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Likely inborn error of metabolism - targeted testing not possible v4.113 | CLCN7 |
Sarah Leigh gene: CLCN7 was added gene: CLCN7 was added to Likely inborn error of metabolism - targeted testing not possible. Sources: Expert Review Amber,Literature watchlist tags were added to gene: CLCN7. Mode of inheritance for gene: CLCN7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: CLCN7 were set to 31155284 Phenotypes for gene: CLCN7 were set to Hypopigmentation, organomegaly, and delayed myelination and development, OMIM:618541 Mode of pathogenicity for gene: CLCN7 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments |
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Likely inborn error of metabolism - targeted testing not possible v4.77 | PIGM | Sarah Leigh Tag promoter tag was added to gene: PIGM. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v4.77 | PIGM |
Sarah Leigh edited their review of gene: PIGM: Added comment: A single PIGM variant (NM_145167.2(PIGM):c.-270C>G)(rs587776528) has been associated with Glycosylphosphatidylinositol deficiency, (OMIM:610293) and as limited Gen2Phen gene for the same condition. To date, this variant has only been reported in people of Arab or Turkish descent. Microsatellite- and SNP-based haplotypes encompassing PIGM reported in PMID:19168132, suggested that a founder effect in the two families (one Arab and one Turkish) was unlikely. However, subsequent occurrences of the variant in two additional unrelated Arab families (PMID: 31445883) might suggest that this variant is confined within the Middle Eastern populations. Functional studies have shown that this variant reduces transcription of PIGM and blocks mannosylation of glycosylphosphatidylinositol anchor (PMID: 16767100).; Changed rating: GREEN |
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Likely inborn error of metabolism - targeted testing not possible v4.77 | PIGM |
Sarah Leigh Tag non-coding-known-pathogenic tag was added to gene: PIGM. Tag Q4_23_promote_green tag was added to gene: PIGM. Tag Q4_23_NHS_review tag was added to gene: PIGM. |
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Likely inborn error of metabolism - targeted testing not possible v4.77 | PIGM | Sarah Leigh Classified gene: PIGM as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v4.77 | PIGM | Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v4.77 | PIGM | Sarah Leigh Gene: pigm has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v4.76 | PIGM | Sarah Leigh Phenotypes for gene: PIGM were changed from Glycosylphosphatidylinositol deficiency 610293 to Glycosylphosphatidylinositol deficiency, OMIM:610293 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v4.75 | PIGM | Sarah Leigh Publications for gene: PIGM were set to 27604308; 16767100; 25293775; 17442906 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v4.74 | PIGM | Hannah Knight reviewed gene: PIGM: Rating: GREEN; Mode of pathogenicity: None; Publications: 31445883; Phenotypes: Glycosylphosphatidylinositol deficiency 610293; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v2.190 | DHDDS | Arina Puzriakova Phenotypes for gene: DHDDS were changed from Retinitis pigmentosa 59, OMIM:613861; ?Congenital disorder of glycosylation, type 1bb, OMIM:613861; Posterior segment abnormalities to Retinitis pigmentosa 59, OMIM:613861; ?Congenital disorder of glycosylation, type 1bb, OMIM:613861 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v2.189 | DHDDS | Arina Puzriakova Phenotypes for gene: DHDDS were changed from Retinitis pigmentosa 59 613861; ?Congenital disorder of glycosylation, type 1bb 613861 to Retinitis pigmentosa 59, OMIM:613861; ?Congenital disorder of glycosylation, type 1bb, OMIM:613861; Posterior segment abnormalities | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v2.111 | MSTO1 | Sarah Leigh Phenotypes for gene: MSTO1 were changed from Myopathy, mitochondrial, and ataxia, 617675 to Myopathy, mitochondrial, and ataxia OMIM:617675; mitochondrial myopathy-cerebellar ataxia-pigmentary retinopathy syndrome MONDO:0044714 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.339 | PIGM | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.254 | ABHD12 | Sarah Leigh reviewed gene: ABHD12: Rating: GREEN; Mode of pathogenicity: ; Publications: 27604308, 20797687, 24697911 ; Phenotypes: Polyneuropathy, hearing loss, ataxia, retinitis pigmentosa, and cataract 612674, Hereditary ataxia, Posterior segment abnormalities, Congenital hearing impairment (profound/severe), PHARC syndrome (Disorders of complex lipid synthesis); Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.232 | PIGM | Sarah Leigh Classified gene: PIGM as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.232 | PIGM |
Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype. Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 1 variant was reported in 2 unrelated families (PMID 16767100), together with supportive functional studies (PMID 17442906 & 25293775). |
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Likely inborn error of metabolism - targeted testing not possible v1.232 | PIGM | Sarah Leigh Gene: pigm has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM | Sarah Leigh Deleted their comment | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM | Sarah Leigh Classified gene: PIGM as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM |
Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype. Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 1 variant was reported in 2 unrelated families (PMID 16767100), together with supportive functional studies (PMID 17442906 & 25293775). |
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Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM | Sarah Leigh Gene: pigm has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM | Sarah Leigh Classified gene: PIGM as Amber List (moderate evidence) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM |
Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype. Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 1 variant was reported in 2 unrelated families (PMID 16767100), together with supportive functional studies (PMID 17442906 & 25293775). |
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Likely inborn error of metabolism - targeted testing not possible v1.231 | PIGM | Sarah Leigh Gene: pigm has been classified as Amber List (Moderate Evidence). | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.230 | PIGM | Sarah Leigh Publications for gene: PIGM were set to 27604308; 16767100; 25293775; 17442906 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.230 | PIGM | Sarah Leigh Publications for gene: PIGM were set to 27604308; 16767100; 25293775; 17442906; 25293775 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.229 | PIGM | Sarah Leigh Publications for gene: PIGM were set to 27604308; 16767100; 25293775 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.228 | PIGM | Sarah Leigh Added comment: Comment on phenotypes: Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation;Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.228 | PIGM | Sarah Leigh Phenotypes for gene: PIGM were changed from Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation; Glycosylphosphatidylinositol deficiency, 610293; Glycosylphosphatidylinositol deficiency 610293; Phosphatidylinositolglycan, class M deficiency (Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation); Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency to Glycosylphosphatidylinositol deficiency 610293 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.115 | DHDDS |
Sarah Leigh Added comment: Comment on list classification: This gene was part of an initial gene list collated by Emma Ashton on behalf of the London North GLH, for GMS Metabolic Consensus Specialist Test Group. Additional information was not provided, such as mode of inheritance and phenotype. Associated with relevant phenotype in OMIM and as probable Gen2Phen gene for Retinitis pigmentosa 59 613861. One variant was reported in at least 15 families with retinitis pigmentosa, but only one compound individual with glycosylation defects was identifed so far (PMID 27343064). |
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Likely inborn error of metabolism - targeted testing not possible v1.114 | DHDDS | Sarah Leigh Added comment: Comment on phenotypes: Posterior segment abnormalities;Retinitis pigmentosa (other congenital disorders of glycosylation) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.114 | DHDDS | Sarah Leigh Phenotypes for gene: DHDDS were changed from ?Congenital disorder of glycosylation, type 1bb 613861; Developmental delay and seizures with or without movement abnormalities 617836; Retinitis pigmentosa 59 613861 to Retinitis pigmentosa 59 613861; ?Congenital disorder of glycosylation, type 1bb 613861 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.110 | DHDDS | Sarah Leigh Phenotypes for gene: DHDDS were changed from Retinitis pigmentosa 59 613861; Posterior segment abnormalities; Retinitis pigmentosa (other congenital disorders of glycosylation) to ?Congenital disorder of glycosylation, type 1bb 613861; Developmental delay and seizures with or without movement abnormalities 617836; Retinitis pigmentosa 59 613861 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v1.47 | PIGM |
