ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.1366G>A (p.Val456Met)

gnomAD frequency: 0.00002  dbSNP: rs398124208
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169330 SCV000220667 likely pathogenic Glycogen storage disease, type V 2014-09-04 criteria provided, single submitter literature only
Eurofins Ntd Llc (ga) RCV000790687 SCV000225355 pathogenic not provided 2013-09-20 criteria provided, single submitter clinical testing
Invitae RCV000169330 SCV001590586 pathogenic Glycogen storage disease, type V 2024-01-09 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 456 of the PYGM protein (p.Val456Met). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with glycogen storage disease, aka polyglucosan body myopathy (PMID: 14568816, 17324573, 17876739, 22250184, 29143597). ClinVar contains an entry for this variant (Variation ID: 95290). 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%. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000169330 SCV004207227 pathogenic Glycogen storage disease, type V 2023-09-27 criteria provided, single submitter clinical testing

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