Williams Gene: ltbp1 has been classified as Amber List (Moderate Evidence).
Ehlers Danlos syndrome with a likely monogenic cause v2.62 LTBP1 Eleanor Williams Phenotypes for gene: LTBP1 were changed from Cutis laxa; craniofacial dysmorphism; altered skeletal development, including short stature; brachydactyly; clinodactyly to Cutis laxa, autosomal recessive, type IIE, OMIM:619451; Joint hyperlaxity
Ehlers Danlos syndrome with a likely monogenic cause v2.61 LTBP1 Eleanor Williams Publications for gene: LTBP1 were set to PMID: 33991472
Ehlers Danlos syndrome with a likely monogenic cause v2.60 LTBP1 Eleanor Williams Tag Q3_21_rating tag was added to gene: LTBP1.
Ehlers Danlos syndrome with a likely monogenic cause v2.60 LTBP1 Eleanor Williams edited their review of gene: LTBP1: Changed rating: GREEN; Changed publications to: 33991472; Changed phenotypes to: Cutis laxa, autosomal recessive, type IIE, OMIM:619451, Joint hyperlaxity; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Ehlers Danlos syndrome with a likely monogenic cause v2.60 LTBP1 Eleanor Williams commented on gene: LTBP1
Skeletal dysplasia v2.110 LTBP1 Eleanor Williams commented on gene: LTBP1: Short stature was noted in 8/8 (100%) of the patients reported in PMID:33991472
Skeletal dysplasia v2.110 LTBP1 Eleanor Williams Added comment: Comment on phenotypes: OMIM phenotype added 28-07-2021
Skeletal dysplasia v2.110 LTBP1 Eleanor Williams Phenotypes for gene: LTBP1 were changed from inherited cutis laxa MONDO:0100237 to inherited cutis laxa MONDO:0100237; Cutis laxa, autosomal recessive, type IIE, OMIM:619451
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.48 LTBP1 Eleanor Williams Tag Q3_21_rating tag was added to gene: LTBP1.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.48 LTBP1 Eleanor Williams Classified gene: LTBP1 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.48 LTBP1 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber but with a recommendation for green rating following GMS review. 4 cases reported with craniosynostosis in 6/8 individuals
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.48 LTBP1 Eleanor Williams Gene: ltbp1 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.47 LTBP1 Eleanor Williams Phenotypes for gene: LTBP1 were changed from Craniosynostosis; cutis laxa; intelectual disability to Cutis laxa, autosomal recessive, type IIE, OMIM:619451; craniosynostosis, MONDO:0015469
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.46 LTBP1 Eleanor Williams edited their review of gene: LTBP1: Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.46 LTBP1 Eleanor Williams reviewed gene: LTBP1: Rating: GREEN; Mode of pathogenicity: None; Publications: 33991472; Phenotypes: Cutis laxa, autosomal recessive, type IIE, OMIM:619451, craniosynostosis, MONDO:0015469; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.46 CHD7 Eleanor Williams Classified gene: CHD7 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.46 CHD7 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from grey to amber with a recommedation of green rating following GMS review. 3 cases reported with a craniosynostosis phenotype and supported model organism data, although incomplete penetrance is noted.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.46 CHD7 Eleanor Williams Gene: chd7 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.45 CHD7 Eleanor Williams Phenotypes for gene: CHD7 were changed from craniosynostosis to CHARGE syndrome, OMIM:214800; CHARGE syndrome, MONDO:0008965
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.44 CHD7 Eleanor Williams Publications for gene: CHD7 were set to 33844462; 30498854; 33288889
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.43 CHD7 Eleanor Williams Tag Q3_21_rating tag was added to gene: CHD7.
Tag Q3_21_NHS_review tag was added to gene: CHD7.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.43 CHD7 Eleanor Williams reviewed gene: CHD7: Rating: GREEN; Mode of pathogenicity: None; Publications: 33844462, 30498854, 33288889, 24975120, 22363697; Phenotypes: CHARGE syndrome, OMIM:214800, CHARGE syndrome, MONDO:0008965; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.43 ZNF462 Eleanor Williams Classified gene: ZNF462 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.43 ZNF462 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber, but with a recommendation for green rating following GMS review. Metopic ridging or craniosynostosis reported in 6 cases with a plausible disease causing variant in ZNF462.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.43 ZNF462 Eleanor Williams Gene: znf462 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.42 ZNF462 Eleanor Williams Phenotypes for gene: ZNF462 were changed from Weiss-Kruszka syndrome, MIM# 618619 to Weiss-Kruszka syndrome, OMIM:618619; weiss-kruszka syndrome, MONDO:0032836
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.41 ZNF462 Eleanor Williams Publications for gene: ZNF462 were set to 28513610
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 ZNF462 Eleanor Williams Tag Q3_21_rating tag was added to gene: ZNF462.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 ZNF462 Eleanor Williams reviewed gene: ZNF462: Rating: GREEN; Mode of pathogenicity: None; Publications: 28513610, 31361404; Phenotypes: Weiss-Kruszka syndrome, OMIM:618619, weiss-kruszka syndrome, MONDO:0032836; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Fetal anomalies v1.697 SMAD3 Eleanor Williams commented on gene: SMAD3
Ehlers Danlos syndrome with a likely monogenic cause v2.60 SMAD3 Eleanor Williams commented on gene: SMAD3: Note one case with a biallelic variant reported:
PMID: 32935439 - Baskin et al 2020 - first report of a LDS patient with biallelic SMAD3 variants (affecting splice site). Proband had classic Loeys-Dietz features, including dysmorphic facial features, significant scoliosis, and pectus excavatum, arachnodactyly, severe aortic root dilation, and diffuse arterial tortuosity. His parents are each heterozygous for the likely pathogenic variant and are more mildly affected.
Skeletal dysplasia v2.109 SMAD3 Eleanor Williams commented on gene: SMAD3: Note one case with a biallelic variant reported:
PMID: 32935439 - Baskin et al 2020 - first report of a LDS patient with biallelic SMAD3 variants (affecting splice site). Proband had classic Loeys-Dietz features, including dysmorphic facial features, significant scoliosis, and pectus excavatum, arachnodactyly, severe aortic root dilation, and diffuse arterial tortuosity. His parents are each heterozygous for the likely pathogenic variant and are more mildly affected.
Arthrogryposis v3.113 SMAD3 Eleanor Williams commented on gene: SMAD3
Thoracic aortic aneurysm or dissection v1.121 SMAD3 Eleanor Williams commented on gene: SMAD3
Thoracic aortic aneurysm or dissection (GMS) v1.15 SMAD3 Eleanor Williams commented on gene: SMAD3
Hereditary neuropathy v1.388 KIF1A Dmitrijs Rots reviewed gene: KIF1A: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: SPASTIC PARAPLEGIA 30, NESCAV SYNDROME; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 SMAD3 Eleanor Williams changed review comment from: Associated with Loeys-Dietz syndrome 3 #613795 (AD) in OMIM but craniosynostosis not listed as a clinical feature.

PMID: 20301312 - Loeys and Dietz (2008 updated 2018) - Gene Reviews - states that in severe presentation, craniofacial anomalies in individuals with LDS are characterized by widely spaced eyes and craniosynostosis.

PMID: 29392890 - Schepers et al 2018 - review of genes/variants associated with Loeys-Dietz syndrome. Table 5 indicates that only SMAD3 variants are associated with craniosynostosis and text says that "craniosynostosis has only been reported once in a SMAD3 patient" but no reference is given.

Looking at reported phenotypes for LDS patients with a SMAD3 variant:
PMID: 31569402 - Camerota et al 2019 - report 4 families with LDS and SMAD3 variants. 3/9 individuals from 3 different Italian families presented with dolichocephaly among other phenotypes. 4 families reported with SMAD3 variants in total, each with a different likely causative variant.

PMID: 32935439 - Baskin et al 2020 - first report of a LDS patient with biallelic SMAD3 variants (affecting splice site). Proband had classic Loeys-Dietz features, including dysmorphic facial features, significant scoliosis, and pectus excavatum, arachnodactyly, severe aortic root dilation, and diffuse arterial tortuosity. His parents are each heterozygous for the likely pathogenic variant and are more mildly affected. Dolichocephaly in the proband is mentioned.; to: Associated with Loeys-Dietz syndrome 3 #613795 (AD) in OMIM but craniosynostosis not listed as a clinical feature.

PMID: 20301312 - Loeys and Dietz (2008 updated 2018) - Gene Reviews - states that in severe presentation, craniofacial anomalies in individuals with LDS are characterized by widely spaced eyes and craniosynostosis.

PMID: 29392890 - Schepers et al 2018 - review of genes/variants associated with Loeys-Dietz syndrome. Table 5 indicates that only SMAD3 variants are associated with craniosynostosis and text says that "craniosynostosis has only been reported once in a SMAD3 patient" but no reference is given.

Looking at reported phenotypes for LDS patients with a SMAD3 variant and craniosynostosis phenotype:
PMID: 31569402 - Camerota et al 2019 - report 4 families with LDS and SMAD3 variants. 3/9 individuals from 3 different Italian families presented with dolichocephaly among other phenotypes. 4 families reported with SMAD3 variants in total, each with a different likely causative variant.

PMID: 32935439 - Baskin et al 2020 - first report of a LDS patient with biallelic SMAD3 variants (affecting splice site). Proband had classic Loeys-Dietz features, including dysmorphic facial features, significant scoliosis, and pectus excavatum, arachnodactyly, severe aortic root dilation, and diffuse arterial tortuosity. His parents are each heterozygous for the likely pathogenic variant and are more mildly affected. Dolichocephaly in the proband is mentioned.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 SMAD3 Eleanor Williams reviewed gene: SMAD3: Rating: AMBER; Mode of pathogenicity: None; Publications: 29392890, 31569402, 32935439; Phenotypes: Loeys-Dietz syndrome 3 OMIM:613795; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability v3.1206 DLL1 Arina Puzriakova Phenotypes for gene: DLL1 were changed from Global developmental delay; Intellectual disability; Morphological abnormality of the central nervous system; Seizures; Behavioral abnormality; Autism; Scoliosis to Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures, OMIM:618709
Early onset or syndromic epilepsy v2.397 DLL1 Arina Puzriakova Phenotypes for gene: DLL1 were changed from Global developmental delay; Intellectual disability; Morphological abnormality of the central nervous system; Seizures; Behavioral abnormality; Autism; Scoliosis to Neurodevelopmental disorder with nonspecific brain abnormalities and with or without seizures, OMIM:618709
Early onset or syndromic epilepsy v2.396 DLL1 Arina Puzriakova Tag Q3_21_rating tag was added to gene: DLL1.
Fetal anomalies v1.697 BMPR1B Arina Puzriakova Phenotypes for gene: BMPR1B were changed from Acromesomelic dysplasia, Demirhan type, OMIM:609441; Brachydactyly, type A1, D, OMIM:616849; Brachydactyly, type A2, OMIM:112600 to Acromesomelic dysplasia, Demirhan type, OMIM:609441
Fetal anomalies v1.696 BMPR1B Arina Puzriakova Added comment: Comment on mode of inheritance: Biallelic variants lead to the Demirhan type of acromesomelic dysplasia (MIM# 609441) which is pertinent to this panel. Monoallelic variants cause brachydactyly (MIM# 616849 and MIM# 112600) with dysplasia of only a single or few phalanges which would be difficult to diagnose prenatally. For this reason the MOI should remain as biallelic only on this panel.
Fetal anomalies v1.696 BMPR1B Arina Puzriakova Mode of inheritance for gene: BMPR1B was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies v1.695 BMPR1B Arina Puzriakova Phenotypes for gene: BMPR1B were changed from BRACHYDACTYLY TYPE A2 to Acromesomelic dysplasia, Demirhan type, OMIM:609441; Brachydactyly, type A1, D, OMIM:616849; Brachydactyly, type A2, OMIM:112600
Limb disorders v2.46 BMPR1B Arina Puzriakova Phenotypes for gene: BMPR1B were changed from Acromesomelic dysplasia, Demirhan type, 609441; Brachydactyly, type A1, D 616849; Brachydactyly, type A2, 112600 to Acromesomelic dysplasia, Demirhan type, OMIM:609441; Brachydactyly, type A1, D, OMIM:616849; Brachydactyly, type A2, OMIM:112600
Intellectual disability v3.1205 BMPR1B Arina Puzriakova Phenotypes for gene: BMPR1B were changed from Brachydactyly, type A2, 112600; Chrondrodysplasia, acromesomelic, with genital anomalies, 609441 to Acromesomelic dysplasia, Demirhan type, OMIM:609441; Brachydactyly, type A1, D, OMIM:616849; Brachydactyly, type A2, OMIM:112600
Skeletal dysplasia v2.109 BMPR1B Arina Puzriakova Phenotypes for gene: BMPR1B were changed from Brachydactyly, type A1, D 616849; Brachydactyly, type A2 112600; Acromesomelic dysplasia, Demirhan type 609441 to Acromesomelic dysplasia, Demirhan type, OMIM:609441; Brachydactyly, type A1, D, OMIM:616849; Brachydactyly, type A2, OMIM:112600
Intellectual disability v3.1204 BMPR1B Arina Puzriakova Mode of inheritance for gene: BMPR1B was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1203 PTPN4 Ivone Leong Phenotypes for gene: PTPN4 were changed from Intellectual disability to Intellectual disability, MONDO:0001071
Primary immunodeficiency or monogenic inflammatory bowel disease v2.452 CXCR2 Arina Puzriakova Phenotypes for gene: CXCR2 were changed from WHIM syndrome 2 619407 to WHIM syndrome 2, OMIM:619407
Intellectual disability v3.1202 PTPN4 Ivone Leong Publications for gene: PTPN4 were set to 17953619; 25424712; 30238967; DOI: https://doi.org/10.1016/j.xhgg.2021.100033
Primary immunodeficiency or monogenic inflammatory bowel disease v2.451 CXCR2 Arina Puzriakova Classified gene: CXCR2 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.451 CXCR2 Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark. Only a single family with variants in this gene and WHIM syndrome described to date. Rating Red until further evidence emerges.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.451 CXCR2 Arina Puzriakova Gene: cxcr2 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.450 PLG Arina Puzriakova Tag founder-effect was removed from gene: PLG.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.450 PLG Arina Puzriakova changed review comment from: Comment on list classification: Discussed with Helen Brittain (Genomics England Clinical Team) regarding the founder effect and reduced penetrance associated with the angioedema-specific variant (c.988A>G, p.K330E) in this gene - 'it goes slightly against our usual rule of needing another source to corroborate that it is the variant itself, but the evidence is reasonably compelling and this is harder if there happens to be a narrow pathogenic variant spectrum e.g. gain of function missense. In view of the reduced penetrance, and this slight doubt, I would prefer to ask the opinion of the evaluation working group'

Therefore rating Amber with the recommendation of expert review at the next GMS panel update (tagged)

Note: this phenotype is also now listed in OMIM (MIM# 619360); to: Comment on list classification: Discussed with Helen Brittain (Genomics England Clinical Team) regarding the reduced penetrance and recurrence of the angioedema-specific variant (c.988A>G, p.K330E) in this gene - 'it goes slightly against our usual rule of needing another source to corroborate that it is the variant itself, but the evidence is reasonably compelling and this is harder if there happens to be a narrow pathogenic variant spectrum e.g. gain of function missense. In view of the reduced penetrance, and this slight doubt, I would prefer to ask the opinion of the evaluation working group'

Therefore rating Amber with the recommendation of expert review at the next GMS panel update (tagged)

Note: this phenotype is also now listed in OMIM (MIM# 619360)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.450 PLG Arina Puzriakova Publications for gene: PLG were set to 28795768; 29548426; 29987869; 31131012; 32066472; 32065705; 32181895
Primary immunodeficiency or monogenic inflammatory bowel disease v2.449 PLG Arina Puzriakova edited their review of gene: PLG: Changed rating: AMBER; Changed publications to: 28795768, 29548426, 29952006, 30809376, 31131012, 32066472, 32065705, 32181895, 33799813
Primary immunodeficiency or monogenic inflammatory bowel disease v2.449 PLG Arina Puzriakova changed review comment from: Bork et al. 2018 (PMID: 28795768) found a recurrent variant (c.988A>G, p.K330E) in 13 German families with hereditary angioedema. Haplotype analysis indicated that this is a likely founder variant. However, the variant is associated with incomplete penetrance as there are several asymptomatic carriers within the families and the variant can be found at low freq in the European population in gnomAD - but has been classified as 'Pathogenic'. There is no evidence of other relevant variants but this seems to be an accepted causal variant in the literature and several subsequent publications have identified additional cases (PMIDs: 29548426; 31131012; 32066472; 32065705; 32181895). There is some data that suggests the variant might affect plasminogen glycosylation (PMIDs: 29548426; 32181895), however multiple patients have also been identified with normal plasminogen activity.; to: Bork et al. 2018 (PMID: 28795768) found a recurrent variant (c.988A>G, p.K330E) in 13 German families with hereditary angioedema. However, the variant is associated with incomplete penetrance as there are several asymptomatic carriers within the families and the variant can be found at low freq in the European population in gnomAD - but has been classified as 'Pathogenic'.

There is no evidence of other relevant variants but this seems to be an accepted causal variant in the literature and several subsequent publications have identified additional cases (PMIDs: 29548426; 29952006; 30809376; 31131012; 32066472; 32065705; 32181895; 33799813). Most cases are of European ancestry and haplotype analysis performed by the original study (Bork et al. 2018) indicated a likely founder effect. However, 2 families in Japan have since been identified indicating the variant may be found in various ethnic populations (PMID: 29987869)

There is some data that suggests the variant might affect plasminogen glycosylation (PMIDs: 29548426; 32181895), however multiple patients have also been identified with normal plasminogen activity.
Corneal abnormalities v1.8 GSN Ivone Leong Phenotypes for gene: GSN were changed from Amyloidosis, Finnish type 105120; to Amyloidosis, Finnish type, OMIM:105120
Paediatric or syndromic cardiomyopathy v1.51 GSN Ivone Leong Phenotypes for gene: GSN were changed from Amyloidosis; cranial neuropathy; peripheral neuropathy; cutis laxa; cardiomyopathy; arrhytmia to Amyloidosis, Finnish type, OMIM:105120; cranial neuropathy; peripheral neuropathy; cutis laxa; cardiomyopathy, MONDO:0004994; arrhythmia
Paediatric or syndromic cardiomyopathy v1.50 GSN Ivone Leong Publications for gene: GSN were set to PMID: 33499149; PMID:26339870
Primary immunodeficiency or monogenic inflammatory bowel disease v2.449 PLG Arina Puzriakova Publications for gene: PLG were set to PMID: 28795768
Primary immunodeficiency or monogenic inflammatory bowel disease v2.448 PLG Arina Puzriakova Classified gene: PLG as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.448 PLG Arina Puzriakova Added comment: Comment on list classification: Discussed with Helen Brittain (Genomics England Clinical Team) regarding the founder effect and reduced penetrance associated with the angioedema-specific variant (c.988A>G, p.K330E) in this gene - 'it goes slightly against our usual rule of needing another source to corroborate that it is the variant itself, but the evidence is reasonably compelling and this is harder if there happens to be a narrow pathogenic variant spectrum e.g. gain of function missense. In view of the reduced penetrance, and this slight doubt, I would prefer to ask the opinion of the evaluation working group'

Therefore rating Amber with the recommendation of expert review at the next GMS panel update (tagged)

Note: this phenotype is also now listed in OMIM (MIM# 619360)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.448 PLG Arina Puzriakova Gene: plg has been classified as Amber List (Moderate Evidence).
Structural eye disease v1.76 ASPH Ivone Leong Tag Q3_21_rating tag was added to gene: ASPH.
Tag Q3_21_NHS_review tag was added to gene: ASPH.
Structural eye disease v1.76 ASPH Ivone Leong Added comment: Comment on publications: Additional case; however, I could not access the article.
Structural eye disease v1.76 ASPH Ivone Leong Publications for gene: ASPH were set to 31274573; 24768550; 31012784
Structural eye disease v1.75 ASPH Ivone Leong Classified gene: ASPH as Amber List (moderate evidence)
Structural eye disease v1.75 ASPH Ivone Leong Added comment: Comment on list classification: New gene added by Julia Baptista (Royal Devon and Exeter NHS Foundation Trust). This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). There are >3 unrelated cases, therefore there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Structural eye disease v1.75 ASPH Ivone Leong Gene: asph has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.447 PLG Arina Puzriakova changed review comment from: Penetrance for gene PLG was set from 'unknown' to 'incomplete'; to: Penetrance for PLG on this panel was set from 'unknown' to 'incomplete'
Primary immunodeficiency or monogenic inflammatory bowel disease v2.447 PLG Arina Puzriakova commented on gene: PLG: Penetrance for gene PLG was set from 'unknown' to 'incomplete'
Primary immunodeficiency or monogenic inflammatory bowel disease v2.447 PLG Arina Puzriakova Penetrance for gene PLG was set from to unknown
Primary immunodeficiency or monogenic inflammatory bowel disease v2.446 PLG Arina Puzriakova Tag founder-effect tag was added to gene: PLG.
Tag Q3_21_expert_review tag was added to gene: PLG.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.446 PLG Arina Puzriakova reviewed gene: PLG: Rating: ; Mode of pathogenicity: None; Publications: 28795768, 29548426, 31131012, 32066472, 32065705, 32181895; Phenotypes: Angioedema, hereditary, 4, OMIM:619360; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Primary immunodeficiency or monogenic inflammatory bowel disease v2.446 PLG Arina Puzriakova Phenotypes for gene: PLG were changed from Angioedema, hereditary, 4, OMIM:619360 to Angioedema, hereditary, 4, OMIM:619360
Primary immunodeficiency or monogenic inflammatory bowel disease v2.445 PLG Arina Puzriakova Phenotypes for gene: PLG were changed from Non-C1 Hereditary Angioedema to Angioedema, hereditary, 4, OMIM:619360
Hydrocephalus v2.115 PLG Arina Puzriakova Phenotypes for gene: PLG were changed from Plasminogen deficiency, type I, OMIM:217090 to Plasminogen deficiency, type I, OMIM:217090; Dysplasminogenemia, OMIM:217090
Thrombophilia with a likely monogenic cause v1.20 PLG Arina Puzriakova Phenotypes for gene: PLG were changed from 217090 Plasminogen deficiency, type I to Plasminogen deficiency, type I, OMIM:217090; Dysplasminogenemia, OMIM:217090
Fetal anomalies v1.694 PLG Arina Puzriakova Phenotypes for gene: PLG were changed from Plasminogen deficiency, type I, OMIM:217090; Hypoplasminogenemia, MONDO:0009009 to Plasminogen deficiency, type I, OMIM:217090; Dysplasminogenemia, OMIM:217090
Inherited bleeding disorders v1.163 PLG Arina Puzriakova Phenotypes for gene: PLG were changed from Plasminogen deficiency to Plasminogen deficiency, type I, OMIM:217090; Dysplasminogenemia, OMIM:217090
Fetal anomalies v1.693 ASPH Ivone Leong Added comment: Comment on phenotypes: Previously:
FACIAL DYSMORPHISM, LENS DISLOCATION, ANTERIOR SEGMENT ABNORMALITIES, AND SPONTANEOUS FILTERING BLEBS
Fetal anomalies v1.693 ASPH Ivone Leong Phenotypes for gene: ASPH were changed from FACIAL DYSMORPHISM, LENS DISLOCATION, ANTERIOR SEGMENT ABNORMALITIES, AND SPONTANEOUS FILTERING BLEBS to Traboulsi syndrome, OMIM:601552
Structural eye disease v1.74 ASPH Ivone Leong Phenotypes for gene: ASPH were changed from ectopia lentis; facial dysmorphism; Traboulsi syndrome to Traboulsi syndrome, OMIM:601552
Fetal anomalies v1.692 MYOD1 Ivone Leong Tag Q3_21_rating was removed from gene: MYOD1.
Tag watchlist tag was added to gene: MYOD1.
Fetal anomalies v1.692 MYOD1 Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics) on Congenital myopathy panel. This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is currently not enough evidence to support a gene-disease association on this panel (Fetal anomalies). Therefore, this gene has been given an Amber rating.
Arthrogryposis v3.113 MYOD1 Ivone Leong Tag Q3_21_rating was removed from gene: MYOD1.
Tag watchlist tag was added to gene: MYOD1.
Arthrogryposis v3.113 MYOD1 Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics) on Congenital myopathy panel. This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is currently not enough evidence to support a gene-disease association on this panel (Arthrogryposis). Therefore, this gene has been given an Amber rating.
Fetal anomalies v1.692 MYOD1 Ivone Leong Entity copied from Congenital myopathy v2.56
Fetal anomalies v1.692 MYOD1 Ivone Leong gene: MYOD1 was added
gene: MYOD1 was added to Fetal anomalies. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: MYOD1.
Mode of inheritance for gene: MYOD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYOD1 were set to 26733463; 30403323; 31260566
Phenotypes for gene: MYOD1 were set to Myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies, OMIM:618975
Arthrogryposis v3.113 MYOD1 Ivone Leong Entity copied from Congenital myopathy v2.56
Arthrogryposis v3.113 MYOD1 Ivone Leong gene: MYOD1 was added
gene: MYOD1 was added to Arthrogryposis. Sources: Expert Review Amber,Literature
Q3_21_rating tags were added to gene: MYOD1.
Mode of inheritance for gene: MYOD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYOD1 were set to 26733463; 30403323; 31260566
Phenotypes for gene: MYOD1 were set to Myopathy, congenital, with diaphragmatic defects, respiratory insufficiency, and dysmorphic facies, OMIM:618975
Congenital myopathy v2.56 MYOD1 Ivone Leong commented on gene: MYOD1: Affected individuals present with hypotonia and respiratory insufficiency. More severe cases develop features in utero and lead to contractures.
Early onset or syndromic epilepsy v2.396 SYNCRIP Konstantinos Varvagiannis gene: SYNCRIP was added
gene: SYNCRIP was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: SYNCRIP was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SYNCRIP were set to 34157790; 30504930; 27479843; 23020937
Phenotypes for gene: SYNCRIP were set to Global developmental delay; Intellectual disability; Autism; Myoclonic atonic seizures; Abnormality of nervous system morphology
Review for gene: SYNCRIP was set to AMBER
Added comment: Semino et al (2021 - PMID: 34157790) provide clinical details on 3 unrelated individuals with de novo SYNCRIP variants and provide a review of 5 additional subjects previously identified within large cohorts in the literature and databases.

Features included DD, ID (7/7 for whom this information was available), ASD or autistic features (4/7). MRI abnormalities were observed in 3 (widening of CSF spaces, periventricular nodular heterotopia, prominent lat. ventricles). Epilepsy (myoclonic-astatic epilepsy / Doose syndrome) was reported for 2(/8) individuals.

The 3 patients here reported were identified following trio/singleton exome with Sanger confirmation of the variants and their de novo occurrence.

Variants are in almost all cases de novo (7/7 for whom this was known) and in 5/8 cases were pLoF, in 2/8 missense SNVs while a case from DECIPHER had a 77.92 kb whole gene deletion not involving other genes with unknown inheritance.

Overall the variants reported to date include [NM_006372.5]:
1 - c.858_859del p.(Gly287Leufs*5)
2 - c.854dupA p.(Asn285Lysfs*8)
3 - c.734T>C p.(Leu245Pro)
4 - chr6:85605276-85683190 deletion (GRCh38)
5 - c.629T>C p.(Phe210Ser)
6 - c.1573_1574delinsTT p.(Gln525Leu)
7 - c.1247_1250del p.(Arg416Lysfs*145)
8 - c.1518_1519insC p.(Ala507Argfs*14)

[P1-3: this report, P4: DECIPHER 254774, P5-6: Guo et al 2019 - PMID: 30504930, P7: Lelieveld et al 2016 - PMID: 27479843, P8: Rauch et al 2012 - PMID: 23020937 / all other Refs not here reviewed, clinical details summarized by Semino et al in table 1]

SYNCRIP (also known as HNRNPQ) encodes synaptotagmin‐binding cytoplasmic RNA‐interacting protein. As the authors note, this RNA-binding protein is involved in multiple pathways associated with neuronal/muscular developmental disorders. Several references are provided for its involvement in regulation of RNA metabolism, among others sequence recognition, pre-mRNA splicing, translation, transport and degradation.

Mutations in other RNA-interacting proteins and hnRNP members (e.g. HNRNPU, HNRNPD) are associated with NDD.

