ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.789G>C (p.Leu263Phe)

gnomAD frequency: 0.00021  dbSNP: rs201073763
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000393924 SCV000343012 uncertain significance not provided 2018-01-02 criteria provided, single submitter clinical testing
Invitae RCV000533176 SCV000649909 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2022-10-13 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 285 of the POMT1 protein (p.Leu285Phe). This variant is present in population databases (rs201073763, gnomAD 0.02%). This missense change has been observed in individual(s) with Walker-Warburg syndrome. This publication describes this variant as a polymorphism (PMID: 16575835). ClinVar contains an entry for this variant (Variation ID: 288794). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt POMT1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital RCV000678830 SCV000805016 uncertain significance Pyridoxine-dependent epilepsy 2017-05-19 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000764804 SCV000895949 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1 2018-10-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001166185 SCV001328532 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2K 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Mayo Clinic Laboratories, Mayo Clinic RCV000393924 SCV001714924 uncertain significance not provided 2019-05-05 criteria provided, single submitter clinical testing
GeneDx RCV000393924 SCV002064167 uncertain significance not provided 2022-01-20 criteria provided, single submitter clinical testing Described as a non-pathogenic variant in a cohort of individuals with Walker-Warburg syndrome (van Reeuwijk et al., 2006); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17878207, 16575835, 30564623)
Revvity Omics, Revvity Omics RCV000393924 SCV003809687 uncertain significance not provided 2023-09-23 criteria provided, single submitter clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000393924 SCV001958656 uncertain significance not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000393924 SCV001965809 uncertain significance not provided no assertion criteria provided clinical testing

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