ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.785T>G (p.Ile262Ser)

gnomAD frequency: 0.00055  dbSNP: rs145406549
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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 RCV001910857 SCV002166298 uncertain significance Glycogen storage disease IXa1 2023-07-05 criteria provided, single submitter clinical testing 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. 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. ClinVar contains an entry for this variant (Variation ID: 1390884). This variant has not been reported in the literature in individuals affected with PHKA2-related conditions. This variant is present in population databases (rs145406549, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces isoleucine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 262 of the PHKA2 protein (p.Ile262Ser).
Mayo Clinic Laboratories, Mayo Clinic RCV003481166 SCV004225650 uncertain significance not provided 2022-06-30 criteria provided, single submitter clinical testing BS1, PP3

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