ClinVar Miner

Submissions for variant NM_002637.4(PHKA1):c.2063G>A (p.Arg688Gln)

gnomAD frequency: 0.00010  dbSNP: rs201234013
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000785102 SCV000923660 uncertain significance Glycogen storage disease IXd 2019-01-01 criteria provided, single submitter clinical testing
Invitae RCV000785102 SCV003452700 uncertain significance Glycogen storage disease IXd 2023-12-11 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 688 of the PHKA1 protein (p.Arg688Gln). This variant is present in population databases (rs201234013, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 634584). 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 PHKA1 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 RCV002535720 SCV003726423 uncertain significance Inborn genetic diseases 2022-12-02 criteria provided, single submitter clinical testing The c.2063G>A (p.R688Q) alteration is located in exon 19 (coding exon 19) of the PHKA1 gene. This alteration results from a G to A substitution at nucleotide position 2063, causing the arginine (R) at amino acid position 688 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Preventiongenetics, part of Exact Sciences RCV003396361 SCV004120178 uncertain significance PHKA1-related condition 2023-08-01 criteria provided, single submitter clinical testing The PHKA1 c.2063G>A variant is predicted to result in the amino acid substitution p.Arg688Gln. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.022% of alleles in individuals of East Asian descent in gnomAD, including two hemizygous individuals (http://gnomad.broadinstitute.org/variant/X-71840649-C-T), which may be too common to be causative of disease. Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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