ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.1A>G (p.Met1Val)

dbSNP: rs2148058081
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001379104 SCV001576838 pathogenic Glycogen storage disease IXa1 2023-07-14 criteria provided, single submitter clinical testing This sequence change affects the initiator methionine of the PHKA2 mRNA. The next in-frame methionine is located at codon 59. This variant is not present in population databases (gnomAD no frequency). Disruption of the initiator codon has been observed in individual(s) with glycogen storage disease (Invitae). ClinVar contains an entry for this variant (Variation ID: 1067758). This variant disrupts a region of the PHKA2 protein in which other variant(s) (p.Arg45Trp) have been determined to be pathogenic (PMID: 21646031, 25070466, 28627441; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
CeGaT Center for Human Genetics Tuebingen RCV002292634 SCV002585113 likely pathogenic not provided 2022-09-01 criteria provided, single submitter clinical testing PHKA2: PM2, PVS1:Moderate, PM3:Supporting, PP4

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