ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.2111C>T (p.Ala704Val)

gnomAD frequency: 0.00001  dbSNP: rs1483102315
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001204475 SCV001375682 pathogenic Glycogen storage disease, type V 2024-01-27 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 704 of the PYGM protein (p.Ala704Val). This variant is present in population databases (no rsID available, gnomAD 0.006%). This missense change has been observed in individual(s) with McArdle disease (PMID: 17221871, 29143597). ClinVar contains an entry for this variant (Variation ID: 935807). 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 PYGM protein function with a negative predictive value of 95%. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV001204475 SCV004207222 likely pathogenic Glycogen storage disease, type V 2023-10-10 criteria provided, single submitter clinical testing

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