ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.1996C>G (p.Gln666Glu)

dbSNP: rs119103256
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000002393 SCV003515532 likely pathogenic Glycogen storage disease, type V 2023-09-22 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with glutamic acid, which is acidic and polar, at codon 666 of the PYGM protein (p.Gln666Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with glycogen storage disease (PMID: 9506549). This variant is also known as p.Gln665Glu. ClinVar contains an entry for this variant (Variation ID: 2303). 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. 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.
Revvity Omics, Revvity RCV000002393 SCV003810406 uncertain significance Glycogen storage disease, type V 2019-06-05 criteria provided, single submitter clinical testing
GeneDx RCV003441700 SCV004170406 uncertain significance not provided 2023-10-05 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); 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: 32075227, 17404776, 31980526, 9506549, 17915571, 27535533)
OMIM RCV000002393 SCV000022551 pathogenic Glycogen storage disease, type V 1998-03-01 no assertion criteria provided literature only

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