ClinVar Miner

Submissions for variant NM_002637.4(PHKA1):c.3149G>A (p.Arg1050His)

gnomAD frequency: 0.00006  dbSNP: rs782453258
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001169830 SCV001332609 likely benign Glycogen storage disease IXd 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV001169830 SCV003267581 uncertain significance Glycogen storage disease IXd 2023-04-14 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 915258). This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. This variant is present in population databases (rs782453258, gnomAD 0.008%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 1050 of the PHKA1 protein (p.Arg1050His).
Mayo Clinic Laboratories, Mayo Clinic RCV003480977 SCV004225668 uncertain significance not provided 2023-06-14 criteria provided, single submitter clinical testing PP3

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