ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.1288_1294del (p.Ser430fs)

dbSNP: rs796052860
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001008452 SCV001168223 likely pathogenic not provided 2023-01-27 criteria provided, single submitter clinical testing Frameshift variant predicted to result in protein truncation, as the last 92 amino acids are replaced with 34 different amino acids, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 22508754)
Invitae RCV001860590 SCV002196270 pathogenic Developmental and epileptic encephalopathy, 12 2023-09-22 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ser430Profs*35) 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 (no rsID available, gnomAD 0.001%). 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: 817332). For these reasons, this variant has been classified as Pathogenic.

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