ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1439A>G (p.Tyr480Cys)

gnomAD frequency: 0.00021  dbSNP: rs145464516
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001061860 SCV001226619 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2022-08-15 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 502 of the POMT1 protein (p.Tyr502Cys). This variant is present in population databases (rs145464516, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with POMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 856405). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Ambry Genetics RCV002553908 SCV003679017 uncertain significance Inborn genetic diseases 2022-01-26 criteria provided, single submitter clinical testing The c.1505A>G (p.Y502C) alteration is located in exon 15 (coding exon 14) of the POMT1 gene. This alteration results from a A to G substitution at nucleotide position 1505, causing the tyrosine (Y) at amino acid position 502 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV003132198 SCV003811840 uncertain significance not provided 2019-06-20 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004735952 SCV005348905 uncertain significance POMT1-related disorder 2024-05-30 no assertion criteria provided clinical testing The POMT1 c.1505A>G variant is predicted to result in the amino acid substitution p.Tyr502Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.048% of alleles in individuals of African descent in gnomAD. Although we suspect that this variant may be benign, the clinical significance of this variant is classified as uncertain at this time due to insufficient functional and genetic evidence.

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