The missense variant (p.Leu245Pro) is within RRM2 one of the 3 RNA recognition motif (RRM) domains of the protein. These 3 domains, corresponding to the central part of the protein (aa 150-400), are relatively intolerant to variation (based on in silico predictions and/or variation in gnomAD). Leu245 localizes within an RNA binding pocket and in silico modeling suggests alteration of the tertiary structure and RNA-binding capacity of RRM2.

There are no additional studies performed.

Overall haploinsufficiency appears to be the underlying disease mechanism based on the truncating variants and the gene deletion. [pLI in gnomAD : 1, %HI : 2.48%]

Animal models are not discussed.

There is no associated phenotype in OMIM or PanelApp AUS.
This gene is included in the DD panel of G2P (monoallelic LoF variants / SYNCRIP-related developmental disorder). SysID also lists SYNCRIP within the current primary ID genes.
Sources: Literature
Intellectual disability v3.1201 SYNCRIP Konstantinos Varvagiannis reviewed gene: SYNCRIP: Rating: AMBER; Mode of pathogenicity: None; Publications: 34157790, 30504930, 27479843, 23020937; Phenotypes: Global developmental delay, Intellectual disability, Autism, Myoclonic atonic seizures, Abnormality of nervous system morphology; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Cerebellar hypoplasia v1.53 L1CAM Dmitrijs Rots gene: L1CAM was added
gene: L1CAM was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: L1CAM was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: L1CAM were set to PMID: 3147431
Phenotypes for gene: L1CAM were set to Cerebellar hypoplasia
Penetrance for gene: L1CAM were set to Complete
Review for gene: L1CAM was set to GREEN
gene: L1CAM was marked as current diagnostic
Added comment: In PMID: 31474318 found 3 patient with DNM variant and cerebellar hypoplasia, and additionally summarized another 13 from the literature (see suplements of the paper).
Sources: Literature
Cerebellar hypoplasia v1.53 PDGFRB Dmitrijs Rots gene: PDGFRB was added
gene: PDGFRB was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: PDGFRB was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: PDGFRB were set to PMID: 31474318
Phenotypes for gene: PDGFRB were set to Cerebellar hypoplasia
Penetrance for gene: PDGFRB were set to Complete
Review for gene: PDGFRB was set to GREEN
Added comment: In PMID: 31474318 found 4 patients with DNM variants and cerebellar hypoplasia, and additionally summarized another 1 from the literature (see suplements of the paper).
Sources: Literature
Cerebellar hypoplasia v1.53 FOXP1 Dmitrijs Rots gene: FOXP1 was added
gene: FOXP1 was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: FOXP1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: FOXP1 were set to PMID: 31474318
Phenotypes for gene: FOXP1 were set to Mental retardation with language impairment and with or without autistic features
Penetrance for gene: FOXP1 were set to Complete
Review for gene: FOXP1 was set to GREEN
gene: FOXP1 was marked as current diagnostic
Added comment: In PMID: 31474318 found 11 patient with DNM AHDC1 variant and cerebellar hypoplasia (see suplements of the paper).
Sources: Literature
Cerebellar hypoplasia v1.53 WDR37 Dmitrijs Rots gene: WDR37 was added
gene: WDR37 was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: WDR37 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: WDR37 were set to PMID: 31474318
Phenotypes for gene: WDR37 were set to Neurooculocardiogenitourinary syndrome
Penetrance for gene: WDR37 were set to Complete
Review for gene: WDR37 was set to GREEN
gene: WDR37 was marked as current diagnostic
Added comment: In PMID: 31474318 found 5 patient with DNM WDR37 variant and cerebellar hypoplasia (see suplements of the paper).
Sources: Literature
Cerebellar hypoplasia v1.53 BCL11A Dmitrijs Rots gene: BCL11A was added
gene: BCL11A was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: BCL11A was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: BCL11A were set to PMID: 31474318
Phenotypes for gene: BCL11A were set to intellectual disability; Cerebellar hypoplasia
Penetrance for gene: BCL11A were set to Complete
Review for gene: BCL11A was set to GREEN
Added comment: In PMID: 31474318 found 3 patient with DNM AHDC1 variant and cerebellar hypoplasia, and additionally summarized another 9 from the literature (see suplements of the paper).
Sources: Literature
Cerebellar hypoplasia v1.53 AUTS2 Dmitrijs Rots gene: AUTS2 was added
gene: AUTS2 was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: AUTS2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: AUTS2 were set to PMID: 31474318
Phenotypes for gene: AUTS2 were set to intellectual disability; Cerebellar hypoplasia
Penetrance for gene: AUTS2 were set to Complete
Review for gene: AUTS2 was set to AMBER
Added comment: In PMID: 31474318 found in 2/5 patient with DNM AUTS2 variant and cerebellar hypoplasia (see suplements of the paper).
Sources: Literature
Cerebellar hypoplasia v1.53 AHDC1 Dmitrijs Rots gene: AHDC1 was added
gene: AHDC1 was added to Cerebellar hypoplasia. Sources: Literature
Mode of inheritance for gene: AHDC1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: AHDC1 were set to PMID: 31474318
Phenotypes for gene: AHDC1 were set to intellectual disability; Cerebellar hypoplasia
Penetrance for gene: AHDC1 were set to Complete
Review for gene: AHDC1 was set to GREEN
Added comment: In PMID: 31474318 found one patient with DNM AHDC1 variant and cerebellar hypoplasia, and additionally summarized another 4 from the literature (see suplements of the paper).
Sources: Literature
Paediatric or syndromic cardiomyopathy v1.49 GSN Dmitrijs Rots gene: GSN was added
gene: GSN was added to Cardiomyopathies - including childhood onset. Sources: Literature
Mode of inheritance for gene: GSN was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: GSN were set to PMID: 33499149; PMID:26339870
Phenotypes for gene: GSN were set to Amyloidosis; cranial neuropathy; peripheral neuropathy; cutis laxa; cardiomyopathy; arrhytmia
Penetrance for gene: GSN were set to Incomplete
Review for gene: GSN was set to GREEN
gene: GSN was marked as current diagnostic
Added comment: Causes Amyloidosis, Finnish type with multisystem involvement. Cardiomyopathy reported in >6% of patients and arrhytmia (without specifying types) in >30% from >200-individual large cohort from Finland. PMID:26339870.
Sources: Literature
Hereditary neuropathy or pain disorder v1.30 GSN Dmitrijs Rots gene: GSN was added
gene: GSN was added to Hereditary neuropathy NOT PMP22 copy number. Sources: Literature
Mode of inheritance for gene: GSN was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: GSN were set to PMID: 33499149; 26339870
Phenotypes for gene: GSN were set to Amyloidosis; cranial neuropathy; peripheral neuropathy; cutis laxa; cardiomyopathy; arrhytmia
Penetrance for gene: GSN were set to Complete
Review for gene: GSN was set to GREEN
gene: GSN was marked as current diagnostic
Added comment: Causes Amyloidosis, Finnish type with multisystem involvement. Peripheral and cranial neuropathy each reported in >70% of patients from >200 big cohort from Finland. PMID:26339870.
Sources: Literature
Intellectual disability v3.1201 CAMK4 Konstantinos Varvagiannis gene: CAMK4 was added
gene: CAMK4 was added to Intellectual disability. Sources: Literature,Other
Mode of inheritance for gene: CAMK4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: CAMK4 were set to 30262571; 33098801; 33211350
Phenotypes for gene: CAMK4 were set to Global developmental delay; Intellectual disability; Autism; Behavioral abnormality; Abnormality of movement; Dystonia; Ataxia; Chorea; Myoclonus
Penetrance for gene: CAMK4 were set to Complete
Review for gene: CAMK4 was set to GREEN
Added comment: 3 publications by Zech et al (2018, 2020 - PMIDs : 30262571, 33098801, 33211350) provide clinical details on 3 individuals, each harboring a private de novo CAMK4 variant.

Overlapping features included DD, ID, behavoral issues, autism and abnormal hyperkinetic movements. Dystonia and chorea in all 3 appeared 3-20 years after initial symptoms.

CAMK4 encodes Calcium/Calmodulin-dependent protein kinase IV, an important mediator of calcium-mediated activity and dynamics, particularly in the brain. It is involved in neuronal transmission, synaptic plasticity, and neuronal gene expression required for brain development and neuronal homeostasis (summary by OMIM based on Zech et al, 2018).

The 473 aa enzyme has a protein kinase domain (aa 46-300) and a C-terminal autoregulatory domain (aa 305-341) the latter comprising an autoinhibitory domain (AID / aa 305-321) and a calmodulin-binding domain (CBD / aa 322-341) [NP_001735.1 / NM_001744.4 - also used below].

Variants in all 3 subjects were identified following trio-WES and were in all cases protein-truncating, mapping to exon 10 or exon 10-intron 10 junction, expected to escape NMD and cause selective abrogation of the autoinhibitory domain (aa 305-321) leading overall to gain-of-function.

Variation databases include pLoF CAMK4 variants albeit in all cases usptream or downstream of this region (pLI of this gene in gnomAD: 0.51). Variants leading to selective abrogation of the autoregulatory domain have not been reported.

Extensive evidence for the GoF effect of the variant has been provided in the first publication. Several previous studies have demonstrated that abrogation of the AID domain leads to consitutive activation (details below).

Mouse models - though corresponding to homozygous loss of function - support a role for CAMKIV in cognitive and motor symptoms. Null mice display tremulous and ataxic movements, deficiencies in balance and sensorimotor performance associated with reduced number of Purkinje neurons (Ribar et al 2000, PMID: 11069976 - not reviewed). Wei et al (2002, PMID: 12006982 - not reviewed) provided evidence for alteration in hippocampal physiology and memory function.

Heterozygous mutations in other genes for calcium/calmodulin-dependent protein kinases (CAMKs) e.g. CAMK2A/CAMK2B (encoding subunits of CAMKII) have been reported in individuals with ID.

---

The proband in the first publication (PMID: 30262571) was a male with DD, ID, behavioral difficulties (ASD, autoaggression, stereotypies) and hyperkinetic movement disorder (myoclonus, chorea, ataxia) with severe generalized dystonia (onset at the age of 13y). Brain MRI demonstrated cerebellar atrophy.

Extensive work-up incl. karyotyping, CMA, DYT-TOR1A, THAP1, GCH1, SCA1/2/3/6/7/8/12/17, Friedreich's ataxia and FMR1 analysis was negative.F

Trio WES identified a dn splice site variant (c.981+1G>A) in the last exon-intron junction. RT-PCR followed by gel electrophoresis and Sanger in fibroblasts from an affected and control subject revealed that the proband had - as predicted by the type/location of the variant - in equal amount 2 cDNA products, a normal as well as a truncated one.

Sequencing of the shortest revealed utilization of a cryptic donor splice site upstream of the mutated donor leading to a 77bp out-of-frame deletion and introduction of a premature stop codon in the last codon (p.Lys303Serfs*28). Western blot in fibroblast cell lines revealed 2 bands corresponding to the normal protein product as well as to the p.Lys303Serfs*28 although expression of the latter was lower than that of the full length protein.

Several previous studies have shown that mutant CAMKIV species that lack the autoinhibitory domain are consitutively active (several Refs provided). Among others Chatila et al (1996, PMID: 8702940) studied an in vitro-engineered truncation mutant (Δ1-317 - truncation at position 317 of the protein) with functionally validated gain-of-function effect.

To prove enhanced activity of the splicing variant, Zech et al assessed phosphorylation of CREB (cyclic AMP-responsive element binding protein), a downstream substrate of CAMKIV. Immunobloting revealed significant increase of CREB phosphorylation in patient fibroblasts compared to controls. Overactivation of CAMKIV signaling was reversed when cells were treated with STO-609 an inhibitor of CAMKK, the ustream activator of CAMKIV.

Overall the authors demonstrated that loss of CAMKIV autoregulatory domain due to this splice variant had a gain-of-function effect.

----

Following trio-WES, Zech et al (2020 - PMID: 33098801) identified another relevant subject within cohort of 764 individuals with dystonia. This 12-y.o. male, harboring a different variant affecting the same donor site (c.981+1G>T), presented DD, ID, dystonia (onset at 3y) and additional movement disorders (myoclonus, ataxia) as well as similar behavior (ASD, autoaggression, stereotypies). [Details in suppl. p20].

----

Finally Zech et al (2020 - PMID: 33211350) reported on a 24-y.o. woman with adolescence onset choreodystonia. Other features included DD, moderate ID, absence seizures in infancy, OCD with anxiety and later diagnosis of ASD. Trio WES revealed a dn stopgain variant (c.940C>T; p.Gln314*).

----

There is no associated phenotype in OMIM, G2P, PanelApp AUS.

In SysID CAMK4 is listed among the current primary ID genes.

----

Please consider inclusion in other relevant panels.
Sources: Literature, Other
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 ACTG2 Zornitza Stark Deleted their review
Intellectual disability v3.1201 ATP9A Konstantinos Varvagiannis edited their review of gene: ATP9A: Changed publications to: http://dx.doi.org/10.1136/jmedgenet-2021-107843
Intellectual disability v3.1201 ATP9A Konstantinos Varvagiannis gene: ATP9A was added
gene: ATP9A was added to Intellectual disability. Sources: Literature,Other
Mode of inheritance for gene: ATP9A was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: ATP9A were set to Global developmental delay; Intellectual disability; Postnatal microcephaly; Failure to thrive; Abnormality of the abdomen
Penetrance for gene: ATP9A were set to Complete
Review for gene: ATP9A was set to AMBER
Added comment: Vogt, Verheyen et al (2021 - http://dx.doi.org/10.1136/jmedgenet-2021-107843) report 3 affected individuals from 2 unrelated consanguineous families.

Features included DD, variable ID (Fam1: sib1-mild, sib2-possible, Fam2: severe), postnatal microcephaly (-2.33 to -3.58 SD), failure to thrive as well as gastrointestinal symptoms (nausea, vomiting, GE reflux).

These subjects were homozygous for pLoF ATP9A variants private to each family.

Previous investigations incl. karyotype, aCGH and transferrin electophoresis (CDGs) and were unremarkable.

Diagnosis was made by exome sequencing and homozygosity mapping. Affected sibs from the first family were homozygous for a stopgain variant [NM_006045.3:c.868C>Τ / p.(Arg290*)]. The subject from the second family was homozygous for a variant affecting the consensus (donor) splice site [c.642+1G>A - same RefSeq]. Both variants were absent from gnomAD. Sanger sequencing was used to confirm variants, carrier status of the parents and unaffected sibs in both families.

Sequencing of cDNA from the individual homozygous for the splicing variant demonstrated skipping of exon 7 with the variant likely leading to frameshift and introduction of a premature stop codon.

qPCR in dermal fibroblasts from affected individuals from both families revealed expression downregulation of ATP9A (14% and 4% respectively for the stopgain and splice variant). Study at the protein level was not possible due to absence of antibody against endogenous ATP9A.

ATP9A encodes ATPase phospholipid transporting 9A (similarly to ATP9B) belonging to the subclass 2 of the P4-ATPase family. As the authors comment, the protein is mainly expressed in the brain although the precise function or subcellular distribution of endogenous ATP9A are unknown.

A previous study showed that overexpressed ATP9A in HeLa cells localizes to early/recycling endosomes and the trans-Golgi network, being required for endocytic recycling of the transferrin receptor to the plasma membrane. ATP9A (in complex with DOP1B and MON2) functionally interacts with the SNX3-retromer. A previous ATP9A knockdown cell line suggested dysregulation of >100 genes with ARPC3 (actin-related protein 2/3 complex subunit 3) being strongly upregulated.

Overall ATP9A appears to have a role in endosome trafficking pathways as well as to inhibit secretion of exosomes at the plasma membrane likely due to alteration of the actin cytoskeleton.

In line with the role of APT9A in early/recycling endosomes and identified interactions, the authors demonstrated overexpression of ARPC3 and SNX3. Study of genes encoding other known interacting proteins was not possible due to poor expression in fibroblasts.

As the authors note, mutations in genes encoding proteins of the Golgi and endosomal trafficking are important for brain development and have been associated with postnatal microcephaly.

In OMIM, G2P, SysID there is no associated phenotype.

The gene is included in the ID panel of PanelApp AUS with amber rating.
Sources: Literature, Other
Mitochondrial disorders v2.47 ACSL4 Andžela Lazdāne gene: ACSL4 was added
gene: ACSL4 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: ACSL4 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: ACSL4 were set to PMID: 33340416
Phenotypes for gene: ACSL4 were set to Long-chain fatty acid-CoA ligase 4 deficiency; Mental retardation; Autistic features; Intellectual disability
Review for gene: ACSL4 was set to GREEN
Added comment: X-linked intellectual disability type 63.
The gene is included in international classification of inherited metabolic disorders (ICIMD), Disorders of lipid metabolism.
IEM Nosology Group (IEMbase): Disorders of cytoplasmic triglyceride metabolism.
Sources: Literature
Likely inborn error of metabolism v2.154 EHHADH Andžela Lazdāne gene: EHHADH was added
gene: EHHADH was added to Inborn errors of metabolism. Sources: Literature
Mode of inheritance for gene: EHHADH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: EHHADH were set to PMID: 33340416
Phenotypes for gene: EHHADH were set to L-bifunctional protein deficiency; Metabolic acidosis; Increased amino acids in urine
Review for gene: EHHADH was set to AMBER
Added comment: Fanconi renotubular syndrome type 3.
The EHHADH gene is included in international classification of inherited metabolic disorders (ICIMD), Disorders of peroxisomal fatty acid oxidation.
IEM Nosology Group (IEMbase): Disorders of peroxisomal β-oxidation.
Sources: Literature
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 MASP1 Eleanor Williams Classified gene: MASP1 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 MASP1 Eleanor Williams Added comment: Comment on list classification: Promoting from red to amber but with a green recommendation for GMS review. Publications from Basdemirci et al and Atik et al suggest further cases where craniosynostosis is a feature.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.40 MASP1 Eleanor Williams Gene: masp1 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.39 MASP1 Eleanor Williams Phenotypes for gene: MASP1 were changed from 3MC syndrome 1 257920 to 3MC syndrome 1, OMIM:257920; 3MC syndrome 1, MONDO:0009770
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.38 MASP1 Eleanor Williams Publications for gene: MASP1 were set to
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.37 MASP1 Eleanor Williams Mode of inheritance for gene: MASP1 was changed from to BIALLELIC, autosomal or pseudoautosomal
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.36 MASP1 Eleanor Williams Tag Q2_21_rating was removed from gene: MASP1.
Tag Q3_21_rating tag was added to gene: MASP1.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.36 MASP1 Eleanor Williams Tag Q2_21_rating tag was added to gene: MASP1.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.36 MASP1 Eleanor Williams edited their review of gene: MASP1: Added comment: Checking for further reported cases:

PMID: 30601195 - Basdemirci et al 2019 - 3 siblings with 3MC syndrome in which a novel homozygous missense mutation, p.V704G, in MASP1 was identified in 2 of the siblings (not clear if the 3rd sibling was analysed). Craniosynostosis/skull asymmetry is reported in 2 siblings but no details given.

PMID: 29407414 - Graul-Neumann et al 2018 - 1adult female with a homozygous 2kb deletion, partially affecting exon 12 of MASP1 found by trio exome sequencing. She has the characteristic facial gestalt and typical multiple congenital anomalies but lacking the key feature cleft lip and palate. At birth craniofacial dysmorphism with skull asymmetry, open sutura metopica and facial asymmetry were noted among other features.

PMID: 26419238 - Atik et al 2015 - report on 6 unrelated children with 3MC1 syndrome. Sanger sequencing of MASP1 found 2 different splice site variants, and 3 different missense variants in the 6 probands. Two are reported to have craniosynostosis/skull asymmetry but no details given.

No mention of craniosynostosis or skull asymmetry:

PMID: 21035106 - Sirmaci et al 2010 - 3 individuals from 2 consanguineous Turkish families with 3MC. A missense and nonsense mutation in MASP1 were found by WES and Sanger sequencing in the two families respectively. Craniosynostosis is NOT mentioned as part of the phenotype.; Changed publications to: 30601195, 29407414, 26419238, 21035106, 21258343, 26789649
Structural eye disease v1.73 ASPH Julia Baptista gene: ASPH was added
gene: ASPH was added to Structural eye disease. Sources: Literature
Mode of inheritance for gene: ASPH was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ASPH were set to 31274573; 24768550; 31012784
Phenotypes for gene: ASPH were set to ectopia lentis; facial dysmorphism; Traboulsi syndrome
Review for gene: ASPH was set to GREEN
gene: ASPH was marked as current diagnostic
Added comment: Sources: Literature
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.36 HNRNPK Eleanor Williams Classified gene: HNRNPK as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.36 HNRNPK Eleanor Williams Added comment: Comment on list classification: Promoting this gene from grey to amber, with a recommendation for green rating following GMS review. 4 cases reported with craniosynostosis and variants in this gene.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.36 HNRNPK Eleanor Williams Gene: hnrnpk has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.35 HNRNPK Eleanor Williams Phenotypes for gene: HNRNPK were changed from Au-Kline syndrome, MIM# 616580 to Au-Kline syndrome, OMIM:616580
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.34 HNRNPK Eleanor Williams Publications for gene: HNRNPK were set to 26173930; 26954065; 29904177
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.33 HNRNPK Eleanor Williams reviewed gene: HNRNPK: Rating: GREEN; Mode of pathogenicity: None; Publications: 26173930, 26954065, 28771707, 29904177, 24501764, 25348648, 28374925; Phenotypes: Au-Kline syndrome, OMIM:616580; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability v3.1201 ZDHHC9 Ivone Leong Phenotypes for gene: ZDHHC9 were changed from Mental retardation, X-linked syndromic, Raymond type, 300799; MENTAL RETARDATION SYNDROMIC X-LINKED ZDHHC9-RELATED (MRXSZ) to Mental retardation, X-linked syndromic, Raymond type, OMIM:300799
Early onset or syndromic epilepsy v2.396 ZDHHC9 Ivone Leong Phenotypes for gene: ZDHHC9 were changed from epilepsy; intellectual disability; Mental retardation, X-linked syndromic, Raymond type, 300799 to epilepsy; intellectual disability; Mental retardation, X-linked syndromic, Raymond type, OMIM:300799
DDG2P v2.39 ZDHHC9 Ivone Leong Added comment: Comment on phenotypes: Previously:
MENTAL RETARDATION SYNDROMIC X-LINKED ZDHHC9-RELATED 300799
DDG2P v2.39 ZDHHC9 Ivone Leong Phenotypes for gene: ZDHHC9 were changed from MENTAL RETARDATION SYNDROMIC X-LINKED ZDHHC9-RELATED 300799 to Mental retardation, X-linked syndromic, Raymond type, OMIM:300799
Hereditary neuropathy v1.388 XK Ivone Leong Phenotypes for gene: XK were changed from McLeod syndrome with or without chronic granulomatous disease, 300842; Mceod syndrome, Onset 25-60, acanthocytes and Huntington-like syndrome, also epilepsy, cardiomyopathy, axonal motor neuropathy to McLeod syndrome with or without chronic granulomatous disease,OMIM:300842; McLeod syndrome, Onset 25-60, acanthocytes and Huntington-like syndrome, also epilepsy, cardiomyopathy, axonal motor neuropathy
Rare anaemia v1.24 XK Ivone Leong Phenotypes for gene: XK were changed from 300842 McLeod syndrome to McLeod syndrome with or without chronic granulomatous disease,OMIM:300842
Cytopenias and congenital anaemias v1.87 XK Ivone Leong Phenotypes for gene: XK were changed from McLeod syndrome with or without chronic granulomatous disease, 300842 to McLeod syndrome with or without chronic granulomatous disease,OMIM:300842
Early onset dystonia v1.88 XK Ivone Leong Phenotypes for gene: XK were changed from McLeod syndrome with or without chronic granulomatous disease OMIM 300842 to McLeod syndrome with or without chronic granulomatous disease,OMIM:300842
DDG2P v2.38 WNT10B Ivone Leong Phenotypes for gene: WNT10B were changed from SPLIT-HAND/FOOT MALFORMATION TYPE 6 225300 to Split-hand/foot malformation 6, OMIM:225300
Fetal anomalies v1.691 WNT10B Ivone Leong Phenotypes for gene: WNT10B were changed from Split-hand/foot malformation 6, OMIM:225300 to Split-hand/foot malformation 6, OMIM:225300
Skeletal dysplasia v2.108 WNT10B Ivone Leong Phenotypes for gene: WNT10B were changed from Split-hand/foot malformation 6 225300 to Split-hand/foot malformation 6, OMIM:225300
Fetal anomalies v1.690 WNT10B Ivone Leong Phenotypes for gene: WNT10B were changed from SPLIT-HAND/FOOT MALFORMATION TYPE 6 to Split-hand/foot malformation 6, OMIM:225300
Limb disorders v2.45 WNT10B Ivone Leong Phenotypes for gene: WNT10B were changed from Split-hand/foot malformation 6 225300 to Split-hand/foot malformation 6, OMIM:225300
Ectodermal dysplasia v1.25 WNT10A Ivone Leong Phenotypes for gene: WNT10A were changed from Schopf-Schulz-Passarge syndrome, OMIM:224750; Odontoonychodermal dysplasia, OMIM:257980 to Schopf-Schulz-Passarge syndrome, OMIM:224750; Odontoonychodermal dysplasia, OMIM:257980
Ectodermal dysplasia v1.24 WNT10A Ivone Leong Phenotypes for gene: WNT10A were changed from Schopf-Schulz-Passarge syndrome 224750; Odontoonychodermal dysplasia 257980 to Schopf-Schulz-Passarge syndrome, OMIM:224750; Odontoonychodermal dysplasia, OMIM:257980
Ectodermal dysplasia without a known gene mutation v1.22 WNT10A Ivone Leong Phenotypes for gene: WNT10A were changed from Odontoonychodermal dysplasia 257980; Schopf-Schulz-Passarge syndrome 224750 to Odontoonychodermal dysplasia, OMIM:257980; Schopf-Schulz-Passarge syndrome, OMIM:224750
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.33 FGF10 Eleanor Williams Classified gene: FGF10 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.33 FGF10 Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber. 2 cases reported.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.33 FGF10 Eleanor Williams Gene: fgf10 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.32 FGF10 Eleanor Williams Phenotypes for gene: FGF10 were changed from Craniosynostosis to craniosynostosis, MONDO:0015469
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.31 FGF10 Eleanor Williams changed review comment from: As expert reviewer reports PMID: 29215649 (Lee et al 2018) conducted a study in which 233 individuals with craniosynostosis where screened with a 20-gene panel which was designed based on the genes' association with craniosynostosis. Heterozygous variants (1 frameshift, 1 nonsense) were identified in 2 patients.; to: As expert reviewer reports PMID: 29215649 (Lee et al 2018) conducted a study in which 233 individuals with craniosynostosis where screened with a 20-gene panel which was designed based on the genes' association with craniosynostosis. Heterozygous variants (1 frameshift, 1 nonsense) in FGF10 were identified in 2 patients.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.31 FGF10 Eleanor Williams reviewed gene: FGF10: Rating: AMBER; Mode of pathogenicity: None; Publications: 29215649; Phenotypes: craniosynostosis, MONDO:0015469; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.31 B3GAT3 Eleanor Williams Tag Q3_21_rating tag was added to gene: B3GAT3.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.31 ACTG2 Eleanor Williams Classified gene: ACTG2 as No list
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.31 ACTG2 Eleanor Williams Added comment: Comment on list classification: Keeping this gene grey as it is not the correct gene for the panel (should be ACTG1).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.31 ACTG2 Eleanor Williams Gene: actg2 has been removed from the panel.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.30 ACTG2 Eleanor Williams commented on gene: ACTG2
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.30 ACTG1 Eleanor Williams Classified gene: ACTG1 as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.30 ACTG1 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from red to amber, with the recommendation of green rating following GMS review. More than 3 cases reported with disease-associated variants in this gene, with Trigonocephaly/metopic ridge reported as part of the phenotype.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.30 ACTG1 Eleanor Williams Gene: actg1 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.29 ACTG1 Eleanor Williams Tag Q3_21_rating tag was added to gene: ACTG1.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.29 ACTG1 Eleanor Williams gene: ACTG1 was added
gene: ACTG1 was added to Craniosynostosis. Sources: Literature
missense tags were added to gene: ACTG1.
Mode of inheritance for gene: ACTG1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ACTG1 were set to 22366783; 25052316; 27240540
Phenotypes for gene: ACTG1 were set to Baraitser-Winter syndrome 2, OMIM:614583
Review for gene: ACTG1 was set to GREEN
Added comment: Associated with Baraitser-Winter syndrome 2 OMIM:614583 (AD) in OMIM.

