ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.2024C>T (p.Ser675Leu)

gnomAD frequency: 0.00001  dbSNP: rs794727189
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000175191 SCV000226633 uncertain significance not provided 2017-05-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV002516665 SCV003512676 pathogenic Glycogen storage disease, type V 2024-10-15 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 675 of the PYGM protein (p.Ser675Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of glycogen storage disease (PMID: 17705025, 32735634; internal data). ClinVar contains an entry for this variant (Variation ID: 194750). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt PYGM protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV002516665 SCV003810350 uncertain significance Glycogen storage disease, type V 2019-10-15 criteria provided, single submitter clinical testing

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