ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.143del (p.Arg48fs)

gnomAD frequency: 0.00001  dbSNP: rs766530579
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000704636 SCV000833592 pathogenic Developmental and epileptic encephalopathy, 12 2023-10-13 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg48Lysfs*17) 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). This variant is present in population databases (rs766530579, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with PNKP-related conditions. ClinVar contains an entry for this variant (Variation ID: 580950). For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV002462056 SCV002756786 pathogenic not provided 2022-11-21 criteria provided, single submitter clinical testing Frameshift 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); This variant is associated with the following publications: (PMID: 34490615)

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