PMID: 22366783 - Rivière et al 2012 - 8 patients with Baraitser-Winter syndrome in which a heterozygous missense mutation was identified in the ACTG1 gene. In 7 patients the mutation was found to have occurred de novo (no parental DNA in 8th patient). Trigonocephaly was noted in 7 of the patients.

PMID: 25052316 - Verloes et al 2015 - report on 1 new case of a patient with a missense variant in ACTG1 (same variant as reported in Riviere et al) and bring together information from the Riviere patients with this one. They state that Trigonocephaly/metopic ridge is reported in 4/8 cases (50%) which contradicts the table in the Riviere paper which puts the number as higher.

PMID: 27240540 - Donato et al 2016 - report on 7 new unrelated patients with 6 mutations in ACTG1. Clinical photographs were available for 6 of these patients, and only 1/6 displayed a metopic ridge.
Sources: Literature
Childhood onset dystonia, chorea or related movement disorder v1.137 C9orf72_GGGGCC Sarah Leigh Tag Q2_21_rating was removed from STR: C9orf72_GGGGCC.
Tag STR tag was added to STR: C9orf72_GGGGCC.
Childhood onset dystonia, chorea or related movement disorder v1.137 C9orf72_GGGGCC Sarah Leigh Tag STR was removed from STR: C9orf72_GGGGCC.
Childhood onset dystonia, chorea or related movement disorder v1.137 C9orf72_GGGGCC Sarah Leigh Classified STR: C9orf72_GGGGCC as Red List (low evidence)
Childhood onset dystonia, chorea or related movement disorder v1.137 C9orf72_GGGGCC Sarah Leigh Added comment: Comment on list classification: Reviews for C9orf72 gene on this panel from Zornitza Stark (Australian Genomics), James Polke (North Thames GLH) & Helen Brittain (Genomics England Clinical Fellow)(https://panelapp.genomicsengland.co.uk/panels/847/gene/C9orf72/#!review), together recommend a Red rating, as the phenotype associated with this variant in this gene has an adult onset and is therefore not appropriate for a childhood gene panel.
Childhood onset dystonia, chorea or related movement disorder v1.137 C9orf72_GGGGCC Sarah Leigh Str: c9orf72_ggggcc has been classified as Red List (Low Evidence).
Childhood onset dystonia, chorea or related movement disorder v1.136 C9orf72 Sarah Leigh edited their review of gene: C9orf72: Added comment: Helen Brittain (Genomics England Clinical Fellow) suggested a Red rating, as the phenotype associated with variants in this gene has an adult onset and therefore is not appropriate for a childhood gene panel.; Changed rating: RED
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.28 ACTB Eleanor Williams Classified gene: ACTB as Amber List (moderate evidence)
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.28 ACTB Eleanor Williams Added comment: Comment on list classification: Promoting from grey to amber, but with a recommendation for green rating following GMS review. There are more than 3 cases with plausible disease causing variants in this gene, and a relevant phenotype.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.28 ACTB Eleanor Williams Gene: actb has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.27 ACTB Eleanor Williams Phenotypes for gene: ACTB were changed from Baraitser-Winter syndrome 1, MIM# 243310 to Baraitser-Winter syndrome 1, OMIM:243310; Baraitser-Winter syndrome 1, MONDO:0009470
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.26 ACTB Eleanor Williams Publications for gene: ACTB were set to
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.25 ACTB Eleanor Williams Tag missense tag was added to gene: ACTB.
Tag Q3_21_rating tag was added to gene: ACTB.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.25 ACTB Eleanor Williams reviewed gene: ACTB: Rating: GREEN; Mode of pathogenicity: None; Publications: 22366783, 23649928, 23756437; Phenotypes: Baraitser-Winter syndrome 1, OMIM:243310, Baraitser-Winter syndrome 1, MONDO:0009470; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Mitochondrial disorders v2.47 CMPK2 Andžela Lazdāne gene: CMPK2 was added
gene: CMPK2 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: CMPK2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CMPK2 were set to PMID: 33340416
Phenotypes for gene: CMPK2 were set to Mitochondrial UMP-CMP kinase 2 deficiency; Developmental delay; Failure to thrive
Review for gene: CMPK2 was set to GREEN
Added comment: Mitochondrial UMP-CMP kinase is a component of the salvage pathway for nucleotide synthesis.
IEM Nosology Group (IEMbase): Disorders of mitochondrial DNA depletion, multiple deletion, or intergenomic communication.
The CMPK2 gene is included in International classification of inherited metabolic disorders (ICIMD), Disorders of mitochondrial DNA maintenance and replication.
Sources: Literature
Clefting v2.46 SEPT9 Eleanor Williams Classified gene: SEPT9 as Green List (high evidence)
Clefting v2.46 SEPT9 Eleanor Williams Added comment: Comment on list classification: There is only 1 report of clefting in a patient with a variant in SEPT9 and a diagnosis of HNA. Other reports of clefting are in patients in which the molecular cause of the disease were not established. Therefore, the recommendation is to demote this gene from green to amber following GMS review.
Clefting v2.46 SEPT9 Eleanor Williams Gene: sept9 has been classified as Green List (High Evidence).
Clefting v2.45 SEPT9 Eleanor Williams Publications for gene: SEPT9 were set to
Clefting v2.44 SEPT9 Eleanor Williams Tag Q3_21_rating tag was added to gene: SEPT9.
Clefting v2.44 SEPT9 Eleanor Williams reviewed gene: SEPT9: Rating: AMBER; Mode of pathogenicity: None; Publications: 11739810, 18492087, 30019529, 31619932, 28503616, 20019224, 19939853, 19451530, 19139049, 16186812; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Clefting v2.44 MED12 Eleanor Williams Phenotypes for gene: MED12 were changed from Lujan-Fryns syndrome, 309520; Opitz-Kaveggia syndrome, 305450; OKS; submucous cleft palate to Hardikar syndrome, OMIM:612726; cholestasis-pigmentary retinopathy-cleft palate syndrome, MONDO:0012997
Clefting v2.43 MED12 Eleanor Williams Publications for gene: MED12 were set to 12784307
Clefting v2.42 MED12 Eleanor Williams Mode of inheritance for gene: MED12 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)
Clefting v2.41 MED12 Eleanor Williams Classified gene: MED12 as Amber List (moderate evidence)
Clefting v2.41 MED12 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from red to amber with the recommendation of a green rating following GMS review. There are 7 reported cases with cleft lip/palate and a variant identified in MED12.
Clefting v2.41 MED12 Eleanor Williams Gene: med12 has been classified as Amber List (Moderate Evidence).
Clefting v2.40 MED12 Eleanor Williams Tag Q3_21_rating tag was added to gene: MED12.
Clefting v2.40 MED12 Eleanor Williams reviewed gene: MED12: Rating: GREEN; Mode of pathogenicity: None; Publications: 33244166; Phenotypes: Hardikar syndrome, OMIM:612726, cholestasis-pigmentary retinopathy-cleft palate syndrome, MONDO:0012997; 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 v2.40 ESCO2 Eleanor Williams Classified gene: ESCO2 as Green List (high evidence)
Clefting v2.40 ESCO2 Eleanor Williams Added comment: Comment on list classification: Leaving rating as green. Sufficient cases reported with clefting a feature in Roberts-SC phocomelia syndrome. Additionally 2 (likely founder) cases reported with clefting in probands with Juberg-Hayward syndrome.
Clefting v2.40 ESCO2 Eleanor Williams Gene: esco2 has been classified as Green List (High Evidence).
Clefting v2.39 ESCO2 Eleanor Williams Phenotypes for gene: ESCO2 were changed from ROBERTS SYNDROME; RBS, SC PHOCOMELIA SYNDROME to Roberts-SC phocomelia syndrome, OMIM:268300; Roberts-SC phocomelia syndrome, MONDO:0100253
Clefting v2.38 ESCO2 Eleanor Williams Publications for gene: ESCO2 were set to
Clefting v2.37 ESCO2 Eleanor Williams reviewed gene: ESCO2: Rating: GREEN; Mode of pathogenicity: None; Publications: 32977150, 32255174, 15821733, 16380922, 18411254, 24864645; Phenotypes: Roberts-SC phocomelia syndrome, OMIM:268300, Roberts-SC phocomelia syndrome, MONDO:0100253; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Likely inborn error of metabolism v2.154 IDH1 Andžela Lazdāne gene: IDH1 was added
gene: IDH1 was added to Inborn errors of metabolism. Sources: Literature
Mode of inheritance for gene: IDH1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IDH1 were set to PMID: 33340416
Phenotypes for gene: IDH1 were set to Failure to thrive; Psychomotor delay; Feeding difficulties; Increased D-2-Hydroxyglutaric acid in urine
Review for gene: IDH1 was set to AMBER
Added comment: Isocitrate dehydrogenase 1 deficiency.

IEM Nosology Group (IEMbase):Disorders of the Krebs cycle. The IDH1 gene is included in International classification of inherited metabolic disorders (ICIMD), Disorders of the Krebs cycle.
Sources: Literature
Hypertrophic cardiomyopathy v2.22 ALPK3 Dmitrijs Rots reviewed gene: ALPK3: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID: 32480058; Phenotypes: Hypertrophic cardiomyopathy; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal; Current diagnostic: yes
Likely inborn error of metabolism v2.154 ACAT2 Andžela Lazdāne reviewed gene: ACAT2: Rating: AMBER; Mode of pathogenicity: None; Publications: PMID:33340416; Phenotypes: Developmental delay; Mode of inheritance: None
Likely inborn error of metabolism v2.154 ACAT2 Andžela Lazdāne Deleted their review
Likely inborn error of metabolism v2.154 ACAT2 Andžela Lazdāne commented on gene: ACAT2: ACAT2 gene is included in international classification of inherited metabolic
disorders (ICIMD).
Likely inborn error of metabolism v2.154 ACAT2 Andžela Lazdāne changed review comment from: Acetoacetyl-CoA thiolase deficiency (cytosolic)

IEM Nosology Group:Disorders of ketone body metabolism
Sources: Literature; to: Acetoacetyl-CoA thiolase deficiency (cytosolic)

IEM Nosology Group:Disorders of ketone body metabolism
Sources: Literature
Likely inborn error of metabolism v2.154 ACAT2 Andžela Lazdāne gene: ACAT2 was added
gene: ACAT2 was added to Inborn errors of metabolism. Sources: Literature
Mode of inheritance for gene: ACAT2 was set to Unknown
Publications for gene: ACAT2 were set to PMID:33340416
Phenotypes for gene: ACAT2 were set to Developmental delay
Review for gene: ACAT2 was set to AMBER
Added comment: Acetoacetyl-CoA thiolase deficiency (cytosolic)

IEM Nosology Group:Disorders of ketone body metabolism
Sources: Literature
Mitochondrial disorders v2.47 IDH1 Andžela Lazdāne edited their review of gene: IDH1: Changed rating: AMBER; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne edited their review of gene: ACAT2: Changed rating: AMBER; Changed mode of inheritance: Unknown
Mitochondrial disorders v2.47 IDH1 Andžela Lazdāne changed review comment from: Cytosolic NADP+-dependent isocitrate dehydrogenase 1 superactivity. IDH1 is a dimeric cytosolic NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) that catalyzes decarboxylation of isocitrate into alpha-ketoglutarate.
The IDH1 gene is included in International classification of inherited metabolic disorders (ICIMD), Disorders of the Krebs cycle.
Sources: Literature; to: Cytosolic NADP+-dependent isocitrate dehydrogenase 1 superactivity. IDH1 is a dimeric cytosolic NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) that catalyzes decarboxylation of isocitrate into alpha-ketoglutarate.
The IDH1 gene is included in International classification of inherited metabolic disorders (ICIMD), Disorders of the Krebs cycle.
Sources: Literature
Mitochondrial disorders v2.47 IDH1 Andžela Lazdāne gene: IDH1 was added
gene: IDH1 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: IDH1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: IDH1 were set to PMID: 33340416
Phenotypes for gene: IDH1 were set to Metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria
Review for gene: IDH1 was set to GREEN
Added comment: Cytosolic NADP+-dependent isocitrate dehydrogenase 1 superactivity. IDH1 is a dimeric cytosolic NADP-dependent isocitrate dehydrogenase (EC 1.1.1.42) that catalyzes decarboxylation of isocitrate into alpha-ketoglutarate.
The IDH1 gene is included in International classification of inherited metabolic disorders (ICIMD), Disorders of the Krebs cycle.
Sources: Literature
Mitochondrial disorders v2.47 SLC13A3 Andžela Lazdāne gene: SLC13A3 was added
gene: SLC13A3 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: SLC13A3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC13A3 were set to PMID: 33340416; PMID: 30635937
Phenotypes for gene: SLC13A3 were set to Sodium dicarboxylate cotransporter 3 deficiency; Increased urinary dicarboxylic acids, alpha-ketoglutarate, fumarate, N-acetylaspartate; Encephalopathy; Ataxia
Penetrance for gene: SLC13A3 were set to Complete
Review for gene: SLC13A3 was set to GREEN
Added comment: Based on the literature SLC13A3 gene variants cause acute reversible leukoencephalopathy and alpha-ketoglutarate accumulation. Patient had hypotonia, abnormal movements, and dysarthria associated with white matter abnormalities and increased urinary alpha-ketoglutarate and NAA. CSF analysis showed increased lactate. Laboratory studies showed increased urinary excretion of alpha-ketoglutarate, succinate, fumarate, and N-acetylaspartate (NAA). These organic acids were also increased in the cerebrospinal fluid (CSF).

The SLC13A3 gene is included an international classification of inherited metabolic disorders (ICIMD), Disorders of the Krebs cycle.
Sources: Literature
Mitochondrial disorders v2.47 SLC13A5 Andžela Lazdāne gene: SLC13A5 was added
gene: SLC13A5 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: SLC13A5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: SLC13A5 were set to PMID: 33340416
Phenotypes for gene: SLC13A5 were set to Plasma membrane citrate transporter deficiency; Epileptic encephalopathy; Delayed psychomotor development.
Penetrance for gene: SLC13A5 were set to Complete
Review for gene: SLC13A5 was set to GREEN
Added comment: The SLC13A5 gene encodes a tricarboxylate plasma transporter with a preference for citrate. The SLC13A5 gene should be include in Mitochondrial disorder panel because it is included in International Classification of Inborn Metabolic Disorders (ICIMD), Disorders of the Krebs cycle.
Sources: Literature
Clefting v2.37 PLCB4 Eleanor Williams Phenotypes for gene: PLCB4 were changed from Cleft palate to Auriculocondylar syndrome 2, OMIM:614669; auriculocondylar syndrome 2, MONDO:0013845
Clefting v2.36 PLCB4 Eleanor Williams Publications for gene: PLCB4 were set to
Clefting v2.35 PLCB4 Eleanor Williams Mode of inheritance for gene: PLCB4 was changed from to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Clefting v2.34 PLCB4 Eleanor Williams Classified gene: PLCB4 as Amber List (moderate evidence)
Clefting v2.34 PLCB4 Eleanor Williams Added comment: Comment on list classification: Promoting this gene from red to amber as there are two cases of auriculocondylar syndrome 2 associated with variants in this gene where cleft palate is part of the phenotype.
Clefting v2.34 PLCB4 Eleanor Williams Gene: plcb4 has been classified as Amber List (Moderate Evidence).
Clefting v2.33 PLCB4 Eleanor Williams edited their review of gene: PLCB4: Changed rating: AMBER; Changed publications to: 16114046, 32201334, 27007857, 23913798, 2560091, 23315542; Changed phenotypes to: Auriculocondylar syndrome 2, OMIM:614669, auriculocondylar syndrome 2, MONDO:0013845; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder v1.136 AFG3L2 Sarah Leigh changed review comment from: The review by Zornitza Stark (5 Sep 2020), has raised concerns about the relevance of the phenotypes associated with variants in AFG3L2 to scope of this panel.
Helen Brittain (Genomics England Clinical Fellow) has suggested this gene should be rated Amber on Childhood onset dystonia or chorea or related movement disorder panel.
AFG3L2 is already Green on Ataxia and cerebellar anomalies - narrow (https://panelapp.genomicsengland.co.uk/panels/477/gene/AFG3L2) and Hereditary ataxia - adult onset (https://panelapp.genomicsengland.co.uk/panels/466/gene/AFG3L2) panels.; to: The review by Emily Jones (9 Jul 2019) and Zornitza Stark (5 Sep 2020), have raised concerns about the relevance of the phenotypes associated with variants in AFG3L2 to scope of this panel.
Helen Brittain (Genomics England Clinical Fellow) has suggested this gene should be rated Amber on Childhood onset dystonia or chorea or related movement disorder panel.
AFG3L2 is already Green on Ataxia and cerebellar anomalies - narrow (https://panelapp.genomicsengland.co.uk/panels/477/gene/AFG3L2) and Hereditary ataxia - adult onset (https://panelapp.genomicsengland.co.uk/panels/466/gene/AFG3L2) panels.
Clefting v2.33 PLCB4 Eleanor Williams commented on gene: PLCB4
Childhood onset dystonia, chorea or related movement disorder v1.136 AFG3L2 Sarah Leigh reviewed gene: AFG3L2: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1200 CEP85L Sarah Leigh Tag Q3_21_rating tag was added to gene: CEP85L.
Childhood onset dystonia, chorea or related movement disorder v1.136 FXN Sarah Leigh reviewed gene: FXN: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.1200 CEP85L Sarah Leigh edited their review of gene: CEP85L: Added comment: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least nine variants reported in nine unrelated families. PMID 32097630 comments that - the CEP85L gene as a whole is tolerant to loss of function and to missense variation. However, the 4 missense variants that have been identified in patients affect a 15-aa region of the protein that is highly intolerant to missense variation, the splicing and start-loss variants are predicted to produce a shortened protein that excludes the same 15-aa region. It is speculated that variants in this constrained region, may act through a dominant-negative mechanism.
Intellectual disability was apparent in eight of the families studied, ranging from mild (three families) to moderate (five families).
Supportive studies were also presented (PMID 32097630, 32097629).; Changed rating: GREEN
Intellectual disability v3.1200 CEP85L Sarah Leigh Classified gene: CEP85L as Amber List (moderate evidence)
Intellectual disability v3.1200 CEP85L 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 v3.1200 CEP85L Sarah Leigh Gene: cep85l has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1199 CEP85L Sarah Leigh Phenotypes for gene: CEP85L were changed from Intellectual disability; epilepsy, lissencephaly to Lissencephaly 10, OMIM:618873; Lissencephaly 10, MONDO:0030031
Skeletal Muscle Channelopathies v1.37 PYGM Eleanor Williams commented on gene: PYGM
Skeletal muscle channelopathy v1.31 PYGM Eleanor Williams Tag Q2_21_rating was removed from gene: PYGM.
Skeletal muscle channelopathy v1.31 PYGM Eleanor Williams changed review comment from: Comment on list classification: Leaving the rating as green, but with a recommendation for a red rating following GMS review because this gene encodes an enzyme not a channel. However, the phenotype may overlap with channelopathies.; to: Comment on list classification: Leaving rating as Green but with a recommendation for review by the GMS test evaluation group as to suitability for this panel. This gene encodes an enzyme not a channel. However, the phenotype may overlap with channelopathies.
Skeletal Muscle Channelopathies v1.37 SLC2A1 Eleanor Williams commented on gene: SLC2A1
Skeletal muscle channelopathy v1.31 SLC2A1 Eleanor Williams changed review comment from: Comment on list classification: Leaving this gene green but with a recommendation for a red rating following GMS review as to whether it is useful to have this gene on panel although variants seem to result in a brain channelopathy rather than a skeletal muscle one; to: Comment on list classification: Leaving rating as Green but with a recommendation for review by the GMS test evaluation group as to suitability for this panel. Variants seem to result in a brain channelopathy rather than a skeletal muscle one
Skeletal muscle channelopathy v1.31 SLC2A1 Eleanor Williams Tag Q2_21_rating was removed from gene: SLC2A1.
Skeletal Muscle Channelopathies v1.37 SLC1A3 Eleanor Williams Classified gene: SLC1A3 as Green List (high evidence)
Skeletal Muscle Channelopathies v1.37 SLC1A3 Eleanor Williams Added comment: Comment on list classification: Leaving as green for consistency with the GMS Skeletal muscle channelopathy panel (panel 542).
Skeletal Muscle Channelopathies v1.37 SLC1A3 Eleanor Williams Gene: slc1a3 has been classified as Green List (High Evidence).
Skeletal muscle channelopathy v1.31 SLC1A3 Eleanor Williams changed review comment from: Comment on list classification: Leaving the rating as Green but with a recommendation for red rating following GMS review as to whether it is useful to have this gene on panel although variants seem to result in a brain channelopathy rather than a skeletal muscle one.; to: Comment on list classification: Leaving rating as Green but with a recommendation for review by the GMS test evaluation group as to suitability for this panel. Variants seem to result in a brain channelopathy rather than a skeletal muscle one.
Skeletal muscle channelopathy v1.31 SLC1A3 Eleanor Williams Tag Q2_21_rating was removed from gene: SLC1A3.
Skeletal Muscle Channelopathies v1.36 CACNA1A Eleanor Williams Classified gene: CACNA1A as Green List (high evidence)
Skeletal Muscle Channelopathies v1.36 CACNA1A Eleanor Williams Added comment: Comment on list classification: Leaving as green for consistency with the GMS Skeletal muscle channelopathy panel (panel 542).
Skeletal Muscle Channelopathies v1.36 CACNA1A Eleanor Williams Gene: cacna1a has been classified as Green List (High Evidence).
Skeletal muscle channelopathy v1.31 CACNA1A Eleanor Williams Tag Q2_21_rating was removed from gene: CACNA1A.
Skeletal muscle channelopathy v1.31 ATP1A2 Eleanor Williams Tag Q2_21_rating was removed from gene: ATP1A2.
Skeletal muscle channelopathy v1.31 CACNA1A Eleanor Williams changed review comment from: Comment on list classification: Leaving rating as green but with a recommendation for red rating following GMS review. As reported by Zornitza Stark variants in this gene appear to be associated with brain channelopathies rather than skeletal muscle.; to: Comment on list classification: Leaving rating as Green but with a recommendation for review by the GMS test evaluation group as to suitability for this panel. As reported by Zornitza Stark variants in this gene appear to be associated with brain channelopathies rather than skeletal muscle.
Skeletal Muscle Channelopathies v1.35 ATP1A2 Eleanor Williams Classified gene: ATP1A2 as Green List (high evidence)
Skeletal Muscle Channelopathies v1.35 ATP1A2 Eleanor Williams Added comment: Comment on list classification: Leaving as green for consistency with the GMS Skeletal muscle channelopathy panel (panel 542).
Skeletal Muscle Channelopathies v1.35 ATP1A2 Eleanor Williams Gene: atp1a2 has been classified as Green List (High Evidence).
Skeletal muscle channelopathy v1.31 ATP1A2 Eleanor Williams changed review comment from: Comment on list classification: Leaving rating as Green but with a recommendation of a red rating following GMS review, as there is only one case reported associated with a skeletal muscle phenotype.; to: Comment on list classification: Leaving rating as Green but with a recommendation for review by GMS evaluation group as to suitability for this panel. There is only one case reported associated with a skeletal muscle phenotype.
Likely inborn error of metabolism v2.154 PEX6 Sarah Leigh Tag Q3_21_MOI was removed from gene: PEX6.
Likely inborn error of metabolism v2.154 PEX6 Sarah Leigh Tag Q3_21_MOI tag was added to gene: PEX6.
Likely inborn error of metabolism v2.154 PEX6 Sarah Leigh Publications for gene: PEX6 were set to 27604308; 29220678; 20301621
Likely inborn error of metabolism v2.153 PEX6 Sarah Leigh Phenotypes for gene: PEX6 were changed from Disorders of peroxisome biogenesis; Peroxisome biogenesis disorder 4B 614863; Peroxisome biogenesis disorder 4A (Zellweger) 614862 to Peroxisome biogenesis disorder 4A (Zellweger) OMIM:614862; peroxisome biogenesis disorder 4A (Zellweger) MONDO:0013930; Peroxisome biogenesis disorder 4B OMIM:614863; peroxisome biogenesis disorder 4B MONDO:0013931
Likely inborn error of metabolism v2.153 PEX6 Sarah Leigh Publications for gene: PEX6 were set to 27604308
Likely inborn error of metabolism v2.152 PEX6 Sarah Leigh reviewed gene: PEX6: Rating: GREEN; Mode of pathogenicity: None; Publications: 29220678, 20301621; Phenotypes: Peroxisome biogenesis disorder 4A (Zellweger) OMIM:614862, peroxisome biogenesis disorder 4A (Zellweger) MONDO:0013930, Peroxisome biogenesis disorder 4B OMIM:614863, peroxisome biogenesis disorder 4B MONDO:0013931; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1198 DPYSL5 Ivone Leong Tag Q3_21_rating tag was added to gene: DPYSL5.
Intellectual disability v3.1198 DPYSL5 Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (probable) but not in OMIM.

PMID: 33894126. 10 individuals (2 of whom are related). 7/7 had severe ID, 9/9 DD and hypotonia, 3/6 ataxia, 3/10 seizures, 6/7 cerebellar hypoplasia and 7/10 corpus callosum agenesis.

Based on literature and expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (probable) but not in OMIM.

PMID: 33894126. 10 individuals (2 of whom are related). 7/7 had severe ID, 9/9 DD and hypotonia, 3/6 ataxia, 3/10 seizures, 6/7 cerebellar hypoplasia and 7/10 corpus callosum agenesis. Age range from 2.5 years to 33 years.

Based on literature and expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1198 DPYSL5 Ivone Leong Classified gene: DPYSL5 as Amber List (moderate evidence)
Intellectual disability v3.1198 DPYSL5 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (probable) but not in OMIM.

PMID: 33894126. 10 individuals (2 of whom are related). 7/7 had severe ID, 9/9 DD and hypotonia, 3/6 ataxia, 3/10 seizures, 6/7 cerebellar hypoplasia and 7/10 corpus callosum agenesis.

Based on literature and expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1198 DPYSL5 Ivone Leong Gene: dpysl5 has been classified as Amber List (Moderate Evidence).
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.25 CHD5 Ivone Leong Tag watchlist tag was added to gene: CHD5.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.25 CHD5 Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (possible) but not in OMIM.

PMID: 33944996. Age ranged from 3 years - 22 years. 9/14 individuals had ID (only 6 of 9 patients were assessed for severity with 2 moderate ID and 4 severe cases). 10/16 individuals had epilepsy. 7/14 had hypotonia and 3/7 had craniosynostosis. 16 different variants were identified (11 missense, 1 frameshift, 2 nonsense and 2 splice site variants).

There are >3 unrelated cases, therefore there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (possible) but not in OMIM.

PMID: 33944996. Age ranged from 3 years - 22 years. 9/14 individuals had ID (only 6 of 9 patients were assessed for severity with 2 moderate ID and 4 severe cases). 10/16 individuals had epilepsy. 7/14 had hypotonia and 3/7 had craniosynostosis. 16 different variants were identified (11 missense, 1 frameshift, 2 nonsense and 2 splice site variants).

As less than half the cases had craniosynostosis, this gene has been given an Amber rating awaiting more cases.
Early onset or syndromic epilepsy v2.395 CHD5 Ivone Leong Tag Q3_21_rating tag was added to gene: CHD5.
Intellectual disability v3.1197 CHD5 Ivone Leong Tag Q3_21_rating tag was added to gene: CHD5.
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.25 CHD5 Ivone Leong Entity copied from Intellectual disability v3.1197
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.25 CHD5 Ivone Leong gene: CHD5 was added
gene: CHD5 was added to Craniosynostosis. Sources: Expert Review Amber,Literature
Mode of inheritance for gene: CHD5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CHD5 were set to 33944996
Phenotypes for gene: CHD5 were set to Intellectual disability, MONDO:0001071; Epilepsy, MONDO:0005027
Early onset or syndromic epilepsy v2.395 CHD5 Ivone Leong Entity copied from Intellectual disability v3.1197
Early onset or syndromic epilepsy v2.395 CHD5 Ivone Leong gene: CHD5 was added
gene: CHD5 was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
Mode of inheritance for gene: CHD5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CHD5 were set to 33944996
Phenotypes for gene: CHD5 were set to Intellectual disability, MONDO:0001071; Epilepsy, MONDO:0005027
Intellectual disability v3.1197 CHD5 Ivone Leong Classified gene: CHD5 as Amber List (moderate evidence)
Intellectual disability v3.1197 CHD5 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (possible) but not in OMIM.

