ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.2971G>A (p.Gly991Arg)

gnomAD frequency: 0.00004  dbSNP: rs750628677
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000809879 SCV000950060 uncertain significance Glycogen storage disease IXa1 2023-12-11 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 991 of the PHKA2 protein (p.Gly991Arg). This variant is present in population databases (rs750628677, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. 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: 654000). 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 not expected to disrupt PHKA2 protein function with a negative 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.
Ambry Genetics RCV003362966 SCV004080779 likely benign Inborn genetic diseases 2023-08-08 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000809879 SCV004171058 likely pathogenic Glycogen storage disease IXa1 2023-11-26 criteria provided, single submitter clinical testing

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