ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.392G>T (p.Gly131Val)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV005198917 SCV005842221 uncertain significance Glycogen storage disease IXa1 2024-03-24 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 131 of the PHKA2 protein (p.Gly131Val). This variant is present in population databases (no rsID available, gnomAD 0.02%). This missense change has been observed in individual(s) with glycogen storage disease (PMID: 33014498). 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 PHKA2 protein function with a positive predictive value of 80%. This variant disrupts the p.Gly131 amino acid residue in PHKA2. Other variant(s) that disrupt this residue have been observed in individuals with PHKA2-related conditions (PMID: 28627441), which suggests that this may be a clinically significant amino acid residue. 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.

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