PMID: 33944996. Age ranged from 3 years - 22 years. 9/14 individuals had ID (only 6 of 9 patients were assessed for severity with 2 moderate ID and 4 severe cases). 10/16 individuals had epilepsy. 7/14 had hypotonia and 3/7 had craniosynostosis. 16 different variants were identified (11 missense, 1 frameshift, 2 nonsense and 2 splice site variants).

There are >3 unrelated cases, therefore there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Intellectual disability v3.1197 CHD5 Ivone Leong Gene: chd5 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1196 CHD5 Ivone Leong Phenotypes for gene: CHD5 were changed from Intellectual disability; Epilepsy to Intellectual disability, MONDO:0001071; Epilepsy, MONDO:0005027
Undiagnosed metabolic disorders v1.469 ABCB7 Ivone Leong Added comment: Comment on mode of inheritance: MOI changed from "X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)" to "X-LINKED: hemizygous mutation in males, biallelic mutations in females" as there is no evidence that carrier females have ataxia.
Undiagnosed metabolic disorders v1.469 ABCB7 Ivone Leong Mode of inheritance for gene: ABCB7 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Hereditary ataxia v1.235 ABCB7 Ivone Leong Added comment: Comment on mode of inheritance: MOI changed from "X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)" to "X-LINKED: hemizygous mutation in males, biallelic mutations in females" as there is no evidence that carrier females have ataxia.
Hereditary ataxia v1.235 ABCB7 Ivone Leong Mode of inheritance for gene: ABCB7 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Hereditary ataxia with onset in adulthood v2.81 ABCB7 Ivone Leong reviewed gene: ABCB7: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Ataxia and cerebellar anomalies - narrow panel v2.222 ABCB7 Ivone Leong Tag Q3_21_MOI tag was added to gene: ABCB7.
Ataxia and cerebellar anomalies - narrow panel v2.222 ABCB7 Ivone Leong reviewed gene: ABCB7: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Rare anaemia v1.23 ABCB7 Ivone Leong Tag Q3_21_MOI tag was added to gene: ABCB7.
Rare anaemia v1.23 ABCB7 Ivone Leong reviewed gene: ABCB7: Rating: ; 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)
Cytopenias and congenital anaemias v1.86 ABCB7 Ivone Leong Added comment: Comment on mode of inheritance: MOI 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)" as some carrier females have ring sideroblasts, dimorphic peripheral bloode smear, hypochromic and microcytic erythrocytes but no evidence of ataxia.
Cytopenias and congenital anaemias v1.86 ABCB7 Ivone Leong Mode of inheritance for gene: ABCB7 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)
Congenital fibrosis of the extraocular muscles v1.12 MYF5 Ivone Leong Tag watchlist tag was added to gene: MYF5.
Congenital fibrosis of the extraocular muscles v1.12 MYF5 Ivone Leong changed review comment from: PMID:29887215. 3 families and 5 patients. All patients have external ophthalmoplegia, 3/5 torticollis, 4/5 scoliosis, 0/5 hypotonia/weakness.

After consulting the Genomics England Clinical Team it was decided to leave this gene as Amber on this panel.; to: PMID:29887215. 3 families and 5 patients. 2 families from the same village Turkey with the same variant (c.23_32delAGTTCTCACC) and 1 family from Yemen (c.283C>T). All patients have external ophthalmoplegia, 3/5 torticollis, 4/5 scoliosis, 0/5 hypotonia/weakness.

After consulting the Genomics England Clinical Team it was decided that this gene is appropriate for the Congenital fibrosis of the extraocular muscles panel. This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). As 2 of the cases could be due to founder effect (Turkish families) and only 1 other case, there is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating until more evidence is available.
Congenital fibrosis of the extraocular muscles v1.12 MYF5 Ivone Leong Entity copied from Congenital myopathy v2.56
Congenital fibrosis of the extraocular muscles v1.12 MYF5 Ivone Leong gene: MYF5 was added
gene: MYF5 was added to Congenital fibrosis of the extraocular muscles. Sources: Expert Review Amber,Expert list,Literature
Mode of inheritance for gene: MYF5 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: MYF5 were set to 29887215
Phenotypes for gene: MYF5 were set to Ophthalmoplegia, external, with rib and vertebral anomalies, OMIM:618155
Mode of pathogenicity for gene: MYF5 was set to Other
Congenital myopathy v2.56 MYF5 Ivone Leong reviewed gene: MYF5: Rating: AMBER; Mode of pathogenicity: None; Publications: 29887215; Phenotypes: ; Mode of inheritance: None
Hydrocephalus v2.114 P4HB Ivone Leong reviewed gene: P4HB: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Ehlers Danlos syndrome with a likely monogenic cause v2.60 IPO8 Ivone Leong Entity copied from Thoracic aortic aneurysm and dissection v1.15
Ehlers Danlos syndrome with a likely monogenic cause v2.60 IPO8 Ivone Leong gene: IPO8 was added
gene: IPO8 was added to Ehlers Danlos syndromes. Sources: Expert Review Amber,Literature
Q2_21_rating tags were added to gene: IPO8.
Mode of inheritance for gene: IPO8 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IPO8 were set to 34010604; 34010605
Phenotypes for gene: IPO8 were set to Loeys-Dietz syndrome-like; cardiovascular, neurologic, skeletal and immunologic abnormalities
Primary immunodeficiency or monogenic inflammatory bowel disease v2.444 IPO8 Ivone Leong Tag Q3_21_expert_review tag was added to gene: IPO8.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.444 IPO8 Ivone Leong Classified gene: IPO8 as Amber List (moderate evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.444 IPO8 Ivone Leong Added comment: Comment on list classification: New gene added by Boaz Palterer (University of Florence). This gene is associated with a phenotype in Gene2Phenotype but not OMIM. As immune dysregulation is not seen in all affected individuals (PMID:34010604) and PMID:34010605 did not investigate the immune status of their cohort this gene has been given an Amber rating until further cases are available.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.444 IPO8 Ivone Leong Gene: ipo8 has been classified as Amber List (Moderate Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.443 IPO8 Ivone Leong Tag watchlist tag was added to gene: IPO8.
Epidermolysis bullosa and congenital skin fragility v1.49 NAXD Ivone Leong Deleted their comment
Epidermolysis bullosa and congenital skin fragility v1.49 NAXD Ivone Leong edited their review of gene: NAXD: Added comment: After consulting the clinical team at Genomics England, this gene has been added to this panel with an Amber rating (pending more evidence) as there is a skin phenotype is present in patients and may be the first things the patient is being seen for (PMID: 33224489).; Changed rating: AMBER
Epidermolysis bullosa and congenital skin fragility v1.49 NAXD Ivone Leong Tag Q2_21_rating was removed from gene: NAXD.
Tag watchlist tag was added to gene: NAXD.
Epidermolysis bullosa and congenital skin fragility v1.49 NAXD Ivone Leong Entity copied from White matter disorders and cerebral calcification - narrow panel v1.189
Epidermolysis bullosa and congenital skin fragility v1.49 NAXD Ivone Leong gene: NAXD was added
gene: NAXD was added to Epidermolysis bullosa and congenital skin fragility. Sources: Expert Review Amber,Expert list
Q2_21_rating tags were added to gene: NAXD.
Mode of inheritance for gene: NAXD was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NAXD were set to 30576410; 33224489; 31755961
Phenotypes for gene: NAXD were set to Encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, 2, OMIM:618321
Hypogonadotropic hypogonadism (GMS) v1.44 CLPP Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). There is currently not enough evidence to support a gene-disease association as the phenotypes among the patients vary. This gene has been given an Amber rating until more cases are available.
Hypogonadotropic hypogonadism (GMS) v1.44 CLPP Ivone Leong Tag Q3_21_rating was removed from gene: CLPP.
Tag watchlist tag was added to gene: CLPP.
Hypogonadotropic hypogonadism (GMS) v1.44 CLPP Ivone Leong Entity copied from White matter disorders and cerebral calcification - narrow panel v1.189
Hypogonadotropic hypogonadism (GMS) v1.44 CLPP Ivone Leong gene: CLPP was added
gene: CLPP was added to Hypogonadotropic hypogonadism idiopathic. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: CLPP.
Mode of inheritance for gene: CLPP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CLPP were set to 27899912; 23541340; 25956234; 26970254; 27087618; 27650058
Phenotypes for gene: CLPP were set to Perrault syndrome 3, OMIM:614129
Hypogonadotropic hypogonadism v1.33 CLPP Ivone Leong changed review comment from: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.; to: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). There is currently not enough evidence to support a gene-disease association as the phenotypes among the patients vary. This gene has been given an Amber rating until more cases are available.
Hypogonadotropic hypogonadism v1.33 CLPP Ivone Leong Tag Q3_21_rating was removed from gene: CLPP.
Tag watchlist tag was added to gene: CLPP.
Hypogonadotropic hypogonadism v1.33 CLPP Ivone Leong Entity copied from White matter disorders and cerebral calcification - narrow panel v1.189
Hypogonadotropic hypogonadism v1.33 CLPP Ivone Leong gene: CLPP was added
gene: CLPP was added to Hypogonadotropic hypogonadism. Sources: Expert list,Expert Review Amber
Q3_21_rating tags were added to gene: CLPP.
Mode of inheritance for gene: CLPP was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CLPP were set to 27899912; 23541340; 25956234; 26970254; 27087618; 27650058
Phenotypes for gene: CLPP were set to Perrault syndrome 3, OMIM:614129
White matter disorders and cerebral calcification - narrow panel v1.189 CLPP Ivone Leong Classified gene: CLPP as Amber List (moderate evidence)
White matter disorders and cerebral calcification - narrow panel v1.189 CLPP Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype (probable). There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
White matter disorders and cerebral calcification - narrow panel v1.189 CLPP Ivone Leong Gene: clpp has been classified as Amber List (Moderate Evidence).
White matter disorders and cerebral calcification - narrow panel v1.188 CLPP Ivone Leong Tag Q3_21_rating tag was added to gene: CLPP.
Nephrocalcinosis or nephrolithiasis v2.21 ATP6V0A4 Arina Puzriakova Publications for gene: ATP6V0A4 were set to
Renal tubulopathies v2.27 ATP6V0A4 Arina Puzriakova Publications for gene: ATP6V0A4 were set to
Nephrocalcinosis or nephrolithiasis v2.20 ATP6V0A4 Arina Puzriakova Tag Q3_21_MOI tag was added to gene: ATP6V0A4.
Tag watchlist_moi tag was added to gene: ATP6V0A4.
Nephrocalcinosis or nephrolithiasis v2.20 ATP6V0A4 Arina Puzriakova Added comment: Comment on mode of inheritance: Literature search showed that a single Japanese individual was reported in 2016 (PMID: 27274828) with a supposedly pathogenic heterozygous variant p.S544L. Hypokalemia, nephrocalcinosis and alkaluria suggesting distal renal tubular acidosis (dRTA) were detected, but metabolic acidosis was not evident. In 2020, a second Han Chinese family with five dRTA patients was reported (PMID: 32123165) who harboured the same p.S544L heterozygous variant. Some patients in this family were more severely affected than the previous case, displaying more severe complete dRTA with hypokalemia, osteoporosis, and kidney stones. Note this family also harboured 3 other homozygous variants in the ATP6V0A4 gene but these were ruled out, presumably due to MAF.

Apart from these two reports’ alternations in ATP6V0A4 have been found to be inherited recessively (heterozygous parent carriers are unaffected), and multiple such cases have been described in literature (references added to publications list).

At this moment there is only enough evidence to support an Amber rating for the monoallelic form - single heterozygous variant identified in 2 families from a similar ethnic background which does not suffice the inclusion criteria.

MOI should be changed from 'BOTH mono- and biallelic' to 'BIALLELIC' only at the next GMS panel review (tagged) until additional evidence emerges supporting heterozygous variants as disease-causing.
Nephrocalcinosis or nephrolithiasis v2.20 ATP6V0A4 Arina Puzriakova Mode of inheritance for gene: ATP6V0A4 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
Bleeding and platelet disorders v1.30 TNXB Arina Puzriakova reviewed gene: TNXB: Rating: GREEN; Mode of pathogenicity: None; Publications: ; Phenotypes: Ehlers-Danlos syndrome, classic-like, 1, OMIM:606408; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Bleeding and platelet disorders v1.30 COL3A1 Arina Puzriakova commented on gene: COL3A1: Correspondence from Dr Neeti Ghali & Dr Fleur van Dijk, Consultant Clinical Geneticists, EDS National Diagnostic Service (15/07/2021) indicating that inclusion of COL3A1 as Green on this panel would be beneficial as they receive referrals from haematologists asking to consider this form of vascular EDS, associated with significant bruising and haematoma formation.
Bleeding and platelet disorders v1.30 TNXB Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: TNXB.
Tag Q3_21_expert_review tag was added to gene: TNXB.
Bleeding and platelet disorders v1.30 COL3A1 Arina Puzriakova Tag Q2_21_expert_review was removed from gene: COL3A1.
Tag Q3_21_NHS_review tag was added to gene: COL3A1.
Tag Q3_21_expert_review tag was added to gene: COL3A1.
Bleeding and platelet disorders v1.30 COL3A1 Arina Puzriakova Tag Q2_21_expert_review tag was added to gene: COL3A1.
Early onset or syndromic epilepsy v2.394 CEP85L Rachel Challis reviewed gene: CEP85L: Rating: GREEN; Mode of pathogenicity: None; Publications: 32097629, 32097630; Phenotypes: Intellectual disability, epilepsy, lissencephaly; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Intellectual disability v3.1195 CEP85L Rachel Challis gene: CEP85L was added
gene: CEP85L was added to Intellectual disability. Sources: NHS GMS
Mode of inheritance for gene: CEP85L was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CEP85L were set to 32097629; 32097630
Phenotypes for gene: CEP85L were set to Intellectual disability; epilepsy, lissencephaly
Penetrance for gene: CEP85L were set to unknown
Review for gene: CEP85L was set to GREEN
gene: CEP85L was marked as current diagnostic
Added comment: Recommend adding as Green gene to GMS - R29 Intellectual disability panel.

Monoallelic missense and loss of function variants in CEP85L are associated with Lissencephaly (OMIM 618873). Over 10 unrelated families have been described with de novo and inherited rare variants in CEP85L. Functional work in cell lines and knockdown of Cep85l in mice confirms the role of CEP85L in neuronal migration.
PMID: 32097629
PMID: 32097630
Sources: NHS GMS
Malformations of cortical development v2.45 CEP85L Rachel Challis reviewed gene: CEP85L: Rating: GREEN; Mode of pathogenicity: None; Publications: PMID 32097629, 32097630; Phenotypes: Intellectual disability, epilepsy, lissencephaly; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes
Nephrocalcinosis or nephrolithiasis v2.19 ATP6V0A4 Arina Puzriakova Phenotypes for gene: ATP6V0A4 were changed from distal renal tubular acidosis; Compensated or uncomensated dRTA and/or recurrent stone formation, usually with hypocitraturia. +/- deafness; Renal tubular acidosis, distal, autosomal recessive to Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722
Monogenic hearing loss v2.179 ATP6V0A4 Arina Puzriakova Publications for gene: ATP6V0A4 were set to
Monogenic hearing loss v2.178 ATP6V0A4 Arina Puzriakova Phenotypes for gene: ATP6V0A4 were changed from to Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722
Differences in sex development v2.49 ATP6V0A4 Arina Puzriakova Phenotypes for gene: ATP6V0A4 were changed from Genital Anomalies and Suspected Adrenal Problems Gene Panel (UKGTN); Renal tubular acidosis, distal, autosomal recessive, 602722 to Genital Anomalies and Suspected Adrenal Problems Gene Panel (UKGTN); Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722
Renal tubulopathies v2.26 ATP6V0A4 Arina Puzriakova Phenotypes for gene: ATP6V0A4 were changed from Distal Renal Tubular Acidosis, Recessive; Renal tubular acidosis, distal, autosomal recessive, 602722; Distal renal tubular acidosis; Autosomal recessive distal renal tubular acidosis to Distal renal tubular acidosis 3, with or without sensorineural hearing loss, OMIM:602722
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.20 CAV3 Ivone Leong Tag Q3_21_MOI tag was added to gene: CAV3.
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.20 CAV3 Ivone Leong edited their review of gene: CAV3: Added comment: MOI should be changed to Both monoallelic and biallelic to match the MOI for CAV3 in Rhabdomyolysis and metabolic muscle disorders panel.; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Rhabdomyolysis and metabolic muscle disorders v1.48 CAV3 Ivone Leong Added comment: Comment on phenotypes: Previously:
Muscular dystrophy, limb-girdle, type IC 607801;Myopathy, distal, Tateyama type 614321;Rippling muscle disease 606072
Rhabdomyolysis and metabolic muscle disorders v1.48 CAV3 Ivone Leong Phenotypes for gene: CAV3 were changed from Muscular dystrophy, limb-girdle, type IC 607801; Myopathy, distal, Tateyama type 614321; Rippling muscle disease 606072 to Myopathy, distal, Tateyama type, OMIM:614321; Rippling muscle disease, OMIM:606072
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.20 CAV3 Ivone Leong Added comment: Comment on phenotypes: Previously: Limb-Girdle Muscular Dystrophy, Dominant;Muscular dystrophy, limb-girdle, type IC, 607801;Rippling muscle disease, 606072;Creatine phosphokinase, elevated serum, 123320;Myopathy, distal, Tateyama type, 614321;Cardiomyopathy, familial hypertrophic, 192600; Limb-girdle muscular dystrophy
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.20 CAV3 Ivone Leong Phenotypes for gene: CAV3 were changed from Limb-Girdle Muscular Dystrophy, Dominant; Muscular dystrophy, limb-girdle, type IC, 607801; Rippling muscle disease, 606072; Creatine phosphokinase, elevated serum, 123320; Myopathy, distal, Tateyama type, 614321; Cardiomyopathy, familial hypertrophic, 192600; Limb-girdle muscular dystrophy to Rippling muscle disease 2, OMIM:606072; Myopathy, distal, Tateyama type, OMIM:614321
Haematological malignancies cancer susceptibility v2.18 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Class: BM failure syndrome (typ AR); Ataxia telangiectasia; leukaemia; lymphoma; medulloblastoma; glioma; ataxia-telangiectasia; Lymphoma, ALL (particularly T-ALL); Leukaemia to Ataxia-telangiectasia, OMIM:208900; T-cell prolymphocytic leukemia, somatic
Adult onset neurodegenerative disorder v2.176 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Dystonia; Ataxia-Telangiectasia; Ataxia telangiectasia; Ataxia-telangiectasia, to Ataxia-telangiectasia, OMIM:208900
Primary immunodeficiency or monogenic inflammatory bowel disease v2.443 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 208900; Ataxia telangiectasia (ATM); immunodeficiency; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations; Combined immunodeficiencies with associated or syndromic features to Ataxia-telangiectasia, OMIM:208900; Combined immunodeficiencies with associated or syndromic features; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations
Hereditary ataxia v1.234 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-Telangiectasia ; Ataxia-telangiectasia, to Ataxia-telangiectasia, OMIM:208900
Hereditary haemorrhagic telangiectasia v2.7 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 208900 to Ataxia-telangiectasia, OMIM:208900
Ataxia and cerebellar anomalies - narrow panel v2.222 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia,; Ataxia-Telangiectasia to Ataxia-telangiectasia, OMIM:208900
Early onset dystonia v1.87 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Dystonia; Ataxia telangiectasia to Ataxia-telangiectasia, OMIM:208900
Primary ovarian insufficiency v1.44 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia 208900 to Ataxia-telangiectasia, OMIM:208900
COVID-19 research v1.79 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia telangiectasia (ATM); immunodeficiency; Combined immunodeficiencies with associated or syndromic features; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations; Ataxia-telangiectasia, 208900 to Ataxia-telangiectasia, OMIM:208900; Combined immunodeficiencies with associated or syndromic features; Ataxia, telangiectasia, pulmonary infections, lymphoreticular and other malignancies, increased alpha fetoprotein, increased radiosensitivity, chromosomal instability and chromosomal translocations
Haematological malignancies for rare disease v1.4 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Class: BM failure syndrome (typ AR); Ataxia telangiectasia; leukaemia; lymphoma; medulloblastoma; glioma; ataxia-telangiectasia; Lymphoma, ALL (particularly T-ALL); Leukaemia to Ataxia-telangiectasia, OMIM:208900; T-cell prolymphocytic leukemia, somatic
Childhood solid tumours v2.22 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia Telangiectasia; 208900 to Ataxia-telangiectasia, OMIM:208900
Adult solid tumours for rare disease v1.24 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia Telangiectasia to Ataxia-telangiectasia, OMIM:208900
Adult solid tumours cancer susceptibility v2.13 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia Telangiectasia to Ataxia-telangiectasia, OMIM:208900
Childhood solid tumours cancer susceptibility v1.15 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia Telangiectasia to Ataxia-telangiectasia, OMIM:208900
Peroxisomal disorders v1.13 PEX6 Julia Baptista reviewed gene: PEX6: Rating: GREEN; Mode of pathogenicity: None; Publications: 29220678, 20301621; Phenotypes: Zellweger syndrome; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal; Current diagnostic: yes
Early onset or syndromic epilepsy v2.394 PCDHGC4 Sarah Leigh Classified gene: PCDHGC4 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.394 PCDHGC4 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 v2.394 PCDHGC4 Sarah Leigh Gene: pcdhgc4 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.393 PCDHGC4 Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least eight variants reported in 19 members of nine unreleted families with a neurodevelopmental syndrome. Severe or moderate intellectual disabilty was found in eight families and seizures were evident in four families. Four of the variants were terminating, in silico analysis of the remaining missense (n=3) and splice variants were predicted to be pathogenic.
Sources: Literature; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO (15/7/2021). At least eight variants reported in 19 members of nine unreleted families with a neurodevelopmental syndrome. Severe or moderate intellectual disabilty was found in eight families and seizures were evident in four families. Four of the variants were terminating, in silico analysis of the remaining missense (n=3) and splice variants were predicted to be pathogenic.
Sources: Literature
Intellectual disability v3.1195 PCDHGC4 Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least eight variants reported in 19 members of nine unreleted families with a neurodevelopmental syndrome. Severe or moderate intellectual disabilty was found in eight families and seizures were evident in four families. Four of the variants were terminating, in silico analysis of the remaining missense (n=3) and splice variants were predicted to be pathogenic.
Sources: Literature; to: Not associated with a phenotype in OMIM, Gen2Phen or MONDO (15/7/2021). At least eight variants reported in 19 members of nine unreleted families with a neurodevelopmental syndrome. Severe or moderate intellectual disabilty was found in eight families and seizures were evident in four families. Four of the variants were terminating, in silico analysis of the remaining missense (n=3) and splice variants were predicted to be pathogenic.
Sources: Literature
Intellectual disability v3.1195 PCDHGC4 Sarah Leigh Classified gene: PCDHGC4 as Amber List (moderate evidence)
Intellectual disability v3.1195 PCDHGC4 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 v3.1195 PCDHGC4 Sarah Leigh Gene: pcdhgc4 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.393 PCDHGC4 Sarah Leigh gene: PCDHGC4 was added
gene: PCDHGC4 was added to Genetic epilepsy syndromes. Sources: Literature
Q3_21_rating tags were added to gene: PCDHGC4.
Mode of inheritance for gene: PCDHGC4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PCDHGC4 were set to 34244665
Phenotypes for gene: PCDHGC4 were set to neurodevelopmental syndrome
Review for gene: PCDHGC4 was set to GREEN
Added comment: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least eight variants reported in 19 members of nine unreleted families with a neurodevelopmental syndrome. Severe or moderate intellectual disabilty was found in eight families and seizures were evident in four families. Four of the variants were terminating, in silico analysis of the remaining missense (n=3) and splice variants were predicted to be pathogenic.
Sources: Literature
Intellectual disability v3.1194 PCDHGC4 Sarah Leigh gene: PCDHGC4 was added
gene: PCDHGC4 was added to Intellectual disability. Sources: Literature
Q3_21_rating tags were added to gene: PCDHGC4.
Mode of inheritance for gene: PCDHGC4 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PCDHGC4 were set to 34244665
Phenotypes for gene: PCDHGC4 were set to neurodevelopmental syndrome
Review for gene: PCDHGC4 was set to GREEN
Added comment: Not associated with a phenotype in OMIM, Gen2Phen or MONDO. At least eight variants reported in 19 members of nine unreleted families with a neurodevelopmental syndrome. Severe or moderate intellectual disabilty was found in eight families and seizures were evident in four families. Four of the variants were terminating, in silico analysis of the remaining missense (n=3) and splice variants were predicted to be pathogenic.
Sources: Literature
Inherited ovarian cancer (without breast cancer) v2.21 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 208900; Lymphoma, B-cell non-Hodgkin, somatic; {Breast cancer, susceptibility to}, 114480; Lymphoma, mantle cell; T-cell prolymphocytic leukemia, somatic; Breast and Ovarian Cancer to {Breast cancer, susceptibility to}, OMIM:114480
Familial breast cancer v1.14 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 208900; Lymphoma, B-cell non-Hodgkin, somatic; {Breast cancer, susceptibility to}, 114480; Lymphoma, mantle cell; T-cell prolymphocytic leukemia, somatic; Breast and Ovarian Cancer to {Breast cancer, susceptibility to}, OMIM:114480
Intellectual disability v3.1193 ATXN2L Ivone Leong Tag watchlist tag was added to gene: ATXN2L.
Intellectual disability v3.1193 ATXN2L Ivone Leong Classified gene: ATXN2L as Amber List (moderate evidence)
Intellectual disability v3.1193 ATXN2L Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not asssociated with a phenotype in OMIM or Gene2Phenotype. There is not enough evidence to support a gene-disease association. This gene has been given a Amber rating.
Intellectual disability v3.1193 ATXN2L Ivone Leong Gene: atxn2l has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1192 EPHA7 Ivone Leong Tag watchlist tag was added to gene: EPHA7.
Intellectual disability v3.1192 EPHA7 Ivone Leong Classified gene: EPHA7 as Amber List (moderate evidence)
Intellectual disability v3.1192 EPHA7 Ivone Leong Added comment: Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. This gene has been given an Amber rating based on expert review.
Intellectual disability v3.1192 EPHA7 Ivone Leong Gene: epha7 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1191 EPHA7 Ivone Leong Phenotypes for gene: EPHA7 were changed from Global developmental delay; Intellectual disability; Delayed speech and language development; Behavioral abnormality to Global developmental delay; Intellectual disability, MONDO:0001071; Delayed speech and language development; Behavioral abnormality
Early onset or syndromic epilepsy v2.392 HEATR5B Ivone Leong Entity copied from Intellectual disability v3.1190
Early onset or syndromic epilepsy v2.392 HEATR5B Ivone Leong gene: HEATR5B was added
gene: HEATR5B was added to Genetic epilepsy syndromes. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: HEATR5B.
Mode of inheritance for gene: HEATR5B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HEATR5B were set to 33824466
Phenotypes for gene: HEATR5B were set to pontocerebellar hypoplasia, MONDO:0020135; intellectual disability, MONDO:0001071; seizures
Intellectual disability v3.1190 ERGIC3 Ivone Leong Tag watchlist tag was added to gene: ERGIC3.
Intellectual disability v3.1190 ERGIC3 Ivone Leong Classified gene: ERGIC3 as Amber List (moderate evidence)
Intellectual disability v3.1190 ERGIC3 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not asssociated with a phenotype in OMIM or Gene2Phenotype. There is not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Intellectual disability v3.1190 ERGIC3 Ivone Leong Gene: ergic3 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1189 ERGIC3 Ivone Leong Phenotypes for gene: ERGIC3 were changed from Intellectual disability to Intellectual disability, MONDO:0001071
Cerebellar hypoplasia v1.53 HEATR5B Ivone Leong Entity copied from Intellectual disability v3.1188
Cerebellar hypoplasia v1.53 HEATR5B Ivone Leong gene: HEATR5B was added
gene: HEATR5B was added to Cerebellar hypoplasia. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: HEATR5B.
Mode of inheritance for gene: HEATR5B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HEATR5B were set to 33824466
Phenotypes for gene: HEATR5B were set to pontocerebellar hypoplasia, MONDO:0020135; intellectual disability, MONDO:0001071; seizures
Ataxia and cerebellar anomalies - narrow panel v2.221 HEATR5B Ivone Leong Entity copied from Intellectual disability v3.1188
Ataxia and cerebellar anomalies - narrow panel v2.221 HEATR5B Ivone Leong gene: HEATR5B was added
gene: HEATR5B was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review Amber,Literature
watchlist tags were added to gene: HEATR5B.
Mode of inheritance for gene: HEATR5B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HEATR5B were set to 33824466
Phenotypes for gene: HEATR5B were set to pontocerebellar hypoplasia, MONDO:0020135; intellectual disability, MONDO:0001071; seizures
Intellectual disability v3.1188 HEATR5B Ivone Leong Classified gene: HEATR5B as Amber List (moderate evidence)
Intellectual disability v3.1188 HEATR5B Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. There is currently not enough evidence to support a gene-disease association. This gene has been given an Amber rating.
Intellectual disability v3.1188 HEATR5B Ivone Leong Gene: heatr5b has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1187 HEATR5B Ivone Leong Tag watchlist tag was added to gene: HEATR5B.
Intellectual disability v3.1187 HEATR5B Ivone Leong Phenotypes for gene: HEATR5B were changed from pontocerebellar hypoplasia; intellectual disability; seizures to pontocerebellar hypoplasia, MONDO:0020135; intellectual disability, MONDO:0001071; seizures
Intellectual disability v3.1186 JPH3 Ivone Leong Classified gene: JPH3 as Red List (low evidence)
Intellectual disability v3.1186 JPH3 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is asssociated with a phenotype in OMIM but not Gene2Phenotype. As there is only one case there is not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Intellectual disability v3.1186 JPH3 Ivone Leong Gene: jph3 has been classified as Red List (Low Evidence).
Intellectual disability v3.1185 KIF1B Ivone Leong Classified gene: KIF1B as Red List (low evidence)
Intellectual disability v3.1185 KIF1B Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is asssociated with a phenotype in OMIM but not Gene2Phenotype. As there is only one case there is not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Intellectual disability v3.1185 KIF1B Ivone Leong Gene: kif1b has been classified as Red List (Low Evidence).
Intellectual disability v3.1184 KIF1B Ivone Leong Phenotypes for gene: KIF1B were changed from Hypotonia; coloboma; hypoplasia of the corpus callosum; severe neurodevelopmental delay to Hypotonia; coloboma, MONDO:0001476; hypoplasia of the corpus callosum; severe neurodevelopmental delay
Intellectual disability v3.1183 SAMD9L Ivone Leong Classified gene: SAMD9L as Red List (low evidence)
Intellectual disability v3.1183 SAMD9L Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in OMIM and Gene2Phenotype, but nothing related to ID. There is currently not enough evidence to support a gene-disease association. This gene has been given a Red status.
Intellectual disability v3.1183 SAMD9L Ivone Leong Gene: samd9l has been classified as Red List (Low Evidence).
Intellectual disability v3.1182 SAMD9L Ivone Leong Phenotypes for gene: SAMD9L were changed from Intellectual disability to Intellectual disability, MONDO:0001071
Bilateral congenital or childhood onset cataracts v2.76 ALDH18A1 Sarah Leigh Phenotypes for gene: ALDH18A1 were changed from Autosomal dominant cutis laxa-3 (ADCL3); autosomal recessive cutis laxa type III (ARCL3) to Cutis laxa, autosomal dominant 3 OMIM:616603; cutis laxa, autosomal dominant 3 MONDO:0014706; Cutis laxa, autosomal recessive, type IIIA OMIM:219150; ALDH18A1-related de Barsy syndrome MONDO:0009053; Spastic paraplegia 9A, autosomal dominant OMIM:601162; hereditary spastic paraplegia 9A MONDO:0011006; Spastic paraplegia 9B, autosomal recessive OMIM:616586; autosomal recessive complex spastic paraplegia type 9B MONDO:0014702
Likely inborn error of metabolism v2.152 ALDH18A1 Sarah Leigh Phenotypes for gene: ALDH18A1 were changed from Hypoprolinaemia, Cutis laxa, autosomal recessive, type IIIa (Disorders of ornithine or proline metabolism); Cutis laxa, autosomal recessive, type IIIA (Delta-1-pyrroline 5 carboxylic acid synthetase deficiency) 219150 to Cutis laxa, autosomal dominant 3 OMIM:616603; cutis laxa, autosomal dominant 3 MONDO:0014706; Cutis laxa, autosomal recessive, type IIIA OMIM:219150; ALDH18A1-related de Barsy syndrome MONDO:0009053; Spastic paraplegia 9A, autosomal dominant OMIM:601162; hereditary spastic paraplegia 9A MONDO:0011006; Spastic paraplegia 9B, autosomal recessive OMIM:616586; autosomal recessive complex spastic paraplegia type 9B MONDO:0014702
Hyperammonaemia v1.9 ALDH18A1 Sarah Leigh Phenotypes for gene: ALDH18A1 were changed from Cutis laxa, autosomal recessive, type IIIA (Delta-1-pyrroline 5 carboxylic acid synthetase deficiency) 219150 to Cutis laxa, autosomal recessive, type IIIA (Delta-1-pyrroline 5 carboxylic acid synthetase deficiency) 219150; ALDH18A1-related de Barsy syndrome MONDO:0009053
Undiagnosed metabolic disorders v1.468 ALDH18A1 Sarah Leigh Added comment: Comment on phenotypes: Hypoprolinaemia, Cutis laxa, autosomal recessive, type IIIa (Disorders of ornithine or proline metabolism);Cutis laxa, autosomal recessive, type IIIA (Delta-1-pyrroline 5 carboxylic acid synthetase deficiency) 219150
Undiagnosed metabolic disorders v1.468 ALDH18A1 Sarah Leigh Phenotypes for gene: ALDH18A1 were changed from Hypoprolinaemia, Cutis laxa, autosomal recessive, type IIIa (Disorders of ornithine or proline metabolism); Cutis laxa, autosomal recessive, type IIIA (Delta-1-pyrroline 5 carboxylic acid synthetase deficiency) 219150 to Cutis laxa, autosomal dominant 3 OMIM:616603; cutis laxa, autosomal dominant 3 MONDO:0014706; Cutis laxa, autosomal recessive, type IIIA OMIM:219150; ALDH18A1-related de Barsy syndrome MONDO:0009053; Spastic paraplegia 9A, autosomal dominant OMIM:601162; hereditary spastic paraplegia 9A MONDO:0011006; Spastic paraplegia 9B, autosomal recessive OMIM:616586; autosomal recessive complex spastic paraplegia type 9B MONDO:0014702
Arthrogryposis v3.112 MED12 Arina Puzriakova Classified gene: MED12 as Amber List (moderate evidence)
Arthrogryposis v3.112 MED12 Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update.
Arthrogryposis v3.112 MED12 Arina Puzriakova Gene: med12 has been classified as Amber List (Moderate Evidence).
Arthrogryposis v3.111 MED12 Arina Puzriakova Phenotypes for gene: MED12 were changed from MED12-related disorders to MED12-related disorders; Opitz-Kaveggia syndrome, OMIM:305450; Ohdo syndrome, X-linked, OMIM:300895; Lujan-Fryns syndrome, OMIM:309520
Arthrogryposis v3.110 MED12 Arina Puzriakova Publications for gene: MED12 were set to 20301719
Arthrogryposis v3.109 MED12 Arina Puzriakova Tag Q3_21_rating tag was added to gene: MED12.
Arthrogryposis v3.109 MED12 Arina Puzriakova reviewed gene: MED12: Rating: GREEN; Mode of pathogenicity: None; Publications: 565138, 7201743, 16700052, 17369503, 19938245, 25790323; Phenotypes: Opitz-Kaveggia syndrome, OMIM:305450, Ohdo syndrome, X-linked, OMIM:300895, Lujan-Fryns syndrome, OMIM:309520; Mode of inheritance: X-LINKED: hemizygous mutation in males, biallelic mutations in females
Thoracic aortic aneurysm or dissection (GMS) v1.15 MED12 Arina Puzriakova Publications for gene: MED12 were set to
Thoracic aortic aneurysm or dissection (GMS) v1.14 MED12 Arina Puzriakova Phenotypes for gene: MED12 were changed from Lujan-Fryns syndrome, 309520; Marfan Syndrome, Thoracic Aortic Aneurysm & Dissection (TAAD), and Related Disorders to Lujan-Fryns syndrome, OMIM:309520; Marfan Syndrome, Thoracic Aortic Aneurysm & Dissection (TAAD), and Related Disorders
Thoracic aortic aneurysm or dissection v1.121 MED12 Arina Puzriakova Phenotypes for gene: MED12 were changed from Lujan-Fryns syndrome, 309520; Marfan Syndrome, Thoracic Aortic Aneurysm & Dissection (TAAD), and Related Disorders to Lujan-Fryns syndrome, OMIM:309520; Marfan Syndrome, Thoracic Aortic Aneurysm & Dissection (TAAD), and Related Disorders
Thoracic aortic aneurysm or dissection v1.120 MED12 Arina Puzriakova Classified gene: MED12 as Red List (low evidence)
Thoracic aortic aneurysm or dissection v1.120 MED12 Arina Puzriakova Added comment: Comment on list classification: MED12 was previously demoted on the GMS equivalent panel (Thoracic aortic aneurysm and dissection v1.2) due to insufficient evidence. Therefore this gene has been demoted from Green to Red to reflect the most up-to-date knowledge here.
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There are reports of patients with Lujan-Fryns syndrome and aortic dilation, but these were not patients with MED12 variants. Patients reported with MED12 c.3020A>G did not have aortic involvement.
Thoracic aortic aneurysm or dissection v1.120 MED12 Arina Puzriakova Gene: med12 has been classified as Red List (Low Evidence).
Periodic fever syndromes v1.13 APOC2 Arina Puzriakova Phenotypes for gene: APOC2 were changed from Amyloidosis; Hyperlipoproteinemia, type Ib 207750 to Amyloidosis
Intellectual disability v3.1181 SPTBN1 Sarah Leigh Classified gene: SPTBN1 as Amber List (moderate evidence)
Intellectual disability v3.1181 SPTBN1 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 v3.1181 SPTBN1 Sarah Leigh Gene: sptbn1 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.391 SPTBN1 Sarah Leigh Classified gene: SPTBN1 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.391 SPTBN1 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 v2.391 SPTBN1 Sarah Leigh Gene: sptbn1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1180 SPTBN1 Sarah Leigh gene: SPTBN1 was added
gene: SPTBN1 was added to Intellectual disability. Sources: Literature
Q3_21_rating tags were added to gene: SPTBN1.
Mode of inheritance for gene: SPTBN1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SPTBN1 were set to 34211179
Phenotypes for gene: SPTBN1 were set to autosomal dominant neurodevelopmental syndrome
Review for gene: SPTBN1 was set to GREEN
Added comment: Not associated with a phenotype in OMIM, Gen2Phen or MONDO (as of 13/07/2021). At least 27 monoallelic variants reported in 29 individuals with neurodevelopmental abnormalities. Developmental delay was reported in 28/28 tested cases. Intellectual disabilty was reported in 21/24 tested cases (including severe in 5 cases, moderate to severe in 2 cases and moderate in 4 cases) and epilepsy/seizures was reported in 9/24 tested cases (including febrile seizures in 2 cases). Extensive supportive functional evidence was also reported (PMID 34211179).
Sources: Literature
Early onset or syndromic epilepsy v2.390 SPTBN1 Sarah Leigh gene: SPTBN1 was added
gene: SPTBN1 was added to Genetic epilepsy syndromes. Sources: Literature
Q3_21_rating tags were added to gene: SPTBN1.
Mode of inheritance for gene: SPTBN1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: SPTBN1 were set to 34211179
Phenotypes for gene: SPTBN1 were set to autosomal dominant neurodevelopmental syndrome
Review for gene: SPTBN1 was set to GREEN
Added comment: Not associated with a phenotype in OMIM, Gen2Phen or MONDO (as of 13/07/2021). At least 27 monoallelic variants reported in 29 individuals with neurodevelopmental abnormalities. Developmental delay was reported in 28/28 tested cases. Intellectual disabilty was reported in 21/24 tested cases (including severe in 5 cases, moderate to severe in 2 cases and moderate in 4 cases) and epilepsy/seizures was reported in 9/24 tested cases (including febrile seizures in 2 cases). Extensive supportive functional evidence was also reported (PMID 34211179).
Sources: Literature
Severe multi-system atopic disease with high IgE v1.8 CARD11 Ivone Leong Phenotypes for gene: CARD11 were changed from multisystem atopic disease, eczema, raised IgE, low IgM, eosinophilia; B-cell expansion with NFKB and T-cell anergy 616452 AD to multisystem atopic disease, eczema, raised IgE, low IgM, eosinophilia; B-cell expansion with NFKB and T-cell anergy, OMIM:616452
Rhabdomyolysis and metabolic muscle disorders v1.47 CACNA1S Ivone Leong Phenotypes for gene: CACNA1S were changed from {Malignant hyperthermia susceptibility 5}, 601887 to {Malignant hyperthermia susceptibility 5}, OMIM:601887
Skeletal Muscle Channelopathies v1.34 CACNA1S Ivone Leong Publications for gene: CACNA1S were set to 15534250; 18835861
Skeletal Muscle Channelopathies v1.33 CACNA1S Ivone Leong Added comment: Comment on mode of inheritance: Changing MOI from "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted" to "BOTH monoallelic and biallelic, autosomal or pseudoautosomal" based on the review by Eleanor Williams for the same gene on the "Skeletal muscle channelopathy" panel:

"PMID: 28012042 - Shartner et al 2017 - report 11 individuals with congenital myopathy from 7 unrelated families (Caucasian, Argentinean, or Vietnamese) and variants in CACNA1S identified through exome sequencing. The s from origin were included in this study. There were 3 sporadic cases (2 compound het, 1 het), 2 families with dominant inheritance, and 2 families with recessive inheritance . 10 different variants were identified.
Eleanor Williams (Genomics England Curator), 17 Mar 2021"
Skeletal Muscle Channelopathies v1.33 CACNA1S Ivone Leong Mode of inheritance for gene: CACNA1S was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Intellectual disability v3.1179 CAMK2A Ivone Leong Tag watchlist_moi tag was added to gene: CAMK2A.
Intellectual disability v3.1179 NAA20 Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature; to: Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 in this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature
Severe microcephaly v2.220 NAA20 Sarah Leigh changed review comment from: Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature; to: Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 in this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature
Intellectual disability v3.1179 NAA20 Sarah Leigh Classified gene: NAA20 as Amber List (moderate evidence)
Intellectual disability v3.1179 NAA20 Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be amber on this panel, based on two missense variants, which have supporting in silico and experimental evidence in cases with mild to severe intellectually disability (PMID 34230638).
Intellectual disability v3.1179 NAA20 Sarah Leigh Gene: naa20 has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.220 NAA20 Sarah Leigh Classified gene: NAA20 as Amber List (moderate evidence)
Severe microcephaly v2.220 NAA20 Sarah Leigh Gene: naa20 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1178 NAA20 Sarah Leigh Added comment: Comment on phenotypes: Currently there is no phenotype associated with this gene in OMIM, Gen2Phen or MONDO (13/07/2021).
Intellectual disability v3.1178 NAA20 Sarah Leigh Phenotypes for gene: NAA20 were changed from autosomal recessive developmental delay, intellectual disability, and microcephaly to autosomal recessive developmental delay, intellectual disability, and microcephaly
Severe microcephaly v2.219 NAA20 Sarah Leigh changed review comment from: Comment on phenotypes: Currently there is not phenotype associated with this gene in OMIM, Gen2Phen or MONDO (13/07/2021).; to: Comment on phenotypes: Currently there is no phenotype associated with this gene in OMIM, Gen2Phen or MONDO (13/07/2021).
Severe microcephaly v2.219 NAA20 Sarah Leigh Added comment: Comment on phenotypes: Currently there is not phenotype associated with this gene in OMIM, Gen2Phen or MONDO (13/07/2021).
Severe microcephaly v2.219 NAA20 Sarah Leigh Phenotypes for gene: NAA20 were changed from autosomal recessive developmental delay, intellectual disability, and microcephaly to autosomal recessive developmental delay, intellectual disability, and microcephaly
Intellectual disability v3.1177 NAA20 Sarah Leigh gene: NAA20 was added
gene: NAA20 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: NAA20 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NAA20 were set to 34230638
Phenotypes for gene: NAA20 were set to autosomal recessive developmental delay, intellectual disability, and microcephaly
Review for gene: NAA20 was set to AMBER
Added comment: Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature
Severe microcephaly v2.218 NAA20 Sarah Leigh gene: NAA20 was added
gene: NAA20 was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: NAA20 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NAA20 were set to 34230638
Phenotypes for gene: NAA20 were set to autosomal recessive developmental delay, intellectual disability, and microcephaly
Review for gene: NAA20 was set to AMBER
Added comment: Not associated with a phenotype in OMIM nor Gen2Phen. Two missense variants reported as homozygotes in one family each. In silico predictions and in vitro functional studies provide evidence that these variants will adversely affect their capacity to form a NatB complex with NAA25, and in vitro acetylation assays revealed reduced catalytic activities toward different NatB substrates (PMID 34230638). Children from these two families had developmental delay, intellectual disability (mild to moderate family 1, severe family 2).
The two children in family 1 in this study had a head circumcernces of -2.3 & -1.9 SD (which is not regarded as severe microcephaly).
The three children from family 2 this study had a head circumcernces of -3.5, -3.0 & -3.5 SD (which is regarded as severe microcephaly). Subtle dysmorphic features were also reported.
Sources: Literature
Intellectual disability v3.1176 CAMK2A Ivone Leong Added comment: Comment on phenotypes: Previously:
Intellectual disability
Intellectual disability v3.1176 CAMK2A Ivone Leong Phenotypes for gene: CAMK2A were changed from Intellectual disability to Mental retardation, autosomal dominant 53, OMIM:617798; ?Mental retardation, autosomal recessive 63, OMIM:618095
Intellectual disability v3.1175 CAMK2A Ivone Leong Added comment: Comment on publications: PMID:29784083. 2 siblings born from consanguineous parents from Jordan with homozygous missense variant. Both had severe ID.
Intellectual disability v3.1175 CAMK2A Ivone Leong Publications for gene: CAMK2A were set to 26350204; 29100089
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.19 CAPN3 Ivone Leong Added comment: Comment on phenotypes: Previously:
Muscular dystrophy, limb-girdle, type 2A, 253600;Limb-Girdle Muscular Dystrophy, Recessive; Limb-girdle muscular dystrophy
Limb girdle muscular dystrophies, myofibrillar myopathies and distal myopathies v2.19 CAPN3 Ivone Leong Phenotypes for gene: CAPN3 were changed from Muscular dystrophy, limb-girdle, type 2A, 253600; Limb-Girdle Muscular Dystrophy, Recessive; Limb-girdle muscular dystrophy to Muscular dystrophy, limb-girdle, autosomal recessive 1, OMIM:253600
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.21 C3 Ivone Leong Added comment: Comment on phenotypes: Previously:
Haemolytic uraemic syndrome; aHUS; Hemolytic uremic syndrome, atypical, susceptibility to, 5,612925; C3 glomerulopathy; C3G; C3 deficiency, 613779; Immune complex MPGN; IC-MPGN
Membranoproliferative glomerulonephritis including C3 glomerulopathy v2.21 C3 Ivone Leong Phenotypes for gene: C3 were changed from Haemolytic uraemic syndrome; aHUS; Hemolytic uremic syndrome, atypical, susceptibility to, 5,612925; C3 glomerulopathy; C3G; C3 deficiency, 613779; Immune complex MPGN; IC-MPGN to Hemolytic uremic syndrome, atypical, susceptibility to, 5, OMIM:612925; C3 glomerulopathy; C3G
Atypical haemolytic uraemic syndrome v2.9 C3 Ivone Leong Phenotypes for gene: C3 were changed from Hemolytic uremic syndrome, atypical, susceptibility to, 5, 612925 to Hemolytic uremic syndrome, atypical, susceptibility to, 5, OMIM:612925
Intellectual disability v3.1174 MYT1 Ivone Leong Classified gene: MYT1 as Red List (low evidence)
Intellectual disability v3.1174 MYT1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype but not in OMIM. There is currently not enough evidence to support a gene-disease association. This gene has been given a Red rating.
Intellectual disability v3.1174 MYT1 Ivone Leong Gene: myt1 has been classified as Red List (Low Evidence).
Intellectual disability v3.1173 MYT1 Ivone Leong Added comment: Comment on publications: PMID:18341605. A case with de novo subtelomeric deletion on chromosome 20 containing MYT1 and PCMTD2. Both genes affect myelination and neural differentiation.

PMID:33710394. Authors also discuss that variants in MYT1 have been identified in patients with oculo-auriculo-vertebral spectrum (OAVS) who have normal intelligence.
Intellectual disability v3.1173 MYT1 Ivone Leong Publications for gene: MYT1 were set to 33710394
Intellectual disability v3.1172 MYT1 Ivone Leong Phenotypes for gene: MYT1 were changed from Intellectual disability to Intellectual disability, MONDO:0001071
Intellectual disability v3.1171 SRCAP Ivone Leong Publications for gene: SRCAP were set to
Severe early-onset obesity v2.40 PHIP Ivone Leong Tag Q3_21_rating tag was added to gene: PHIP.
Severe early-onset obesity v2.40 PHIP Ivone Leong Classified gene: PHIP as Amber List (moderate evidence)
Severe early-onset obesity v2.40 PHIP Ivone Leong Added comment: Comment on list classification: New gene added by David Hunt (Wessex Clinical Genetics Service). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Severe early-onset obesity v2.40 PHIP Ivone Leong Gene: phip has been classified as Amber List (Moderate Evidence).
Severe early-onset obesity v2.39 PHIP Ivone Leong Tag Q3_21_NHS_review tag was added to gene: PHIP.
Familial non syndromic congenital heart disease v1.63 FLNA Arina Puzriakova Publications for gene: FLNA were set to 17190868, 8230166
Familial non syndromic congenital heart disease v1.62 FLNA Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'X-LINKED... biallelic mutations in females' to 'X-LINKED... monoallelic mutations in females may cause disease'.

Heterozygous females are more mildly affected than hemizygous males, but some healthy female carriers have also been described.
Familial non syndromic congenital heart disease v1.62 FLNA Arina Puzriakova Mode of inheritance for gene: FLNA 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)
Pigmentary skin disorders v1.13 FLNA Arina Puzriakova Publications for gene: FLNA were set to
Pigmentary skin disorders v1.12 FLNA Arina Puzriakova Tag Q3_21_expert_review tag was added to gene: FLNA.
Pigmentary skin disorders v1.12 FLNA Arina Puzriakova edited their review of gene: FLNA: Added comment: Pigmentary abnormalities of the skin are a feature of terminal osseous dysplasia (MIM# 300244). Although the number of unrelated cases (>3) reaches the threshold for inclusion as diagnostic-grade, FLNA is associated with multiple phenotypes which do not include pigmentary anomalies. This gene is already Green on other relevant GMS panels such as Skeletal dysplasia v2.107, which should be sufficient for detecting this phenotype. Nonetheless, as there may be some added clinical benefit of inclusion, FLNA will be flagged for review at the next GMS panel update with regard to the most appropriate rating on this panel.; Changed rating: AMBER; Changed publications to: 17152064, 18792982, 20598277, 30561107; Changed phenotypes to: Terminal osseous dysplasia, OMIM:300244; 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)
Cutaneous photosensitivity with a likely genetic cause v1.8 HMBS Ivone Leong Tag Q3_21_expert_review tag was added to gene: HMBS.
Cutaneous photosensitivity with a likely genetic cause v1.8 HMBS Ivone Leong commented on gene: HMBS
Bleeding and platelet disorders v1.30 FLNA Arina Puzriakova Publications for gene: FLNA were set to 29449050; 21960593; 32299270
Inherited bleeding disorders v1.162 FLNA Arina Puzriakova Publications for gene: FLNA were set to
Bleeding and platelet disorders v1.29 FLNA Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'X-LINKED... biallelic mutations in females' to 'X-LINKED... monoallelic mutations in females may cause disease'.

FLNA-related periventricular nodular heterotopia (MIM# 300049) can be associated with macrothrombocytopenia and a bleeding tendency in some cases (PMID: 16684786; 21960593; 29449050; 32299270). Affected females with heterozygous variants in FLNA have been identified indicating XLD inheritance.

The association with macrothrombocytopenia has been supported by in vitro assays and animal model (PMID: 21652675; 21960593; 30602618; 31471375)
Bleeding and platelet disorders v1.29 FLNA Arina Puzriakova Mode of inheritance for gene: FLNA 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)
Inherited bleeding disorders v1.161 FLNA Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'X-LINKED... biallelic mutations in females' to 'X-LINKED... monoallelic mutations in females may cause disease'.

FLNA-related periventricular nodular heterotopia (MIM# 300049) can be associated with macrothrombocytopenia and a bleeding tendency in some cases (PMID: 16684786; 21960593; 29449050; 32299270). Affected females with heterozygous variants in FLNA have been identified indicating XLD inheritance.

