ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.1499G>A (p.Arg500Gln)

gnomAD frequency: 0.00001  dbSNP: rs753412659
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV002248096 SCV002519122 uncertain significance not specified 2022-05-04 criteria provided, single submitter clinical testing
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV003138121 SCV003807020 uncertain significance Glycogen storage disease IXa1 2022-08-17 criteria provided, single submitter clinical testing ACMG classification criteria: PS4 supporting, PM2 moderated, PP3 supporting
Labcorp Genetics (formerly Invitae), Labcorp RCV003138121 SCV005823335 uncertain significance Glycogen storage disease IXa1 2024-11-02 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 500 of the PHKA2 protein (p.Arg500Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with glycogen storage disease type IXa (PMID: 34093448). ClinVar contains an entry for this variant (Variation ID: 1685004). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on PHKA2 protein function. 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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