ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.559G>A (p.Gly187Arg)

dbSNP: rs2147972085
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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 RCV001940035 SCV002177969 likely pathogenic Glycogen storage disease IXa1 2023-03-23 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 187 of the PHKA2 protein (p.Gly187Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Glycogen storage disease (PMID: 21646031; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1410249). 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. 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.

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