The association with macrothrombocytopenia has been supported by in vitro assays and animal model (PMID: 21652675; 21960593; 30602618; 31471375)
Inherited bleeding disorders v1.161 FLNA Arina Puzriakova Mode of inheritance for gene: FLNA 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)
Cutaneous photosensitivity with a likely genetic cause v1.8 GATA1 Ivone Leong Tag Q3_21_rating tag was added to gene: GATA1.
Cutaneous photosensitivity with a likely genetic cause v1.8 GATA1 Ivone Leong Tag Q3_21_expert_review tag was added to gene: GATA1.
Cutaneous photosensitivity with a likely genetic cause v1.8 GATA1 Ivone Leong reviewed gene: GATA1: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Inherited bleeding disorders v1.160 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Macrothrombocytopenia to Heterotopia, periventricular, 1, OMIM:300049; Macrothrombocytopenia
Cytopenia - NOT Fanconi anaemia v1.42 FLNA Arina Puzriakova Mode of inheritance for gene: FLNA was changed from Unknown to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Cytopenia - NOT Fanconi anaemia v1.41 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from to Heterotopia, periventricular, 1, OMIM:300049; Macrothrombocytopenia
Bleeding and platelet disorders v1.28 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from (NO OMIM NUMBER); Macrothrombocytopenia to Heterotopia, periventricular, 1, OMIM:300049; Macrothrombocytopenia
Cutaneous photosensitivity with a likely genetic cause v1.8 GATA1 Ivone Leong Publications for gene: GATA1 were set to
Arthrogryposis v3.109 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from FLNA-related disorders; Otopalatodigital syndrome, type I 311300; Otopalatodigital syndrome, type II 304120; Terminal osseous dysplasia 300244 to Frontometaphyseal dysplasia 1, OMIM:305620; Otopalatodigital syndrome, type I, OMIM:311300; Otopalatodigital syndrome, type II, OMIM:304120; Terminal osseous dysplasia, OMIM:300244
Intellectual disability v3.1170 ASCC3 Ivone Leong Classified gene: ASCC3 as Amber List (moderate evidence)
Intellectual disability v3.1170 ASCC3 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber. New publication (https://doi.org/10.1016/j.xhgg.2021.100024) describing 11 individuals from 7 unrelated families (1 family was originally described in PMID: 21937992 and had mild ID). Patients had phenotypes ranging from mild to severe developmental dealys. As ID is not the prominant phenotype, this gene has been given an Amber rating.
Intellectual disability v3.1170 ASCC3 Ivone Leong Gene: ascc3 has been classified as Amber List (Moderate Evidence).
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne edited their review of gene: ACAT2: Changed rating: GREEN
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne changed review comment from: Cytosolic acetoacetyl-CoA thiolase deficiency.
Inheritance - isolated cases.
Based on literature the ACAT2 gene encodes cytosolic acetoacetyl-CoA thiolase, which is important in the utilization of ketone bodies. ACAT2 gene can cause disorders of ketone body metabolism. ACAT2 gene is included in international classification of inherited metabolic
disorders (ICIMD).; to: Cytosolic acetoacetyl-CoA thiolase deficiency.
Inheritance - isolated cases.
Based on literature the ACAT2 gene encodes cytosolic acetoacetyl-CoA thiolase, which is important in the utilization of ketone bodies. ACAT2 gene can cause disorders of ketone body metabolism. ACAT2 gene is included in international classification of inherited metabolic
disorders (ICIMD).
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne reviewed gene: ACAT2: Rating: ; Mode of pathogenicity: None; Publications: PMID:33340416, PMID:20597, PMID:6150136; Phenotypes: Increased serum lactate and pyruvate, High levels of ketones, Low levels of cytosolic acetoacetyl-CoA thiolase, Hypotonia, Severe developmental delay; Mode of inheritance: None
Arthrogryposis v3.108 FLNA Arina Puzriakova Classified gene: FLNA as Amber List (moderate evidence)
Arthrogryposis v3.108 FLNA Arina Puzriakova Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant disorder on OMIM and G2P. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Arthrogryposis v3.108 FLNA Arina Puzriakova Gene: flna has been classified as Amber List (Moderate Evidence).
Arthrogryposis v3.107 FLNA Arina Puzriakova Tag Q3_21_rating tag was added to gene: FLNA.
Intellectual disability v3.1169 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Frontometaphyseal dysplasia, 305620Heterotopia, periventricular, ED variant, 300537FG syndrome 2, 300321Cardiac valvular dysplasia, X-linked, 314400Terminal osseous dysplasia, 300244Congenital short bowel syndrome, 300048; EPILEPTIC ENCEPHALOPATHY to Heterotopia, periventricular, 1, OMIM:300049; Otopalatodigital syndrome, type II, OMIM:304120; ?FG syndrome 2, OMIM:300321
Intellectual disability v3.1168 ASCC3 Ivone Leong Publications for gene: ASCC3 were set to 21937992; 26350204
Congenital myopathy v2.56 ASCC3 Ivone Leong Classified gene: ASCC3 as Amber List (moderate evidence)
Congenital myopathy v2.56 ASCC3 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a phenotype in Gene2Phenotype (possible gene-disease association) but not OMIM. There is enough evidence for this gene to be Green.
Congenital myopathy v2.56 ASCC3 Ivone Leong Gene: ascc3 has been classified as Amber List (Moderate Evidence).
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne Deleted their review
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne Deleted their comment
Mitochondrial disorders v2.47 ACAT2 Andžela Lazdāne gene: ACAT2 was added
gene: ACAT2 was added to Mitochondrial disorders. Sources: Literature
Mode of inheritance for gene: ACAT2 was set to Other
Publications for gene: ACAT2 were set to 33340416; 20597; 6150136
Phenotypes for gene: ACAT2 were set to Increased serum lactate and pyruvate; high levels of ketones
Review for gene: ACAT2 was set to GREEN
Added comment: Cytosolic acetoacetyl-CoA thiolase deficiency
Inheritance - isolated cases
Sources: Literature
Malformations of cortical development v2.45 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Periventricular Heterotopia 300049; Melnick-Needles syndrome 309350; Otopalatodigital syndrome, type I 311300; Otopalatodigital syndrome, type II 304120 to Heterotopia, periventricular, 1, OMIM:300049
Intestinal failure or congenital diarrhoea v1.42 FLNA Arina Puzriakova Added comment: Comment on mode of inheritance: Female carriers do not exhibit gastrointestinal defects indicating XLR inheritance
Intestinal failure or congenital diarrhoea v1.42 FLNA Arina Puzriakova Mode of inheritance for gene: FLNA was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Ehlers Danlos syndrome with a likely monogenic cause v2.59 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from to Cardiac valvular dysplasia, X-linked, OMIM:314400; Heterotopia, periventricular, 1, OMIM:300049
Congenital myopathy v2.55 ASCC3 Ivone Leong Tag Q3_21_rating tag was added to gene: ASCC3.
Pigmentary skin disorders v1.12 FLNA Arina Puzriakova Added comment: Comment on mode of inheritance: Terminal osseous dysplasia (associated with pigmentary skin defects) is an X-linked dominant male-lethal disease
Pigmentary skin disorders v1.12 FLNA Arina Puzriakova Mode of inheritance for gene: FLNA 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)
Pigmentary skin disorders v1.11 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Terminal osseous dysplasia with pigmentary defects to Terminal osseous dysplasia, OMIM:300244
Thoracic aortic aneurysm or dissection (GMS) v1.13 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Marfan Syndrome, Thoracic Aortic Aneurysm & Dissection (TAAD), and Related Disorders; Cardiac valvular dysplasia, X-linked 314400 to Cardiac valvular dysplasia, X-linked, OMIM:314400; Heterotopia, periventricular, 1, OMIM:300049
Thoracic aortic aneurysm or dissection v1.119 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Marfan Syndrome, Thoracic Aortic Aneurysm & Dissection (TAAD), and Related Disorders to Cardiac valvular dysplasia, X-linked, OMIM:314400; Heterotopia, periventricular, 1, OMIM:300049
Familial non syndromic congenital heart disease v1.61 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Cardiac valvular dysplasia, X-linked 314400 to Cardiac valvular dysplasia, X-linked, OMIM:314400
Intestinal failure or congenital diarrhoea v1.41 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Congenital short bowel syndrome, OMIM:300048 to Congenital short bowel syndrome, OMIM:300048; Intestinal pseudoobstruction, neuronal, OMIM:300048; ?FG syndrome 2, OMIM:300321
Gastrointestinal neuromuscular disorders v1.15 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Intestinal pseudoobstruction, neuronal 300048; Congenital short bowel syndrome 300048 to Congenital short bowel syndrome, OMIM:300048; Intestinal pseudoobstruction, neuronal, OMIM:300048
Congenital myopathy v2.55 TPM2 Ivone Leong commented on gene: TPM2: As there are only currently 2 homozygous cases, there is currently not enough evidence to support a change in MOI. It should also be noted that the parents (heterozygous for the variants) were asymptomatic.
Intellectual disability v3.1167 ACSL4 Ivone Leong reviewed gene: ACSL4: Rating: ; Mode of pathogenicity: None; Publications: 12525535, 11889465; Phenotypes: ; Mode of inheritance: None
Intellectual disability v3.1167 ACSL4 Ivone Leong Deleted their review
Intellectual disability v3.1167 ACSL4 Ivone Leong changed review comment from: ACSL4 is said to be X-linked dominant in OMIM.

PMID: 12525535 - a family with 4 affected males, 1 unaffected male, 2 carrier females and 1 non-carrier female. All affected males full scale IQ (FSIQ) ranged from 43-71, unaffected male FSIQ is 116, carrier females ranged from 74-83 and non-carrier female is 133. All carrier females showed 100% skewed inactivation.

PMID: 11889465 - Family MRX63, all carrier females showed complete skewed X-inactivation. All affected males showed non-specific, non-progressive mental deficiency (moderate - severe). Carrier females showed highly variable cognitive capacities (normal to moderate).

Based on the available evidence the MOI should be 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)".; to: ACSL4 is said to be X-linked dominant in OMIM.

PMID: 12525535 - a family with 4 affected males, 1 unaffected male, 2 carrier females and 1 non-carrier female. All affected males full scale IQ (FSIQ) ranged from 43-71, unaffected male FSIQ is 116, carrier females ranged from 74-83 and non-carrier female is 133. All carrier females showed 100% skewed inactivation.

PMID: 11889465 - Family MRX63, all carrier females showed complete skewed X-inactivation. All affected males showed non-specific, non-progressive mental deficiency (moderate - severe). Carrier females showed highly variable cognitive capacities (normal to moderate).

As there are only 2 cases where carrier females have a phenotype, the MOI should be kept as "X-LINKED: hemizygous mutation in males, biallelic mutations in females".
Clefting v2.33 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Orofacial Clefting with skeletal anomalies; Otopalatodigital syndrome, type I, 311300 (includes clefting); Otopalatodigital syndrome, type II, 304120 (includes clefting); Melnick-Needles syndrome, 309350 (includes clefting); OTOPALATODIGITAL SYNDROME, TYPE I; OPD1, OTOPALATODIGITAL SYNDROME, TYPE II; OPD2, FRONTOMETAPHYSEAL DYSPLASIA 1; FMD1 to Frontometaphyseal dysplasia 1, OMIM:305620; Melnick-Needles syndrome, OMIM:309350; Otopalatodigital syndrome, type I, OMIM:311300; Otopalatodigital syndrome, type II, OMIM:304120
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.24 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from frontometaphyseal dysplasia; oto-palato-digital syndromes; melnick-needles syndrome to Frontometaphyseal dysplasia 1, OMIM:305620; Melnick-Needles syndrome, OMIM:309350; Otopalatodigital syndrome, type I, OMIM:311300; Otopalatodigital syndrome, type II, OMIM:304120
Skeletal dysplasia v2.107 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Terminal osseous dysplasia 300244; Otopalatodigital syndrome, type II -304120; Otopalatodigital syndrome, type II 304120 XLD; Otopalatodigital syndrome, type I -311300; Melnick Needles syndrome 309350; Frontometaphyseal dysplasia 305620; Frontometaphyseal dysplasia 305620 XLR; Osteodysplasty Melnick Needles 309350 XLD to Frontometaphyseal dysplasia 1, OMIM:305620; Melnick-Needles syndrome, OMIM:309350; Otopalatodigital syndrome, type I, OMIM:311300; Otopalatodigital syndrome, type II, OMIM:304120; Terminal osseous dysplasia, OMIM:300244
Limb disorders v2.44 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Frontometaphyseal dysplasia 305620 XLR; Melnick-Needles syndrome, 309350; Osteodysplasty Melnick Needles 309350 XLD; Otopalatodigital syndrome, type II 304120 XLD; Terminal osseous dysplasia 300244 to Frontometaphyseal dysplasia 1, OMIM:305620; Melnick-Needles syndrome, OMIM:309350; Otopalatodigital syndrome, type I, OMIM:311300; Otopalatodigital syndrome, type II, OMIM:304120; Terminal osseous dysplasia, OMIM:300244
Radial dysplasia v1.14 FLNA Arina Puzriakova Phenotypes for gene: FLNA were changed from Melnick-Needles syndrome, 309350 to Frontometaphyseal dysplasia 1, OMIM:305620; Melnick-Needles syndrome, OMIM:309350; Otopalatodigital syndrome, type I, OMIM:311300; Otopalatodigital syndrome, type II, OMIM:304120; Terminal osseous dysplasia, OMIM:300244
Congenital myopathy v2.55 TPM2 Ivone Leong Phenotypes for gene: TPM2 were changed from CAP myopathy 2, OMIM:609285; Nemaline myopathy 4, autosomal dominant, OMIM:609285; Arthrogryposis multiplex congenita, distal, type1, OMIM:108120: Arthrogryposis, distal, type 2B, OMIM:601680; Congenital myopathy, MONDO:0019952; Multiple pterygium syndrome, MONDO:0017415 to CAP myopathy 2, OMIM:609285; Nemaline myopathy 4, autosomal dominant, OMIM:609285; Congenital myopathy, MONDO:0019952; Multiple pterygium syndrome, MONDO:0017415
Congenital myopathy v2.54 TPM2 Ivone Leong Phenotypes for gene: TPM2 were changed from CAP myopathy 2, OMIM:609285; Nemaline myopathy 4, autosomal dominant, OMIM:609285; Arthrogryposis multiplex congenita, distal, type1, OMIM:108120: Arthrogryposis, distal, type 2B, OMIM:601680 to CAP myopathy 2, OMIM:609285; Nemaline myopathy 4, autosomal dominant, OMIM:609285; Arthrogryposis multiplex congenita, distal, type1, OMIM:108120: Arthrogryposis, distal, type 2B, OMIM:601680; Congenital myopathy, MONDO:0019952; Multiple pterygium syndrome, MONDO:0017415
Congenital myopathy v2.53 TPM2 Ivone Leong Added comment: Comment on publications: PMID: 19155175 and 33558124 describe the 2 homozygous cases
Congenital myopathy v2.53 TPM2 Ivone Leong Publications for gene: TPM2 were set to 12592607; 11738357; 17434307; 24692096; 32092148; 27726070
Congenital myopathy v2.52 TPM2 Ivone Leong Phenotypes for gene: TPM2 were changed from CAP myopathy 2 609285; Nemaline myopathy 4, autosomal dominant 609285; Arthrogryposis multiplex congenita, distal, type1 108120: Arthrogryposis, distal, type 2B 601680 to CAP myopathy 2, OMIM:609285; Nemaline myopathy 4, autosomal dominant, OMIM:609285; Arthrogryposis multiplex congenita, distal, type1, OMIM:108120: Arthrogryposis, distal, type 2B, OMIM:601680
Congenital myopathy v2.51 TNNC2 Ivone Leong Tag Q3_21_rating tag was added to gene: TNNC2.
Congenital myopathy v2.51 TNNC2 Ivone Leong Classified gene: TNNC2 as Amber List (moderate evidence)
Congenital myopathy v2.51 TNNC2 Ivone Leong Added comment: Comment on list classification: Promoted from Red to Amber. This gene is currently not associated with a phenotype in OMIM or Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Congenital myopathy v2.51 TNNC2 Ivone Leong Gene: tnnc2 has been classified as Amber List (Moderate Evidence).
Congenital myopathy v2.50 TNNC2 Ivone Leong Phenotypes for gene: TNNC2 were changed from congenital myopathy to congenital myopathy, MONDO:0019952
Congenital myopathy v2.49 TNNC2 Ivone Leong Added comment: Comment on publications: PMID:26924529 was incorrectly entered for TNNC2
Congenital myopathy v2.49 TNNC2 Ivone Leong Publications for gene: TNNC2 were set to 26924529
Skeletal Muscle Channelopathies v1.32 DMPK Arina Puzriakova Phenotypes for gene: DMPK were changed from Myotonia; MYOTONIC DYSTROPHY 1 (DM1) to Myotonic dystrophy 1, OMIM:160900
Distal myopathies v1.31 DMPK Arina Puzriakova Phenotypes for gene: DMPK were changed from MYOTONIC DYSTROPHY 1 (DM1) to Myotonic dystrophy 1, OMIM:160900
Paroxysmal central nervous system disorders v1.16 DMPK Arina Puzriakova Phenotypes for gene: DMPK were changed from MYOTONIC DYSTROPHY 1 (DM1); Myotonia to Myotonic dystrophy 1, OMIM:160900
Paediatric motor neuronopathies v1.69 DMPK Arina Puzriakova Phenotypes for gene: DMPK were changed from spinal muscular atrophy, myotonic dystrophy (type 1), Prader-Willi syndrome, Angelman syndrome, and maternal UPD 14. to Myotonic dystrophy 1, OMIM:160900
Paediatric motor neuronopathies v1.68 DMPK Arina Puzriakova Mode of inheritance for gene: DMPK was changed from to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Fetal anomalies v1.689 DMPK_CTG Arina Puzriakova Tag STR tag was added to STR: DMPK_CTG.
Tag Q3_21_rating tag was added to STR: DMPK_CTG.
Tag Q3_21_expert_review tag was added to STR: DMPK_CTG.
DDG2P v2.37 DMPK_CTG Arina Puzriakova Tag STR tag was added to STR: DMPK_CTG.
Tag Q3_21_rating tag was added to STR: DMPK_CTG.
Tag Q3_21_expert_review tag was added to STR: DMPK_CTG.
Fetal anomalies v1.689 DMPK_CTG Arina Puzriakova Classified STR: DMPK_CTG as Amber List (moderate evidence)
Fetal anomalies v1.689 DMPK_CTG Arina Puzriakova Added comment: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1. The DMPK gene was demoted and this STR was added to this panel to ensure that cases are appropriately detected.

Only relevant prenatally if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel.
Fetal anomalies v1.689 DMPK_CTG Arina Puzriakova Str: dmpk_ctg has been classified as Amber List (Moderate Evidence).
DDG2P v2.37 DMPK_CTG Arina Puzriakova changed review comment from: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1). As DDG2P is a component of the Paediatric disorders super panel, the the DMPK gene was demoted and this STR was added to capture this entity and ensure that cases are detected.

Only relevant in a paediatric setting if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel.; to: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1). As DDG2P is a component of the Paediatric disorders super panel, the DMPK gene was demoted and this STR was added to ensure that cases are appropriately captured.

Only relevant in a paediatric setting if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel.
DDG2P v2.37 DMPK_CTG Arina Puzriakova changed review comment from: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1). As DDG2P is a component of the Paediatric disorders super panel, the DMPK_CTG STR has been added to capture this entity and ensure that cases are detected.

Only relevant in a paediatric setting if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel.; to: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1). As DDG2P is a component of the Paediatric disorders super panel, the the DMPK gene was demoted and this STR was added to capture this entity and ensure that cases are detected.

Only relevant in a paediatric setting if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel.
DDG2P v2.37 DMPK_CTG Arina Puzriakova Classified STR: DMPK_CTG as Amber List (moderate evidence)
DDG2P v2.37 DMPK_CTG Arina Puzriakova Added comment: Comment on list classification: The genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (normal range: 5–37; pathological: >50–>2000). Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1). As DDG2P is a component of the Paediatric disorders super panel, the DMPK_CTG STR has been added to capture this entity and ensure that cases are detected.

Only relevant in a paediatric setting if it is a large expansion. A small expansion has adult onset and would be an incidental finding. Therefore, this STR will be flagged for GMS expert review to determine the appropriate 'pathogenic number of repeats' relevant to this panel.
DDG2P v2.37 DMPK_CTG Arina Puzriakova Str: dmpk_ctg has been classified as Amber List (Moderate Evidence).
Fetal anomalies v1.688 DMPK_CTG Arina Puzriakova Entity copied from Skeletal muscle channelopathy v1.31
Fetal anomalies v1.688 DMPK_CTG Arina Puzriakova STR: DMPK_CTG was added
STR: DMPK_CTG was added to Fetal anomalies. Sources: Expert Review Green,Expert list
Mode of inheritance for STR: DMPK_CTG was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for STR: DMPK_CTG were set to 7825566
Phenotypes for STR: DMPK_CTG were set to Myotonic dystrophy 1, OMIM:160900
DDG2P v2.36 DMPK_CTG Arina Puzriakova Entity copied from Skeletal muscle channelopathy v1.31
DDG2P v2.36 DMPK_CTG Arina Puzriakova STR: DMPK_CTG was added
STR: DMPK_CTG was added to DDG2P. Sources: Expert Review Green,Expert list
Mode of inheritance for STR: DMPK_CTG was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for STR: DMPK_CTG were set to 7825566
Phenotypes for STR: DMPK_CTG were set to Myotonic dystrophy 1, OMIM:160900
Skeletal muscle channelopathy v1.31 DMPK_CTG Arina Puzriakova Phenotypes for STR: DMPK_CTG were changed from Myotonic dystrophy 1, 16090 to Myotonic dystrophy 1, OMIM:160900
Fetal anomalies v1.687 DMPK Arina Puzriakova changed review comment from: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.; to: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.

DMPK_CTG STR will be added to the panel to capture this entity and ensure that cases are detected.
DDG2P v2.35 DMPK Arina Puzriakova Tag Q3_21_rating tag was added to gene: DMPK.
DDG2P v2.35 DMPK Arina Puzriakova Tag nucleotide-repeat-expansion tag was added to gene: DMPK.
Tag currently-ngs-unreportable tag was added to gene: DMPK.
DDG2P v2.35 DMPK Arina Puzriakova Classified gene: DMPK as Green List (high evidence)
DDG2P v2.35 DMPK Arina Puzriakova Added comment: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene.

However, the evidence level for this expansion is high (it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1), and as DDG2P is a component of the Paediatric disorders super panel, the DMPK_CTG STR will be added to the panel to capture this entity and ensure that cases are detected.
DDG2P v2.35 DMPK Arina Puzriakova Gene: dmpk has been classified as Green List (High Evidence).
Childhood onset dystonia, chorea or related movement disorder v1.136 DMPK Arina Puzriakova changed review comment from: Comment on list classification: Demoted from Green to Red due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.; to: Comment on list classification: Demoted from Amber to Red due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.
Childhood onset dystonia, chorea or related movement disorder v1.136 DMPK Arina Puzriakova Tag nucleotide-repeat-expansion tag was added to gene: DMPK.
Tag currently-ngs-unreportable tag was added to gene: DMPK.
Childhood onset dystonia, chorea or related movement disorder v1.136 DMPK Arina Puzriakova Phenotypes for gene: DMPK were changed from Myotonic dystrophy 1, 16090 to Myotonic dystrophy 1, OMIM:160900
Childhood onset dystonia, chorea or related movement disorder v1.135 DMPK Arina Puzriakova Classified gene: DMPK as Red List (low evidence)
Childhood onset dystonia, chorea or related movement disorder v1.135 DMPK Arina Puzriakova Added comment: Comment on list classification: Demoted from Green to Red due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.
Childhood onset dystonia, chorea or related movement disorder v1.135 DMPK Arina Puzriakova Gene: dmpk has been classified as Red List (Low Evidence).
Fetal anomalies v1.687 DMPK Arina Puzriakova Classified gene: DMPK as Green List (high evidence)
Fetal anomalies v1.687 DMPK Arina Puzriakova Added comment: Comment on list classification: This gene should be demoted from Green to Red at the next GMS review due to the disease-causing mechanism - genetic defect is an amplified trinucleotide CTG repeat in the 3'UTR (currently NGS unreportable), rather than SNVs within the gene. Evidence level for this is high - it is a confirmed DD gene for DYSTROPHIA MYOTONICA TYPE 1.
Fetal anomalies v1.687 DMPK Arina Puzriakova Gene: dmpk has been classified as Green List (High Evidence).
Fetal anomalies v1.686 DMPK Arina Puzriakova Tag nucleotide-repeat-expansion tag was added to gene: DMPK.
Tag currently-ngs-unreportable tag was added to gene: DMPK.
Tag Q3_21_rating tag was added to gene: DMPK.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.442 CD28 Arina Puzriakova Classified gene: CD28 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.442 CD28 Arina Puzriakova Added comment: Comment on list classification: New gene added by Boaz Palterer. Rating Red as only a single family has been reported to date (PMID: 34214472). Some supportive functional data, but additional cases required prior to promoting this gene.
Primary immunodeficiency or monogenic inflammatory bowel disease v2.442 CD28 Arina Puzriakova Gene: cd28 has been classified as Red List (Low Evidence).
Primary immunodeficiency or monogenic inflammatory bowel disease v2.441 CXCR2 Zornitza Stark gene: CXCR2 was added
gene: CXCR2 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: CXCR2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CXCR2 were set to 24777453
Phenotypes for gene: CXCR2 were set to WHIM syndrome 2 619407
Review for gene: CXCR2 was set to RED
Added comment: 2 sisters with neutropaenia, myelokathexis, and recurrent bacterial infections and homozygous frameshift variant in this gene.
Sources: Literature
Intellectual disability v3.1167 HID1 Zornitza Stark gene: HID1 was added
gene: HID1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: HID1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HID1 were set to 33999436
Phenotypes for gene: HID1 were set to Syndromic infantile encephalopathy; Hypopituitarism
Review for gene: HID1 was set to GREEN
Added comment: 7 individuals from 6 unrelated families reported. Clinical features included: hypopituitarism in combination with brain atrophy, thin corpus callosum, severe developmental delay, visual impairment, and epilepsy.
Sources: Literature
Intellectual disability v3.1167 KIF1B Zornitza Stark gene: KIF1B was added
gene: KIF1B was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: KIF1B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: KIF1B were set to 33710394
Phenotypes for gene: KIF1B were set to Hypotonia; coloboma; hypoplasia of the corpus callosum; severe neurodevelopmental delay
Review for gene: KIF1B was set to RED
Added comment: Compound heterozygous missense variants reported in a woman with severe hypotonia, hypsarrhythmia, coloboma, hypoplasia of corpus callosum, severe neurodevelopmental delay.
Sources: Literature
Intellectual disability v3.1167 JPH3 Zornitza Stark gene: JPH3 was added
gene: JPH3 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: JPH3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: JPH3 were set to 33824468
Phenotypes for gene: JPH3 were set to Intellectual disability; dystonia
Review for gene: JPH3 was set to RED
Added comment: One homozygous truncating variant (NM_020655.4: c.1740dup; p.(Val581Argfs*137)) found in a female individual affected with neurodevelopmental anomalies (including delayed motor milestones, abnormal social communication, language difficulties and borderline cognitive impairment) and paroxysmal attacks of dystonia since her early infancy. No functional work.

STRs in this gene are associated with HD-like disorder.
Sources: Literature
Intellectual disability v3.1167 ERGIC3 Zornitza Stark gene: ERGIC3 was added
gene: ERGIC3 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ERGIC3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ERGIC3 were set to 33710394; 31585110
Phenotypes for gene: ERGIC3 were set to Intellectual disability
Review for gene: ERGIC3 was set to AMBER
Added comment: PMID: 33710394 - two homozygous sibs with mild ID, a novel canonical splice (c.717+1G>A). Absent in gnomAD, no splice studies. Classed as a VUS.

PMID: 31585110 - 1 hom (p.Gln233Argfs*10) in a male 8yo with Growth retardation, Microcephaly, Learning disability, Facial dysmorphism, Abnormal pigmentation.
Sources: Literature
Severe microcephaly v2.217 NUF2 Zornitza Stark gene: NUF2 was added
gene: NUF2 was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: NUF2 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: NUF2 were set to 33721060
Phenotypes for gene: NUF2 were set to microcephaly; short stature; bilateral vocal cord paralysis; micrognathia; atrial septal defect
Review for gene: NUF2 was set to RED
Added comment: PMID: 33721060 - de novo missense variant identified in one male patient with microcephaly and short stature, with additional features, such as bilateral vocal cord paralysis, micrognathia and atrial septal defect.
Sources: Literature
Intellectual disability v3.1167 ZC3H14 Zornitza Stark reviewed gene: ZC3H14: Rating: AMBER; Mode of pathogenicity: None; Publications: 21734151, 33710394, 28666327; Phenotypes: Mental retardation, autosomal recessive 56 MIM#617125; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Intellectual disability v3.1167 MYT1 Zornitza Stark gene: MYT1 was added
gene: MYT1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: MYT1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: MYT1 were set to 33710394
Phenotypes for gene: MYT1 were set to Intellectual disability
Review for gene: MYT1 was set to RED
Added comment: Missense variant reported de novo in a patient with mild ID reported in a cohort study. Patient also had a COL9A2 variant and skeletal features. Authors referred to it as an extended phenotype and dual diagnosis.
Sources: Literature
Intellectual disability v3.1167 ATP1A2 Zornitza Stark changed review comment from: Although some of the symptoms of this condition are episodic, intellectual disability is a recognised feature.; to: Alternating hemiplegia: Although some of the symptoms of this condition are episodic, intellectual disability is a recognised feature.
Intellectual disability v3.1167 ATP1A2 Zornitza Stark edited their review of gene: ATP1A2: Added comment: PMID 33880529: six individuals with de novo missense variants reported and DD/EE/PMG.; Changed publications to: 33880529; Changed phenotypes to: Alternating hemiplegia of childhood 1, MIM# 104290, Developmental and epileptic encephalopathy
Intellectual disability v3.1167 HEATR5B Zornitza Stark gene: HEATR5B was added
gene: HEATR5B was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: HEATR5B was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: HEATR5B were set to 33824466
Phenotypes for gene: HEATR5B were set to pontocerebellar hypoplasia; intellectual disability; seizures
Review for gene: HEATR5B was set to AMBER
Added comment: Four affected children from two families presenting with pontocerebellar hypoplasiawith neonatal seizures, severe ID and motor delay. Two homozygous splice variants were reported (c.5051–1G>A and c.5050+4A>G) in intron 31 of HEATR5B gene. Aberrant splicing was found in patient fibroblasts, which correlated with reduced levels of HEATR5B protein. Homozygous knockout mice were not viable
Sources: Literature
Intellectual disability v3.1167 RING1 Eleanor Williams gene: RING1 was added
gene: RING1 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: RING1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RING1 were set to 29386386
Phenotypes for gene: RING1 were set to microcephaly; intellectual disability
Review for gene: RING1 was set to RED
Added comment: Not associated with any phenotype in OMIM.

PMID: 29386386 - Pierce et al 2018 - report a 13 yo female with a de novo RING1 p.R95Q variant and syndromic neurodevelopmental disabilities. Early motor and language development were normal but were delayed after the first year of life. Cognitive testing showed a verbal IQ of 55 and a visual performance IQ of 63. Head circumference at birth was -4.9 SD, and -4.2 SD at age 13 which falls into the severe microcephaly category. C. elegans with either the missense mutation or complete knockout of spat-3 (the suggested RING1 ortholog) were defective in monoubiquitylation of histone H2A and had defects in neuronal migration and axon guidance.
Sources: Literature
Severe microcephaly v2.217 RING1 Eleanor Williams changed review comment from: Not associated with any phenotype in OMIM.

PMID: 29386386 - Pierce et al 2018 - report a 13 yo female with a de novo RING1 p.R95Q variant and syndromic neurodevelopmental disabilities. Head circumference at birth was -4.9 SD, and -4.2 SD at age 13. C. elegans with either the missense mutation or complete knockout of spat-3 (the suggested RING1 ortholog) were defective in monoubiquitylation of histone H2A and had defects in neuronal migration and axon guidance.
Sources: Literature; to: Not associated with any phenotype in OMIM.

