ClinVar Miner

Submissions for variant NM_002637.4(PHKA1):c.892C>T (p.Arg298Ter)

dbSNP: rs1256371424
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000701851 SCV000830672 pathogenic Glycogen storage disease IXd 2022-08-05 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 578746). This variant has not been reported in the literature in individuals affected with PHKA1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg298*) in the PHKA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PHKA1 are known to be pathogenic (PMID: 9731190, 15637709).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003317349 SCV004020885 pathogenic Glycogen phosphorylase kinase deficiency 2023-06-12 criteria provided, single submitter clinical testing Variant summary: PHKA1 c.892C>T (p.Arg298X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 183265 control chromosomes (gnomAD). To our knowledge, no occurrence of c.892C>T in individuals affected with Glycogen Phosphorylase Kinase Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Institute of Human Genetics, University of Wuerzburg RCV000701851 SCV004232368 pathogenic Glycogen storage disease IXd no assertion criteria provided clinical testing

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