ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.580C>T (p.Arg194Trp)

gnomAD frequency: 0.00001  dbSNP: rs376581557
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001239256 SCV001412114 likely pathogenic Glycogen storage disease, type V 2023-12-30 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 194 of the PYGM protein (p.Arg194Trp). This variant is present in population databases (rs376581557, gnomAD 0.005%). This missense change has been observed in individuals with glycogen storage disease (PMID: 10679948, 22250184, 26944031). This variant is also known as R193W. ClinVar contains an entry for this variant (Variation ID: 964929). 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 expected to disrupt PYGM protein function with a positive predictive value of 95%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
GeneDx RCV001751473 SCV001986113 uncertain significance not provided 2020-08-03 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); 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: 26944031, 10679948, 22250184, 29143597)
Revvity Omics, Revvity RCV001239256 SCV003818069 uncertain significance Glycogen storage disease, type V 2019-08-14 criteria provided, single submitter clinical testing
Natera, Inc. RCV001239256 SCV002092340 uncertain significance Glycogen storage disease, type V 2020-12-29 no assertion criteria provided clinical testing

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