PMID: 29386386 - Pierce et al 2018 - report a 13 yo female with a de novo RING1 p.R95Q variant and syndromic neurodevelopmental disabilities. Head circumference at birth was -4.9 SD, and -4.2 SD at age 13 which falls into the severe microcephaly category. C. elegans with either the missense mutation or complete knockout of spat-3 (the suggested RING1 ortholog) were defective in monoubiquitylation of histone H2A and had defects in neuronal migration and axon guidance.
Sources: Literature
Severe microcephaly v2.217 RING1 Eleanor Williams gene: RING1 was added
gene: RING1 was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: RING1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RING1 were set to 29386386
Phenotypes for gene: RING1 were set to microcephaly; intellectual disability
Review for gene: RING1 was set to RED
Added comment: Not associated with any phenotype in OMIM.

PMID: 29386386 - Pierce et al 2018 - report a 13 yo female with a de novo RING1 p.R95Q variant and syndromic neurodevelopmental disabilities. Head circumference at birth was -4.9 SD, and -4.2 SD at age 13. C. elegans with either the missense mutation or complete knockout of spat-3 (the suggested RING1 ortholog) were defective in monoubiquitylation of histone H2A and had defects in neuronal migration and axon guidance.
Sources: Literature
Early onset or syndromic epilepsy v2.389 RNF2 Eleanor Williams Classified gene: RNF2 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v2.389 RNF2 Eleanor Williams Added comment: Comment on list classification: Promoting to amber as there are 2 cases reported
Early onset or syndromic epilepsy v2.389 RNF2 Eleanor Williams Gene: rnf2 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v2.388 RNF2 Eleanor Williams gene: RNF2 was added
gene: RNF2 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: RNF2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: RNF2 were set to 33864376
Phenotypes for gene: RNF2 were set to epilepsy; intellectual disability; intrauterine growth retardation
Review for gene: RNF2 was set to AMBER
Added comment: Not associated with any phenotype in OMIM.

PMID:33864376 (Luo et al 2021) report 2 cases of children with de novo missense variants (p.R70H and p.S82R) in RNF2 and a phenotype of intrauterine growth retardation, severe intellectual disabilities, behavioral problems, seizures, feeding difficulties and dysmorphic features. Seizures started in infancy. Both variants are absent from gnomad. Functional studies in Drosophila showed that the disease-linked variants (p.R70H and p.S82R) behave as LoF alleles.
Sources: Literature
Retinal disorders v2.193 IRX6 Eleanor Williams Tag cnv tag was added to gene: IRX6.
Skeletal dysplasia v2.106 DLX5 Tracy Lester edited their review of gene: DLX5: Added comment: This gene is primarily monoallelic inheritance, many families reported. Biallelic inheritance has been rarely reported and seems to result in a more severe phenotype with deafness as well. Please update mode of inheritance to include monoallelic as well as biallelic, as a variant in this gene was almost missed because it was not in the tier 1 and 2. Thanks; Changed mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal; Set current diagnostic: yes
Retinal disorders v2.193 IRX5 Eleanor Williams edited their review of gene: IRX5: Changed phenotypes to: cone dystrophy, MONDO:0000455, retinitis pigmentosa, MONDO:0019200
Retinal disorders v2.193 IRX6 Eleanor Williams changed review comment from: Not associated with any disorder in OMIM or Gene2Phenotype.

PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.
Sources: Literature; to: Not associated with any disorder in OMIM or Gene2Phenotype.

PMID: 33891002 - Kohl et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.
Sources: Literature
Retinal disorders v2.193 IRX5 Eleanor Williams changed review comment from: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Duplication of gene
-------------------
PMID: 33891002 - Kohl et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

Loss of function/gene
---------
PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa.

PMID: 32045705 - Apuzzo et al 2020 - report 2 cases of loss of a region in 16q12.1q21 which encompasses IRX5 and IRX6 and many other genes, which together with 3 other previous reports of deletions in this region help define a syndrome with features that include dysmorphic features, short stature, microcephaly, global developmental delay/intellectual disability, autism spectrum disorder (ASD) and ocular abnormalities (nystagmus and strabismus).
; to: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition (PMID: 22581230;17230486)

Duplication of gene
-------------------
PMID: 33891002 - Kohl et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

Loss of function/gene
---------
PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa.

PMID: 32045705 - Apuzzo et al 2020 - report 2 cases of loss of a region in 16q12.1q21 which encompasses IRX5 and IRX6 and many other genes, which together with 3 other previous reports of deletions in this region help define a syndrome with features that include dysmorphic features, short stature, microcephaly, global developmental delay/intellectual disability, autism spectrum disorder (ASD) and ocular abnormalities (nystagmus and strabismus).
Retinal disorders v2.193 IRX5 Eleanor Williams edited their review of gene: IRX5: Changed publications to: 33891002, 28041643, 32045705, 22581230, 17230486
Retinal disorders v2.193 IRX5 Eleanor Williams changed review comment from: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Cone dystrophy
-------------------
PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa. ; to: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Duplication of gene
-------------------
PMID: 33891002 - Kohl et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

Loss of function/gene
---------
PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa.

PMID: 32045705 - Apuzzo et al 2020 - report 2 cases of loss of a region in 16q12.1q21 which encompasses IRX5 and IRX6 and many other genes, which together with 3 other previous reports of deletions in this region help define a syndrome with features that include dysmorphic features, short stature, microcephaly, global developmental delay/intellectual disability, autism spectrum disorder (ASD) and ocular abnormalities (nystagmus and strabismus).
Paediatric disorders - additional genes v1.94 WBP11 Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227
Fetal anomalies v1.686 WBP11 Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227
CAKUT v1.163 WBP11 Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227
Skeletal dysplasia v2.106 WBP11 Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227
VACTERL-like phenotypes v1.32 WBP11 Ivone Leong Phenotypes for gene: WBP11 were changed from malformation syndrome affecting the cardiac, skeletal, gastrointestinal and renal systems to Vertebral, cardiac, tracheoesophageal, renal, and limb defects, OMIM:619227
Fetal anomalies v1.685 TMEM94 Ivone Leong Phenotypes for gene: TMEM94 were changed from Intellectual developmental disorder with cardiac defects and dysmorphic facies to Intellectual developmental disorder with cardiac defects and dysmorphic facies, OMIM:618316
Unexplained young onset end-stage renal disease v1.19 TBC1D8B Ivone Leong Added comment: Comment on phenotypes: Previously:
Steroid-resistant nephrotic syndrome
Unexplained young onset end-stage renal disease v1.19 TBC1D8B Ivone Leong Phenotypes for gene: TBC1D8B were changed from Steroid-resistant nephrotic syndrome to Nephrotic syndrome, type 20, OMIM:301028
Proteinuric renal disease v2.51 TBC1D8B Ivone Leong Added comment: Comment on phenotypes: Previously:
Steroid-resistant nephrotic syndrome
Proteinuric renal disease v2.51 TBC1D8B Ivone Leong Phenotypes for gene: TBC1D8B were changed from Steroid-resistant nephrotic syndrome to Nephrotic syndrome, type 20, OMIM:301028
Intellectual disability v3.1166 PPP1R21 Ivone Leong Added comment: Comment on phenotypes: Previously:
Hepatosplenomegaly;Abnormality of the respiratory system;Generalized hypotonia, Feeding difficulties, Profound global developmental delay, Abnormality of the face, Abnormality of vision, Abnormal heart morphology
Intellectual disability v3.1166 PPP1R21 Ivone Leong Phenotypes for gene: PPP1R21 were changed from Hepatosplenomegaly; Abnormality of the respiratory system; Generalized hypotonia, Feeding difficulties, Profound global developmental delay, Abnormality of the face, Abnormality of vision, Abnormal heart morphology to Neurodevelopmental disorder with hypotonia, facial dysmorphism, and brain abnormalities, OMIM:619383
Intellectual disability v3.1165 NTNG2 Ivone Leong Phenotypes for gene: NTNG2 were changed from Central hypotonia; Global developmental delay; Intellectual disability; Behavioral abnormality; Microcephaly; Seizures to Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia, OMIM:618718
Mitochondrial disorders v2.47 NDUFAF8 Ivone Leong Phenotypes for gene: NDUFAF8 were changed from No OMIM phenotype to Mitochondrial complex I deficiency, nuclear type 34, OMIM:618776
Likely inborn error of metabolism v2.151 NDUFAF8 Ivone Leong Phenotypes for gene: NDUFAF8 were changed from No OMIM phenotype to Mitochondrial complex I deficiency, nuclear type 34, OMIM:618776
Possible mitochondrial disorder - nuclear genes v1.49 NDUFAF8 Ivone Leong Phenotypes for gene: NDUFAF8 were changed from No OMIM phenotype to Mitochondrial complex I deficiency, nuclear type 34, OMIM:618776
Mitochondrial disorder with complex I deficiency v1.14 NDUFAF8 Ivone Leong Phenotypes for gene: NDUFAF8 were changed from No OMIM phenotype to Mitochondrial complex I deficiency, nuclear type 34, OMIM:618776
Primary immunodeficiency or monogenic inflammatory bowel disease v2.441 PDCD1 Arina Puzriakova Classified gene: PDCD1 as Red List (low evidence)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.441 PDCD1 Arina Puzriakova Added comment: Comment on list classification: New gene added by Boaz Palterer. Rating Red as only a single patient reported to date with relevant phenotype (PMID: 34183838)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.441 PDCD1 Arina Puzriakova Gene: pdcd1 has been classified as Red List (Low Evidence).
Congenital myopathy v2.48 TPM2 Ivone Leong Publications for gene: TPM2 were set to 12592607; 11738357; 17434307; 24692096
Intellectual disability v3.1164 CUX2 Arina Puzriakova Tag Q3_21_NHS_review tag was added to gene: CUX2.
Intellectual disability v3.1164 CUX2 Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'Monoallelic... paternally imprinted (maternal allele expressed)' to 'Monoallelic... NOT imprinted', in line with Tracy Lester's recent review highlighting there is no evidence of imprinting in this gene.
Intellectual disability v3.1164 CUX2 Arina Puzriakova Mode of inheritance for gene: CUX2 was changed from MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed) to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Congenital myopathy v2.47 ASCC3 Ivone Leong Phenotypes for gene: ASCC3 were changed from congenital myopathy to congenital myopathy, MONDO:0019952
Congenital myopathy v2.46 MYOD1 Ivone Leong Tag Q3_21_rating tag was added to gene: MYOD1.
Congenital myopathy v2.46 MYOD1 Ivone Leong Classified gene: MYOD1 as Amber List (moderate evidence)
Congenital myopathy v2.46 MYOD1 Ivone Leong Added comment: Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM but not in Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Congenital myopathy v2.46 MYOD1 Ivone Leong Gene: myod1 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1163 ATP1A3 Zornitza Stark edited their review of gene: ATP1A3: Changed phenotypes to: Developmental and epileptic encephalopathy
Intellectual disability v3.1163 ATP1A3 Zornitza Stark edited their review of gene: ATP1A3: Added comment: Sixteen individuals reported with DD/EE.; Changed publications to: 33880529; Changed phenotypes to: Alternating hemiplegia of childhood 2, MIM#614820, Developmental and epileptic encephalopathy
Intellectual disability v3.1163 SAMD9L Zornitza Stark gene: SAMD9L was added
gene: SAMD9L was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: SAMD9L was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SAMD9L were set to 33710394
Phenotypes for gene: SAMD9L were set to Intellectual disability
Review for gene: SAMD9L was set to RED
Added comment: Missense variant reported de novo in a patient with moderate ID, in a large cohort study. Authors described it as a phenotype expansion as ataxia-pancytopenia not found in that patient.
Sources: Literature
Skeletal ciliopathies v1.10 GRK2 Zornitza Stark gene: GRK2 was added
gene: GRK2 was added to Skeletal ciliopathies. Sources: Literature
Mode of inheritance for gene: GRK2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: GRK2 were set to 33200460
Phenotypes for gene: GRK2 were set to Jeune asphyxiating thoracic dystrophy (ATD)
Review for gene: GRK2 was set to AMBER
Added comment: Two unrelated families reported and some functional data.
Sources: Literature
Primary lymphoedema v2.13 TIE1 Zornitza Stark gene: TIE1 was added
gene: TIE1 was added to Primary lymphoedema. Sources: Literature
Mode of inheritance for gene: TIE1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: TIE1 were set to 32947856; 24764452
Phenotypes for gene: TIE1 were set to Lymphatic malformation 11, MIM# 619401
Review for gene: TIE1 was set to AMBER
Added comment: Three families reported, supportive animal model, though variants are missense and present at a low frequency in gnomad, hence Amber rating suggested.
Sources: Literature
Rare multisystem ciliopathy disorders v1.142 TTC26 Zornitza Stark gene: TTC26 was added
gene: TTC26 was added to Rare multisystem ciliopathy disorders. Sources: Literature
Mode of inheritance for gene: TTC26 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: TTC26 were set to 34177428; 32617964; 31595528; 24596149; 22718903
Phenotypes for gene: TTC26 were set to Ciliopathy Syndrome with Biliary, Renal, Neurological, and Skeletal Manifestations
Review for gene: TTC26 was set to GREEN
Added comment: 9 families and functional data including zebrafish model.
Sources: Literature
Rare syndromic craniosynostosis or isolated multisuture synostosis v2.23 RNU12 Zornitza Stark gene: RNU12 was added
gene: RNU12 was added to Craniosynostosis. Sources: Literature
Mode of inheritance for gene: RNU12 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RNU12 were set to 34085356
Phenotypes for gene: RNU12 were set to CDAGS syndrome MIM#603116; Craniosynostosis, Delayed closure of the fontanelles, cranial defects, clavicular hypoplasia, Anal and Genitourinary malformations, and Skin manifestations
Review for gene: RNU12 was set to GREEN
Added comment: 5 CDAGS syndrome families with biallelic variants all including NC_000022.10:g.43011402C>T and another variant on the second allele. Whole transcriptome sequencing analysis of patient lymphoblastoid cells identified differentially expressed genes, and differential alternative splicing analysis indicated there was an enrichment of alternative splicing events. Craniosynostosis is a major feature of the condition.
Sources: Literature
Renal tubulopathies v2.25 KCNJ16 Zornitza Stark gene: KCNJ16 was added
gene: KCNJ16 was added to Renal tubulopathies. Sources: Literature
Mode of inheritance for gene: KCNJ16 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: KCNJ16 were set to 33811157; 33840812
Phenotypes for gene: KCNJ16 were set to Renal tubulopathy; deafness
Review for gene: KCNJ16 was set to GREEN
Added comment: 8 unrelated families reported.
Sources: Literature
Skeletal dysplasia v2.105 SLCO2A1 Zornitza Stark reviewed gene: SLCO2A1: Rating: GREEN; Mode of pathogenicity: None; Publications: 23509104, 27134495, 33852188, 22331663, 27134495; Phenotypes: Hypertrophic osteoarthropathy, primary, autosomal dominant, MIM# 167100, Hypertrophic osteoarthropathy, primary, autosomal recessive 2, MIM# 614441; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Likely inborn error of metabolism v2.150 CLPB Zornitza Stark reviewed gene: CLPB: Rating: GREEN; Mode of pathogenicity: None; Publications: 25597510, 34140661; Phenotypes: 3-methylglutaconic aciduria, type VII, with cataracts, neurologic involvement and neutropaenia, MIM# 616271; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Neurological ciliopathies v1.15 IFT74 Zornitza Stark gene: IFT74 was added
gene: IFT74 was added to Neurological ciliopathies. Sources: Literature
Mode of inheritance for gene: IFT74 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: IFT74 were set to 33531668
Phenotypes for gene: IFT74 were set to Joubert syndrome
Review for gene: IFT74 was set to GREEN
Added comment: Gene is associated with BBS. Note new publication:

PMID 33531668: Identified IFT74 as a JBTS-associated gene in 3 unrelated families through WES. All the affected individuals carried truncated variants and shared one missense variant (p.Q179E) found only in East Asians. The expression of the human p.Q179E-IFT74 variant displayed compromised rescue effects in zebrafish ift74 morphants. Attenuated ciliogenesis; altered distribution of IFT proteins and ciliary membrane proteins, including ARL13B, INPP5E, and GPR161; and disrupted hedgehog signaling were observed in patient fibroblasts with IFT74 variants.
Sources: Literature
Intellectual disability v3.1163 RFX4 Zornitza Stark gene: RFX4 was added
gene: RFX4 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: RFX4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: RFX4 were set to 33658631
Phenotypes for gene: RFX4 were set to ID, ASD, ADHD
Review for gene: RFX4 was set to GREEN
Added comment: Report of 38 individuals (from 33 unrelated families) with de novo or inherited loss of function variants in RFX3 (15 families), RFX4 (4 families), and RFX7 (14 families), identified through WES. Individuals share neurobehavioural features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. These genes are potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis.
Sources: Literature
Intellectual disability v3.1163 RFX3 Zornitza Stark gene: RFX3 was added
gene: RFX3 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: RFX3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: RFX3 were set to 33658631
Phenotypes for gene: RFX3 were set to ID, ASD, ADHD
Review for gene: RFX3 was set to GREEN
Added comment: Report of 38 individuals (from 33 unrelated families) with de novo or inherited loss of function variants in RFX3 (15 families), RFX4 (4 families), and RFX7 (14 families), identified through WES. Individuals share neurobehavioural features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. These genes are potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis.
Sources: Literature
Intellectual disability v3.1163 RFX7 Zornitza Stark gene: RFX7 was added
gene: RFX7 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: RFX7 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: RFX7 were set to 33658631
Phenotypes for gene: RFX7 were set to ID, ASD, ADHD
Review for gene: RFX7 was set to GREEN
Added comment: Report of 38 individuals (from 33 unrelated families) with de novo or inherited loss of function variants in RFX3 (15 families), RFX4 (4 families), and RFX7 (14 families), identified through WES. Individuals share neurobehavioural features including ASD, intellectual disability, and/or ADHD; other frequent features include hypersensitivity to sensory stimuli and sleep problems. RFX3, RFX4, and RFX7 are strongly expressed in developing and adult human brain, and X-box binding motifs as well as RFX ChIP-seq peaks are enriched in the cis-regulatory regions of known ASD risk genes. These genes are potentially critical transcriptional regulators of neurobiological pathways associated with neurodevelopmental disease pathogenesis.
Sources: Literature
Hypogonadotropic hypogonadism (GMS) v1.43 SEMA3F Zornitza Stark gene: SEMA3F was added
gene: SEMA3F was added to Hypogonadotropic hypogonadism idiopathic. Sources: Literature
Mode of inheritance for gene: SEMA3F was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SEMA3F were set to 33495532
Phenotypes for gene: SEMA3F were set to Hypogonadotropic hypogonadism
Review for gene: SEMA3F was set to GREEN
Added comment: Screened 216 patients with Idiopathic hypogonadotropic hypogonadism by exome sequencing. Identified 10 individuals from 7 families with heterozygous SEMA3F missense variants. In 4 of the kindreds, there was at least one more gene known to be associated with IHH (oligogenecity). Provide unequivocal human embryonic data showing the expression of SEMA3F along the developing human GnRH migratory pathway. SEMA3Fs harboring the P452T, T29M, and T724M missense variants showed impaired SEMA3F secretion in whole cell lysates.
Sources: Literature
Hypogonadotropic hypogonadism (GMS) v1.43 PLXNA3 Zornitza Stark gene: PLXNA3 was added
gene: PLXNA3 was added to Hypogonadotropic hypogonadism idiopathic. Sources: Literature
Mode of inheritance for gene: PLXNA3 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: PLXNA3 were set to 33495532
Phenotypes for gene: PLXNA3 were set to Hypogonadotropic hypogonadism
Review for gene: PLXNA3 was set to GREEN
Added comment: Screened 216 patients with Idiopathic hypogonadotropic hypogonadism by exome sequencing. Identified 7 individuals from 5 families with hemizygous PLXNA3 missense variants.
In 2 of the kindreds, there was at least one more gene known to be associated with IHH (oligogenecity). Data provided with evidence that PLXNA3, a key component of the SEMA3F holoreceptor complex,31 is expressed by the human GnRH and olfactory/vomeronasal systems. S646P variant showed PLXNA3 localization exclusively in the ER, indicating that the variant S646P disrupts cell surface localization of PLXNA3.
Sources: Literature
White matter disorders and cerebral calcification - narrow panel v1.188 FARSA Zornitza Stark edited their review of gene: FARSA: Added comment: PMID 33598926: three additional families reported. Functional evidence was obtained with reduced FARS1 enzyme activity levels in fibroblasts or EBV-transformed lymphoblastoid cell lines (EBV-LCLs) of patients. Common to all was a chronic interstitial lung disease starting early in life and characterized by bilateral ground-glass opacification on HR-CT, and cholesterol pneumonitis in lung histology. Additional abnormalities in other organ systems include liver disease, neurological manifestations, and growth restriction.; Changed rating: GREEN; Changed publications to: 31355908, 33598926; Changed phenotypes to: Rajab interstitial lung disease with brain calcifications 2, MIM# 619013
Retinal disorders v2.193 IRX5 Eleanor Williams Phenotypes for gene: IRX5 were changed from cone dystrophy, MONDO:0000455 to cone dystrophy, MONDO:0000455; retinitis pigmentosa, MONDO:0019200
Retinal disorders v2.192 IRX5 Eleanor Williams changed review comment from: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Cone dystrophy
-------------------
PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.; to: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Cone dystrophy
-------------------
PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.

PMID: 28041643 - Carss et al 2017 - screened a cohort of 722 individuals with inherited retinal disease using WES/WGS. 1 case reported with a biallelic deletion in IRX5 reported which leads to a frameshift ENST00000394636.4; c.1362_1366delTAAAG, p.Lys455ProfsTer19 in a patient with retinitis pigmentosa.
Retinal disorders v2.192 IRX5 Eleanor Williams Tag cnv tag was added to gene: IRX5.
Tag Q3_21_rating tag was added to gene: IRX5.
Retinal disorders v2.192 IRX5 Eleanor Williams Phenotypes for gene: IRX5 were changed from Retinitis pigmentosa to cone dystrophy, MONDO:0000455
Retinal disorders v2.191 IRX5 Eleanor Williams Publications for gene: IRX5 were set to 28041643
Retinal disorders v2.190 IRX5 Eleanor Williams Mode of pathogenicity for gene: IRX5 was changed from to Other
Retinal disorders v2.189 IRX5 Eleanor Williams Mode of inheritance for gene: IRX5 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Severe early-onset obesity v2.39 PHIP David Hunt gene: PHIP was added
gene: PHIP was added to Severe early-onset obesity. Sources: Literature
Mode of inheritance for gene: PHIP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: PHIP were set to 27900362; 29209020; 31167805; 32492392; 33867250
Phenotypes for gene: PHIP were set to Obesity; global developmental delay; intellectual disability; behavioral abnormality; dysmorphic facies
Penetrance for gene: PHIP were set to unknown
Review for gene: PHIP was set to GREEN
Added comment: Multiple peer-reviewed publications reporting a high rate of childhood-onset obesity in PHIP-related neurodevelopmental disorder (a.k.a. Chung-Jansen syndrome).
Sources: Literature
Retinal disorders v2.188 IRX6 Eleanor Williams changed review comment from: PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.
Sources: Literature; to: Not associated with any disorder in OMIM or Gene2Phenotype.

PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.
Sources: Literature
Retinal disorders v2.188 IRX6 Eleanor Williams edited their review of gene: IRX6: Changed rating: GREEN
Retinal disorders v2.188 IRX6 Eleanor Williams gene: IRX6 was added
gene: IRX6 was added to Retinal disorders. Sources: Literature
Mode of inheritance for gene: IRX6 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: IRX6 were set to 33891002
Phenotypes for gene: IRX6 were set to cone dystrophy, MONDO:0000455
Mode of pathogenicity for gene: IRX6 was set to Other
Added comment: PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.
Sources: Literature
Retinal disorders v2.187 IRX5 Eleanor Williams edited their review of gene: IRX5: Changed mode of pathogenicity: Other
Retinal disorders v2.187 IRX5 Eleanor Williams changed review comment from: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Cone dystrophy
-------------------
PMID: 33891002 - Khol et al 2021 - report 3 families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.; to: Associated with Hamamy syndrome #611174 (AR) in OMIM. Hamamy syndrome is characterised by craniofacial dysmorphism, hearing loss, skeletal anomalies, microcytic hypochromic anemia and congenital heart defects. Severe myopia has also been reported. Homozygous missense variants in IRX5 were reported in 2 families with this condition.

Cone dystrophy
-------------------
PMID: 33891002 - Khol et al 2021 - report 3 unrelated families with duplications of a region covering the genes IRX5 and IRX6 completely, and the proximal exons of MMP2 and cone dystrophy. They propose that overexpression of IRX5 and IRX6 may be the cause of the disease, and this is supported by expression analysis in patient-derived fibroblasts and zebrafish experiments.

Initial family is a large 5 generation German family with 14 members with autosomal dominant cone dystrophy in which a 600kb duplicated region covering IRX5/IRX6 and part of MMP2 was identified. 2 additional families of Chinese and Dutch descent with copy number gains of ~700 and ~850 kb, covering the same region were then identified. The smallest region of overlap is 608kb. In addition another family of German decent is reported with adCD and the same duplication as the first German family. It is not known if they are distantly related. Segregation analysis on available members of all families showed the duplication in affected members and not in unaffected.

They find that IRX5, IRX6 and MMP2 are expressed in human adult retina. Several lincRNA within the locus are also expressed. In patient derived fibroblasts IRX5 and IRX6 showed increased expression levels. Over expression of IRX5 and IRX6 results in impaired visual performance in zebrafish larvae.
Retinal disorders v2.187 IRX5 Eleanor Williams reviewed gene: IRX5: Rating: GREEN; Mode of pathogenicity: None; Publications: 33891002; Phenotypes: cone dystrophy, MONDO:0000455; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability v3.1163 GNB2 Arina Puzriakova Classified gene: GNB2 as Amber List (moderate evidence)
Intellectual disability v3.1163 GNB2 Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update.
Intellectual disability v3.1163 GNB2 Arina Puzriakova Gene: gnb2 has been classified as Amber List (Moderate Evidence).
Intellectual disability v3.1162 GNB2 Arina Puzriakova gene: GNB2 was added
gene: GNB2 was added to Intellectual disability. Sources: Literature
Q3_21_rating tags were added to gene: GNB2.
Mode of inheritance for gene: GNB2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: GNB2 were set to 31698099; 33971351; 34183358
Phenotypes for gene: GNB2 were set to Intellectual disability
Review for gene: GNB2 was set to GREEN
Added comment: GNB2 is not yet associated with any phenotype in OMIM, but has a 'confirmed' disease confidence rating for 'GNB2-related developmental disorder (monoallelic)' in G2P.