Ivone Leong Source NHS GMS was added to PIGM. Source London North GLH was added to PIGM. |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | TRNT1 |
Ellen McDonagh Added phenotypes congenital sideroblastic anemia with B cell immunodeficiency, fevers, and developmental delay (SIFD); retinitis pigmentosa with erythrocytic microcytosis for gene: TRNT1 Publications for gene TRNT1 were changed from PMID: 26494905; PMID: 25652405 to 25652405; 26494905 |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | TRNT1 |
Ellen McDonagh gene: TRNT1 was added gene: TRNT1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: TRNT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TRNT1 were set to PMID: 26494905; PMID: 25652405 Phenotypes for gene: TRNT1 were set to congenital sideroblastic anemia with B cell immunodeficiency, fevers, and developmental delay (SIFD); retinitis pigmentosa with erythrocytic microcytosis |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | POMGNT1 |
Ellen McDonagh Added phenotypes Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 253280; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C 3 613157; Protein-O-mannose beta-1,2-N-acetyglucosaminyltransferase deficiency (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies); Retinitis pigmentosa 76 617123 for gene: POMGNT1 Publications for gene POMGNT1 were changed from 27604308 to 27421908 |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | POMGNT1 |
Ellen McDonagh gene: POMGNT1 was added gene: POMGNT1 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: POMGNT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: POMGNT1 were set to 27604308 Phenotypes for gene: POMGNT1 were set to Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3 253280; Muscular dystrophy-dystroglycanopathy (congenital with mental retardation), type B; Muscular dystrophy-dystroglycanopathy (limb-girdle), type C 3 613157; Protein-O-mannose beta-1,2-N-acetyglucosaminyltransferase deficiency (Disorders of protein O-glycosylation, O-mannosylglycan synthesis deficiencies); Retinitis pigmentosa 76 617123 |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | PIGM | Ellen McDonagh Added phenotypes Phosphatidylinositolglycan, class M deficiency (Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation); Glycosylphosphatidylinositol deficiency 610293 for gene: PIGM | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Likely inborn error of metabolism - targeted testing not possible v0.4 | PIGM |
Ellen McDonagh gene: PIGM was added gene: PIGM was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: PIGM was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PIGM were set to 27604308; 16767100; 25293775 Phenotypes for gene: PIGM were set to Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation; Glycosylphosphatidylinositol deficiency, 610293; Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | HGSNAT |
Ellen McDonagh gene: HGSNAT was added gene: HGSNAT was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: HGSNAT was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: HGSNAT were set to 27604308 Phenotypes for gene: HGSNAT were set to Mucopolysaccharidosis Type III; Mucopolysaccharidosis, Type III; Retinitis Pigmentosa 73; Mucopolysaccharidosis type IIIC (Sanfilippo C), 252930; Mucopolysaccharidosis Type IIIC; MPS IIIC, Sanfilippo C disease (Mucopolysaccharidoses) |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | EPG5 |
Ellen McDonagh gene: EPG5 was added gene: EPG5 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: EPG5 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: EPG5 were set to 28624465; 23222957; 26917586; 23674064; 25331754; 23838600; 26395118 Phenotypes for gene: EPG5 were set to Vici syndrome, 242840; IMMUNODEFICIENCY WITH CLEFT LIP/PALATE, CATARACT, HYPOPIGMENTATION, AND ABSENT CORPUS CALLOSUM |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | DHDDS |
Ellen McDonagh Added phenotypes Retinitis pigmentosa 59 613861 for gene: DHDDS Publications for gene DHDDS were changed from 27604308 to 21295282; 21295283; 27343064 |
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Likely inborn error of metabolism - targeted testing not possible v0.4 | DHDDS |
Ellen McDonagh gene: DHDDS was added gene: DHDDS was added to Inborn errors of metabolism. Sources: Expert Review Amber Mode of inheritance for gene: DHDDS was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DHDDS were set to 27604308 Phenotypes for gene: DHDDS were set to Posterior segment abnormalities; Retinitis pigmentosa (other congenital disorders of glycosylation) |