ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.2785G>C (p.Ala929Pro)

dbSNP: rs1324893950
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000990492 SCV001141494 pathogenic Glycogen storage disease IXa1 2021-08-30 criteria provided, single submitter clinical testing Pathogenic in haplotype with Met912Thr. Haplotype p.[Met912Thr; Ala929Pro]
Invitae RCV000990492 SCV001395521 uncertain significance Glycogen storage disease IXa1 2023-12-04 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 929 of the PHKA2 protein (p.Ala929Pro). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PHKA2-related conditions. ClinVar contains an entry for this variant (Variation ID: 803726). 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%. 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.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV000990492 SCV002512212 uncertain significance Glycogen storage disease IXa1 2021-05-31 criteria provided, single submitter clinical testing ACMG classification criteria: PM2 moderate, PP3 supporting

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