ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.58C>A (p.Pro20Thr)

dbSNP: rs3739168
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000533660 SCV000650118 uncertain significance Developmental and epileptic encephalopathy, 12 2022-11-29 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 471506). This variant has not been reported in the literature in individuals affected with PNKP-related conditions. This variant is present in population databases (rs3739168, gnomAD 0.01%). This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 20 of the PNKP protein (p.Pro20Thr).
GeneDx RCV001770464 SCV001992356 uncertain significance not provided 2023-08-11 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 22508754)
Fulgent Genetics, Fulgent Genetics RCV002483467 SCV002783474 uncertain significance Charcot-Marie-Tooth disease type 2B2; Microcephaly, seizures, and developmental delay; Ataxia - oculomotor apraxia type 4 2022-04-01 criteria provided, single submitter clinical testing

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