ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.1537A>G (p.Ile513Val) (rs139570786)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000675632 SCV000225874 uncertain significance not provided 2018-08-16 criteria provided, single submitter clinical testing
GeneDx RCV000174555 SCV000567874 likely benign not specified 2017-12-08 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
GenomeConnect, ClinGen RCV000509394 SCV000606998 not provided Glycogen storage disease, type V no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Invitae RCV000509394 SCV000835576 uncertain significance Glycogen storage disease, type V 2018-06-21 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with valine at codon 513 of the PYGM protein (p.Ile513Val). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and valine. This variant is present in population databases (rs139570786, ExAC 0.5%). This variant has been observed on the opposite chromosome (in trans) from a pathogenic variant in an individual affected with McArdle disease (PMID: 23653251, Invitae). This finding is consistent with autosomal recessive inheritance, and suggests that this variant contributes to disease. ClinVar contains an entry for this variant (Variation ID: 194233). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000675632 SCV000801333 uncertain significance not provided 2017-05-03 no assertion criteria provided clinical testing

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