ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.610C>T (p.Arg204Ter)

gnomAD frequency: 0.00001  dbSNP: rs796052850
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188430 SCV000242043 pathogenic not provided 2014-02-12 criteria provided, single submitter clinical testing p.Arg204Stop (CGA>TGA): c.610 C>T in exon 6 of the PNKP gene (NM_007254.2) The Arg204Stop nonsense mutation in the PNKP gene is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Although this mutation has not been reported previously to our knowledge, it is considered a disease-causing mutation.The variant is found in EPILEPSY panel(s).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001175506 SCV001339109 likely pathogenic not specified 2020-03-20 criteria provided, single submitter clinical testing Variant summary: PNKP c.610C>T (p.Arg204X) 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. Truncations downstream of this position have been reported as disease-associated mutations in HGMD and in the literature and have been classified as pathogenic in ClinVar. The variant allele was found at a frequency of 4e-06 in 251368 control chromosomes (gnomAD). To our knowledge, no occurrence of c.610C>T in individuals affected with PNKP-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submitter (evaluation in 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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