ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.1207C>T (p.Gln403Ter)

gnomAD frequency: 0.00001  dbSNP: rs372404688
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000420352 SCV000523376 likely pathogenic not provided 2022-04-27 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV001231907 SCV001404444 pathogenic Developmental and epileptic encephalopathy, 12 2023-03-26 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: 383110). This variant has not been reported in the literature in individuals affected with PNKP-related conditions. This variant is present in population databases (rs372404688, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Gln403*) in the PNKP gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PNKP are known to be pathogenic (PMID: 20118933, 25728773).

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