ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.134G>A (p.Arg45Gln)

dbSNP: rs1601781024
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 4
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000808960 SCV000949094 pathogenic Glycogen storage disease IXa1 2023-12-07 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 45 of the PHKA2 protein (p.Arg45Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with glycogen storage disease (PMID: 28627441; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 653226). 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%. This variant disrupts the p.Arg45 amino acid residue in PHKA2. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21646031, 22899091, 25070466, 28627441; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Centre for Human Genetics RCV000808960 SCV001482506 pathogenic Glycogen storage disease IXa1 2020-09-17 criteria provided, single submitter clinical testing Likely affecting
Revvity Omics, Revvity RCV000808960 SCV002024602 likely pathogenic Glycogen storage disease IXa1 2019-03-27 criteria provided, single submitter clinical testing
Laboratory of Medical Genetics, National & Kapodistrian University of Athens RCV000808960 SCV002577594 pathogenic Glycogen storage disease IXa1 2022-04-06 criteria provided, single submitter clinical testing PM2, PM5, PP2, PP3, PP5

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.