At least 14 unrelated individuals with de novo monoallelic variants, including 5 recurrent variants in 13 individuals (PMIDs: 31698099; 33971351; 34183358). All patients (except one fetus owing to termination of pregnancy) have DD/ID of variable severity (mild to severe) which appeared to correlate with the variant each individual harboured. Other variable features include non-specific facial dysmorphism, hypotonia, and autistic behaviour.
Sources: Literature
Early onset or syndromic epilepsy v2.387 DNM1 Arina Puzriakova Publications for gene: DNM1 were set to EuroEPINOMICS-RES Consortium (2014) AJHG 95:1-11; 25262651; 27066543
Early onset or syndromic epilepsy v2.386 DNM1 Arina Puzriakova Tag watchlist tag was added to gene: DNM1.
Early onset or syndromic epilepsy v2.386 DNM1 Arina Puzriakova Classified gene: DNM1 as Green List (high evidence)
Early onset or syndromic epilepsy v2.386 DNM1 Arina Puzriakova Added comment: Comment on list classification: Currently, there is only enough evidence for an Amber rating for the biallelic form and so I have kept the MOI as just 'Monoallelic' at this time. If this is a genuine association, biallelic cases would still be picked by the Genomics England pipeline under this MOI. Added watchlist tag in anticipation of further biallelic cases emerging.
Early onset or syndromic epilepsy v2.386 DNM1 Arina Puzriakova Gene: dnm1 has been classified as Green List (High Evidence).
Early onset or syndromic epilepsy v2.385 DNM1 Arina Puzriakova reviewed gene: DNM1: Rating: AMBER; Mode of pathogenicity: None; Publications: 34172529; Phenotypes: Developmental and epileptic encephalopathy 31, OMIM:616346; Mode of inheritance: None
Hereditary ataxia v1.233 ABCB7 Ivone Leong Phenotypes for gene: ABCB7 were changed from Anemia, sideroblastic, with ataxia, ; Sideroblastic Anemia and Ataxia to Anemia, sideroblastic, with ataxia, OMIM:301310
Ataxia and cerebellar anomalies - narrow panel v2.220 ABCB7 Ivone Leong Phenotypes for gene: ABCB7 were changed from Anemia, sideroblastic, with ataxia,; Sideroblastic Anemia and Ataxia to Anemia, sideroblastic, with ataxia, OMIM:301310
Intellectual disability v3.1161 DNM1 Arina Puzriakova Phenotypes for gene: DNM1 were changed from EPILEPTIC ENCEPHALOPATHY to Developmental and epileptic encephalopathy 31, OMIM:616346
Early onset or syndromic epilepsy v2.385 DNM1 Arina Puzriakova Phenotypes for gene: DNM1 were changed from Epileptic encephalopathy, early infantile, 31, 616346 to Developmental and epileptic encephalopathy 31, OMIM:616346
Cytopenias and congenital anaemias v1.85 ABCB7 Ivone Leong Added comment: Comment on phenotypes: Previously:
Sideroblastic Anemia and Ataxia
Cytopenias and congenital anaemias v1.85 ABCB7 Ivone Leong Phenotypes for gene: ABCB7 were changed from Sideroblastic Anemia and Ataxia; Anemia, sideroblastic, with ataxia, 301310 to Anemia, sideroblastic, with ataxia, OMIM:301310
Severe microcephaly v2.216 ATP9A Arina Puzriakova changed review comment from: Vogt et al. 2021 report on 3 individuals from 2 unrelated consanguineous families with different homozygous truncating variants in ATP9A, presenting with DD/ID of variable degree, postnatal microcephaly (OFC range: −2.33 SD to −3.58 SD), failure to thrive, and gastrointestinal symptoms. Patient-derived fibroblasts showed reduced expression of ATP9A, and consistent with previous findings also overexpression of interacting partners, ARPC3 and SNX3.
Sources: Literature; to: Vogt et al. 2021 report on 3 individuals from 2 unrelated consanguineous families with different homozygous truncating variants in ATP9A, presenting with DD/ID of variable degree (2 mild, 1 severe), postnatal microcephaly (OFC range: −2.33 SD to −3.58 SD), failure to thrive, and gastrointestinal symptoms. Patient-derived fibroblasts showed reduced expression of ATP9A, and consistent with previous findings also overexpression of interacting partners, ARPC3 and SNX3.
Sources: Literature
Severe microcephaly v2.216 ATP9A Arina Puzriakova Classified gene: ATP9A as Amber List (moderate evidence)
Severe microcephaly v2.216 ATP9A Arina Puzriakova Added comment: Comment on list classification: Rating Amber, awaiting further cases/clinical evidence.
Severe microcephaly v2.216 ATP9A Arina Puzriakova Gene: atp9a has been classified as Amber List (Moderate Evidence).
Severe microcephaly v2.215 ATP9A Arina Puzriakova gene: ATP9A was added
gene: ATP9A was added to Severe microcephaly. Sources: Literature
Mode of inheritance for gene: ATP9A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ATP9A were set to http://dx.doi.org/10.1136/jmedgenet-2021-107843
Phenotypes for gene: ATP9A were set to Neurodevelopmental delay; Postnatal microcephaly; Failure to thrive; Gastrointestinal symptoms
Review for gene: ATP9A was set to AMBER
Added comment: Vogt et al. 2021 report on 3 individuals from 2 unrelated consanguineous families with different homozygous truncating variants in ATP9A, presenting with DD/ID of variable degree, postnatal microcephaly (OFC range: −2.33 SD to −3.58 SD), failure to thrive, and gastrointestinal symptoms. Patient-derived fibroblasts showed reduced expression of ATP9A, and consistent with previous findings also overexpression of interacting partners, ARPC3 and SNX3.
Sources: Literature
DDG2P v2.34 ATP6V1A Arina Puzriakova edited their review of gene: ATP6V1A: Changed rating: GREEN; Changed publications to: 28065471, 33320377, 29668857, 32045939
DDG2P v2.34 ATP6V1A Arina Puzriakova Classified gene: ATP6V1A as Amber List (moderate evidence)
DDG2P v2.34 ATP6V1A Arina Puzriakova Added comment: Comment on list classification: There is sufficient evidence to promote this gene to Green at the next GMS panel update.
DDG2P v2.34 ATP6V1A Arina Puzriakova Gene: atp6v1a has been classified as Amber List (Moderate Evidence).
DDG2P v2.33 ATP6V1A Arina Puzriakova Tag Q2_21_rating was removed from gene: ATP6V1A.
Tag Q3_21_rating tag was added to gene: ATP6V1A.
DDG2P v2.33 ATP6V1A Arina Puzriakova Tag Q2_21_rating tag was added to gene: ATP6V1A.
DDG2P v2.33 ATP6V1A Arina Puzriakova Publications for gene: ATP6V1A were set to 28065471
DDG2P v2.32 ATP6V1A Arina Puzriakova Added comment: Comment on mode of inheritance: Despite the different disease confidence ratings associated with each MOI in G2P, there is enough evidence in the literature to support pathogenicity of both biallelic and monoallelic variants in ATP6V1A.

As DDG2P is a component panel of the Paediatric disorders super panel, the MOI has been updated from 'Biallelic' to 'Both mono- and biallelic' to ensure that all cases are captured.
DDG2P v2.32 ATP6V1A Arina Puzriakova Mode of inheritance for gene: ATP6V1A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
DDG2P v2.31 ATP6V1A Arina Puzriakova reviewed gene: ATP6V1A: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
DDG2P v2.31 ATP6V1A Arina Puzriakova Phenotypes for gene: ATP6V1A were changed from Autosomal Recessive Cutis Laxa to Autosomal Recessive Cutis Laxa (AR); Epileptic encephalopathy, infantile or early childhood, 3 (AD)
Ehlers Danlos syndrome with a likely monogenic cause v2.58 ATP6V1A Arina Puzriakova Publications for gene: ATP6V1A were set to 28065471
Intellectual disability v3.1160 ATP6V1A Arina Puzriakova Phenotypes for gene: ATP6V1A were changed from Epileptic encephalopathy, infantile or early childhood, 3 618012; Cutis laxa, autosomal recessive, type IID 617403 to Developmental and epileptic encephalopathy 93, OMIM:618012
Intellectual disability v3.1159 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from ATAXIA-TELANGIECTASIA; AT to Ataxia-telangiectasia, OMIM:208900
Hereditary neuropathy v1.387 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Hereditary Neuropathies; Ataxia-telangiectasia to Ataxia-telangiectasia, OMIM:208900; Hereditary Neuropathies
Hereditary ataxia with onset in adulthood v2.81 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Ataxia-telangiectasia, 607585; Ataxia-Telangiectasia to Ataxia-telangiectasia, OMIM:208900
Hereditary neuropathy or pain disorder v1.30 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Hereditary Neuropathies; Ataxia-telangiectasia to Ataxia-telangiectasia, OMIM:208900; Hereditary Neuropathies
Childhood onset dystonia, chorea or related movement disorder v1.134 ATM Arina Puzriakova Phenotypes for gene: ATM were changed from Dystonia; Ataxia telangiectasia, 208900 to Ataxia-telangiectasia, OMIM:208900
Intellectual disability v3.1158 ATP2C2 Eleanor Williams gene: ATP2C2 was added
gene: ATP2C2 was added to Intellectual disability. Sources: Literature
Mode of inheritance for gene: ATP2C2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: ATP2C2 were set to 33864365; 28440294
Phenotypes for gene: ATP2C2 were set to language impairment, HP:0002463
Review for gene: ATP2C2 was set to RED
Added comment: PMID: 33864365 - Martinelli et al 2021 - report a family with a missense variant NM_001286527.2:c.304G>A, p.(Val102Met) in ATP2C2 in a father and two siblings with specific language impairment. However two other affected siblings did not have this variant. This variant was also reported by Chen et al. They found that the variant had a higher frequency in language cases (1.8%, N = 360) compared with cohorts selected for dyslexia (0.8%, N = 520) and ADHD (0.7%, N = 150), which presented frequencies comparable to reference databases (0.9%, N = 24 046 gnomAD controls). They postulate that variant is not sufficient on its own to cause a disorder but is a susceptibility factor which increases the risk for language impairment.

PMID: 28440294 - Chen et al 2017 - report 2 probands with severe learning impairment, and missense variants in ATP2C2 (NM_001286527: c.G304A:p.V102M and NM_001291454:exon21: c.C1936T:p.R646W).
Sources: Literature
Rhabdomyolysis and metabolic muscle disorders v1.46 OBSCN Eleanor Williams reviewed gene: OBSCN: Rating: RED; Mode of pathogenicity: None; Publications: 33438037; Phenotypes: ; Mode of inheritance: None
Monogenic hearing loss v2.177 P2RX2 Eleanor Williams reviewed gene: P2RX2: Rating: ; Mode of pathogenicity: None; Publications: 33791800; Phenotypes: ; Mode of inheritance: None
Childhood onset hereditary spastic paraplegia v2.45 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome, 617183 to Harel-Yoon syndrome, OMIM:617183; Spastic paraplegia
Childhood onset hereditary spastic paraplegia v2.44 ATAD3A Arina Puzriakova reviewed gene: ATAD3A: Rating: ; Mode of pathogenicity: None; Publications: 28158749, 27640307, 33845882; Phenotypes: Harel-Yoon syndrome, OMIM:617183, Spastic paraplegia; Mode of inheritance: None
Possible mitochondrial disorder - nuclear genes v1.48 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome, 617183 to Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810
Mitochondrial disorders v2.46 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome 617183 to Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810
Likely inborn error of metabolism v2.150 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome 617183 to Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810; Lactic acidosis; Methylglutaconic aciduria
Cerebral vascular malformations v2.55 CBL Zornitza Stark reviewed gene: CBL: Rating: GREEN; Mode of pathogenicity: None; Publications: 28343148, 25283271, 28589114; Phenotypes: early-onset moyamoya angiopathy, Noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia, 613563; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Undiagnosed metabolic disorders v1.467 ATAD3A Arina Puzriakova Publications for gene: ATAD3A were set to 27640307
Undiagnosed metabolic disorders v1.466 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Lactic acidosis; Methylglutaconic aciduria; Neurological abnormalities; Cerebellar hypoplasia; Optic atrophy; Hypertrophic cardiomyopathy; Scoliosis; Spinal muscular atrophy to Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810; Lactic acidosis; Methylglutaconic aciduria
Undiagnosed metabolic disorders v1.465 ATAD3A Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'Biallelic' to 'Both mono- and biallelic'.

At least 6 families with heterozygous variants (PMID: 27640307; 28158749) and 7 unrelated families with biallelic SNVs in this gene (PMID: 27640307; 29053797; 31727539; 32607449; 33845882). Metabolic evaluation often show elevated 3-methylglutaconate and lactate in patients with variants in this gene.
Undiagnosed metabolic disorders v1.465 ATAD3A Arina Puzriakova Mode of inheritance for gene: ATAD3A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Optic neuropathy v2.46 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome: optic atrophy, peripheral neuropathy, delayed psychomotor development, intellectual disability, spastic paraplegia (HAYOS), 617183 to Harel-Yoon syndrome, OMIM:617183
Hypertrophic cardiomyopathy v2.22 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome, 617183 to Harel-Yoon syndrome, OMIM:617183
Bilateral congenital or childhood onset cataracts v2.75 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome, 617183 to Harel-Yoon syndrome, OMIM:617183
Fetal anomalies v1.684 ATAD3A Arina Puzriakova Publications for gene: ATAD3A were set to 27640307; 28327206
Fetal anomalies v1.683 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from ATAD3A disorder - global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy; ATAD3A disorder - global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy; Harel-Yoon syndrome, 617183 to ATAD3A disorder - global developmental delay, hypotonia, optic atrophy, axonal neuropathy, and hypertrophic cardiomyopathy; Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810
DDG2P v2.30 ATAD3A Arina Puzriakova Tag watchlist was removed from gene: ATAD3A.
Tag Q3_21_MOI tag was added to gene: ATAD3A.
Fetal anomalies v1.682 ATAD3A Arina Puzriakova Tag watchlist was removed from gene: ATAD3A.
Tag Q3_21_MOI tag was added to gene: ATAD3A.
Fetal anomalies v1.682 ATAD3A Arina Puzriakova Added comment: Comment on mode of inheritance: MOI should be updated from 'Monoallelic' to 'Both mono- and biallelic' at the next GMS panel review.

At least 7 unrelated families have now been reported with biallelic SNVs in ATAD3A, including 5 families with Harel-Yoon syndrome, MIM# 617183 (PMID: 27640307; 32607449; 33845882) and 2 families with neonatal lethal pontocerebellar hypoplasia, MIM# 618810 (PMID: 29053797; 31727539). Both of these phenotypes are pertinent to this panel.
Fetal anomalies v1.682 ATAD3A Arina Puzriakova Mode of inheritance for gene: ATAD3A was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
DDG2P v2.30 ATAD3A Arina Puzriakova Added comment: Comment on mode of inheritance: Although the MOI has been set to 'Monoallelic' only, to reflect the different disease confidence ratings associated with each MOI in G2P, there is enough evidence in the literature to support pathogenicity of biallelic variants in ATAD3A.

As DDG2P is a component panel of the Paediatric disorders super panel, the MOI should be updated to 'Both mono- and biallelic' to ensure that all cases are captured.
DDG2P v2.30 ATAD3A Arina Puzriakova Mode of inheritance for gene: ATAD3A was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Ataxia and cerebellar anomalies - narrow panel v2.219 ATAD3A Arina Puzriakova changed review comment from: Comment on mode of inheritance: Changed MOI from 'Both mono- and biallelic' to 'Biallelic' only.

ATAD3A is associated with Harel-Yoon syndrome (MIM# 617183) with both dominant and recessive patterns of inheritance. However, only families with the biallelic form displayed cerebellar atrophy (PMID: 27640307; 32607449; 33845882). Brain MRI results have been normal in heterozygous cases to date.

Furthermore, biallelic variants in ATAD3A are also associated with another phenotype comprising neonatal lethal pontocerebellar hypoplasia (MIM# 618810) - at least 13 unrelated families in literature, including 2 families with SNVs (PMID: 29053797; 31727539) and 11 families with deletions affecting ATAD3A (PMID: 27640307; 28549128; 29053797; 33845882); to: ATAD3A is associated with Harel-Yoon syndrome (MIM# 617183) with both dominant and recessive patterns of inheritance. However, only families with the biallelic form displayed cerebellar atrophy (PMID: 27640307; 32607449; 33845882). Brain MRI results have been normal in heterozygous cases to date (MOI set to 'Biallelic' only).

Furthermore, biallelic variants in ATAD3A are also associated with another phenotype comprising neonatal lethal pontocerebellar hypoplasia (MIM# 618810) - at least 13 unrelated families in literature, including 2 families with SNVs (PMID: 29053797; 31727539) and 11 families with deletions affecting ATAD3A (PMID: 27640307; 28549128; 29053797; 33845882)
Ataxia and cerebellar anomalies - narrow panel v2.219 ATAD3A Arina Puzriakova changed review comment from: Comment on list classification: Upgraded from Amber to Green, as the number of unrelated families (at least 7) with cerebellar/pontocerebellar hypoplasia and biallelic SNVs in ATAD3A reaches the threshold for inclusion on this panel.; to: Comment on list classification: There is enough evidence to promote this gene to Green at the next GMS panel update - the number of unrelated families (at least 7) with cerebellar/pontocerebellar hypoplasia and biallelic SNVs in ATAD3A reaches the threshold for inclusion on this panel.
Ataxia and cerebellar anomalies - narrow panel v2.219 ATAD3A Arina Puzriakova Tag Q2_21_rating tag was added to gene: ATAD3A.
Ataxia and cerebellar anomalies - narrow panel v2.219 ATAD3A Arina Puzriakova Classified gene: ATAD3A as Amber List (moderate evidence)
Ataxia and cerebellar anomalies - narrow panel v2.219 ATAD3A Arina Puzriakova Gene: atad3a has been classified as Amber List (Moderate Evidence).
Ataxia and cerebellar anomalies - narrow panel v2.218 ATAD3A Arina Puzriakova Entity copied from Cerebellar hypoplasia v1.52
Ataxia and cerebellar anomalies - narrow panel v2.218 ATAD3A Arina Puzriakova gene: ATAD3A was added
gene: ATAD3A was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Expert Review Green,Expert Review
Mode of inheritance for gene: ATAD3A was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: ATAD3A were set to 27640307; 28549128; 29053797; 31727539; 32607449; 33845882
Phenotypes for gene: ATAD3A were set to Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810
Cerebellar hypoplasia v1.52 ATAD3A Arina Puzriakova Classified gene: ATAD3A as Green List (high evidence)
Cerebellar hypoplasia v1.52 ATAD3A Arina Puzriakova Added comment: Comment on list classification: Upgraded from Amber to Green, as the number of unrelated families (at least 7) with cerebellar/pontocerebellar hypoplasia and biallelic SNVs in ATAD3A reaches the threshold for inclusion on this panel.
Cerebellar hypoplasia v1.52 ATAD3A Arina Puzriakova Gene: atad3a has been classified as Green List (High Evidence).
Cerebellar hypoplasia v1.51 ATAD3A Arina Puzriakova changed review comment from: Comment on mode of inheritance: Changed MOI from 'Both mono- and biallelic' to 'Biallelic' only.

ATAD3A is associated with Harel-Yoon syndrome (MIM# 617183) with both dominant and recessive patterns of inheritance. However, only the family with the biallelic form displayed cerebellar atrophy (PMID: 27640307; 32607449; 33845882). Brain MRI results have been normal in heterozygous cases to date.

Furthermore, biallelic variants in ATAD3A are also associated with another phenotype comprising neonatal lethal pontocerebellar hypoplasia (MIM# 618810) - at least 13 unrelated families in literature, including 2 families with SNVs (PMID: 29053797; 31727539) and 11 families with deletions affecting ATAD3A (PMID: 27640307; 28549128; 29053797; 33845882); to: Comment on mode of inheritance: Changed MOI from 'Both mono- and biallelic' to 'Biallelic' only.

ATAD3A is associated with Harel-Yoon syndrome (MIM# 617183) with both dominant and recessive patterns of inheritance. However, only families with the biallelic form displayed cerebellar atrophy (PMID: 27640307; 32607449; 33845882). Brain MRI results have been normal in heterozygous cases to date.

Furthermore, biallelic variants in ATAD3A are also associated with another phenotype comprising neonatal lethal pontocerebellar hypoplasia (MIM# 618810) - at least 13 unrelated families in literature, including 2 families with SNVs (PMID: 29053797; 31727539) and 11 families with deletions affecting ATAD3A (PMID: 27640307; 28549128; 29053797; 33845882)
Cerebellar hypoplasia v1.51 ATAD3A Arina Puzriakova edited their review of gene: ATAD3A: Changed rating: GREEN; Changed publications to: 27640307, 28549128, 29053797, 31727539, 32607449, 33845882; Changed phenotypes to: Harel-Yoon syndrome, OMIM:617183, Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810; Changed mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Cerebellar hypoplasia v1.51 ATAD3A Arina Puzriakova Publications for gene: ATAD3A were set to 27640307; 25529582; 28549128; 29898916
Cerebellar hypoplasia v1.50 ATAD3A Arina Puzriakova Added comment: Comment on mode of inheritance: Changed MOI from 'Both mono- and biallelic' to 'Biallelic' only.

ATAD3A is associated with Harel-Yoon syndrome (MIM# 617183) with both dominant and recessive patterns of inheritance. However, only the family with the biallelic form displayed cerebellar atrophy (PMID: 27640307; 32607449; 33845882). Brain MRI results have been normal in heterozygous cases to date.

Furthermore, biallelic variants in ATAD3A are also associated with another phenotype comprising neonatal lethal pontocerebellar hypoplasia (MIM# 618810) - at least 13 unrelated families in literature, including 2 families with SNVs (PMID: 29053797; 31727539) and 11 families with deletions affecting ATAD3A (PMID: 27640307; 28549128; 29053797; 33845882)
Cerebellar hypoplasia v1.50 ATAD3A Arina Puzriakova Mode of inheritance for gene: ATAD3A was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal
Cerebellar hypoplasia v1.49 ATAD3A Arina Puzriakova Phenotypes for gene: ATAD3A were changed from Harel-Yoon syndrome, 617183 to Harel-Yoon syndrome, OMIM:617183; Pontocerebellar hypoplasia, hypotonia, and respiratory insufficiency syndrome, neonatal lethal, OMIM:618810
Intellectual disability v3.1157 ACSL4 Ivone Leong Publications for gene: ACSL4 were set to
Intellectual disability v3.1156 ACSL4 Ivone Leong reviewed gene: ACSL4: Rating: ; Mode of pathogenicity: None; Publications: 12525535, 11889465; 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)
Primary immunodeficiency or monogenic inflammatory bowel disease v2.440 PDCD1 Boaz Palterer gene: PDCD1 was added
gene: PDCD1 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: PDCD1 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PDCD1 were set to 34183838
Phenotypes for gene: PDCD1 were set to Autoimmunity; splenomegaly; pneumonitis; tubercolosis
Penetrance for gene: PDCD1 were set to unknown
Added comment: Ogishi et al. described a patient with a homozygous frameshift mutation in the PDCD1 encoding the PD-1 protein. The patient presented with polyautoimmunity and tubercolosis, similarly to mice models of PD-1 deficiency and to patients treated with anti-PD-1 cancer immunotherapy.
Sources: Literature
Primary immunodeficiency or monogenic inflammatory bowel disease v2.440 CD28 Boaz Palterer gene: CD28 was added
gene: CD28 was added to Primary immunodeficiency. Sources: Literature
Mode of inheritance for gene: CD28 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: CD28 were set to 34214472
Phenotypes for gene: CD28 were set to cutaneous horn; immunodeficiency; papillomavirus infection; tree man syndrome; warts
Penetrance for gene: CD28 were set to unknown
Review for gene: CD28 was set to RED
Added comment: Beziat et al. describe 3 patients from a large kindred with homozygous mutations in CD28 causing loss of protein expression. The patients have severe HPV warts or tree man syndrome.
Extensive ex vivo functional data and mouse model are provided.
Sources: Literature
Intellectual disability v3.1156 ACSL4 Ivone Leong Tag Skewed X-inactivation tag was added to gene: ACSL4.
Intellectual disability v3.1156 ACSL4 Ivone Leong Phenotypes for gene: ACSL4 were changed from Mental retardation, X-linked 63, OMIM:300387; ALPORT SYNDROME WITH MENTAL RETARDATION MIDFACE HYPOPLASIA AND ELLIPTOCYTOSIS (ATS-MR) to Mental retardation, X-linked 63, OMIM:300387; Alport syndrome-intellectual disability-midface hypoplasia-elliptocytosis syndrome, MONDO:0010263
Intellectual disability v3.1155 ACSL4 Ivone Leong Phenotypes for gene: ACSL4 were changed from Mental retardation, X-linked 63, 300387; ALPORT SYNDROME WITH MENTAL RETARDATION MIDFACE HYPOPLASIA AND ELLIPTOCYTOSIS (ATS-MR) to Mental retardation, X-linked 63, OMIM:300387; ALPORT SYNDROME WITH MENTAL RETARDATION MIDFACE HYPOPLASIA AND ELLIPTOCYTOSIS (ATS-MR)
Paediatric or syndromic cardiomyopathy v1.49 ACTA1 Ivone Leong commented on gene: ACTA1: Reviewed a number of publications about the association of ACTA1 with cardiomyopathy. All affected patients have heterozygous variants in ACTA1. Therefore, MOI should stay as Monoallelic.
Paediatric or syndromic cardiomyopathy v1.49 ACTA1 Ivone Leong Publications for gene: ACTA1 were set to 26888179; 16945537; 32969603
Paediatric or syndromic cardiomyopathy v1.48 ACTA1 Ivone Leong Publications for gene: ACTA1 were set to 26888179; 16945537
Arthrogryposis v3.107 ACTA1 Ivone Leong Tag Q3_21_MOI tag was added to gene: ACTA1.
Arthrogryposis v3.107 ACTA1 Ivone Leong reviewed gene: ACTA1: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Paediatric or syndromic cardiomyopathy v1.47 ACTA1 Ivone Leong Phenotypes for gene: ACTA1 were changed from Dilated cardiomyopathy; Hypertrophic cardiomyopathy; Nemaline myopathy 3, autosomal dominant or recessive 161800; CMD with rigid spine; Myopathy, congenital, with fiber-type disproportion 1 255310 to Dilated cardiomyopathy, MONDO:0005021; Hypertrophic cardiomyopathy, MONDO:0005045; Nemaline myopathy 3, autosomal dominant or recessive, OMIM:161800; CMD with rigid spine; Myopathy, congenital, with fiber-type disproportion 1, OMIM:255310
Paediatric or syndromic cardiomyopathy v1.46 ACTA1 Ivone Leong Publications for gene: ACTA1 were set to doi:10. 1007/ s12265-016-9673-5; 16945537
Fetal anomalies v1.681 ACTA1 Ivone Leong Phenotypes for gene: ACTA1 were changed from NEMALINE MYOPATHY 3 to Nemaline myopathy 3, autosomal dominant or recessive, OMIM:161800
Arthrogryposis v3.107 ACTA1 Ivone Leong Phenotypes for gene: ACTA1 were changed from Nemaline myopathy 3, autosomal dominant or recessive 161800; Myopathy, actin, congenital, with excess of thin myofilaments 161800; Myopathy, actin, congenital, with cores 161800; nemaline myopathy; Nemaline myopathy 3, autosomal dominant or recessive, 161800Myopathy, actin, congenital, with excess of thin myofilaments, 161800Myopathy, actin, congenital, with cores, 161800Myopathy, congenital, with fiber-type disproportion 1, 255310; Nemaline Myopathy; CMD with rigid spine to Myopathy, actin, congenital, with cores, OMIM:161800; Myopathy, actin, congenital, with excess of thin myofilaments, OMIM:161800; Myopathy, congenital, with fiber-type disproportion 1, OMIM:255310; Nemaline myopathy 3, autosomal dominant or recessive, OMIM:161800; CMD with rigid spine
Congenital myopathy v2.45 ACTA1 Ivone Leong Phenotypes for gene: ACTA1 were changed from Myopathy, actin, congenital, with cores; Myopathy, actin, congenital, with excess of thin myofilaments; Myopathy, congenital, with fiber-type disproportion 1; Nemaline myopathy 3 to Myopathy, actin, congenital, with cores, OMIM:161800; Myopathy, actin, congenital, with excess of thin myofilaments, OMIM:161800; Myopathy, congenital, with fiber-type disproportion 1, OMIM:255310; Nemaline myopathy 3, autosomal dominant or recessive, OMIM:161800
Distal myopathies v1.30 ACTA1 Ivone Leong Phenotypes for gene: ACTA1 were changed from Nemaline myopathy 3, 161800 to Nemaline myopathy 3, autosomal dominant or recessive, OMIM:161800
Bleeding and platelet disorders v1.27 ACTB Ivone Leong Tag Q3_21_MOI tag was added to gene: ACTB.
Bleeding and platelet disorders v1.27 ACTB Ivone Leong reviewed gene: ACTB: Rating: ; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Bleeding and platelet disorders v1.27 ACTB Ivone Leong Phenotypes for gene: ACTB were changed from (NO OMIM NUMBER); AD thrombocytopenia to thrombocytopenia, MONDO:0002049 (AD)
Early onset or syndromic epilepsy v2.384 ACOX1 Ivone Leong edited their review of gene: ACOX1: Changed phenotypes to: Mitchell syndrome, OMIM:618960
Early onset or syndromic epilepsy v2.384 ACOX1 Ivone Leong reviewed gene: ACOX1: Rating: ; Mode of pathogenicity: None; Publications: 32169171; Phenotypes: ; Mode of inheritance: BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Early onset or syndromic epilepsy v2.384 ACOX1 Ivone Leong Tag Q3_21_MOI tag was added to gene: ACOX1.
Early onset or syndromic epilepsy v2.384 ACOX1 Ivone Leong Phenotypes for gene: ACOX1 were changed from Peroxisomal acyl-CoA oxidase deficiency 264470 to Peroxisomal acyl-CoA oxidase deficiency, OMIM:264470
Early onset or syndromic epilepsy v2.383 ACOX1 Ivone Leong Publications for gene: ACOX1 were set to 18536048
Early onset or syndromic epilepsy v2.382 ACOX1 Ivone Leong Publications for gene: ACOX1 were set to 18536048
Early onset or syndromic epilepsy v2.382 ACOX1 Ivone Leong Publications for gene: ACOX1 were set to
Early onset or syndromic epilepsy v2.381 ACOX1 Ivone Leong Tag Q3_21_MOI was removed from gene: ACOX1.