ClinVar Miner

Submissions for variant NM_002863.5(PYGL):c.698G>A (p.Gly233Asp)

gnomAD frequency: 0.00001  dbSNP: rs113993975
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000020504 SCV000952766 pathogenic Glycogen storage disease, type VI 2023-12-20 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 233 of the PYGL protein (p.Gly233Asp). This variant is present in population databases (rs113993975, gnomAD 0.02%). This missense change has been observed in individuals with clinical features of PYGL-related conditions (PMID: 12809646; Invitae). ClinVar contains an entry for this variant (Variation ID: 21339). 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 PYGL protein function with a positive predictive value of 80%. This variant disrupts the p.Gly233 amino acid residue in PYGL. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 31508908; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
GeneReviews RCV000020504 SCV000040955 not provided Glycogen storage disease, type VI no assertion provided literature only

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