ClinVar Miner

Submissions for variant NM_000292.3(PHKA2):c.2137+5G>A

gnomAD frequency: 0.00005  dbSNP: rs372314504
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001591161 SCV001814484 uncertain significance not provided 2019-10-30 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes splice predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV003640904 SCV004512920 uncertain significance Glycogen storage disease IXa1 2024-02-23 criteria provided, single submitter clinical testing This sequence change falls in intron 19 of the PHKA2 gene. It does not directly change the encoded amino acid sequence of the PHKA2 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs372314504, gnomAD 0.005%). 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: 440944). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004782412 SCV005394117 uncertain significance not specified 2024-09-03 criteria provided, single submitter clinical testing
GenomeConnect, ClinGen RCV000578927 SCV000681400 not provided Glycogen phosphorylase kinase deficiency no assertion provided phenotyping only Variant interpretted as Uncertain significance and reported on 11-13-2019 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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