ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.179G>A (p.Arg60Gln)

gnomAD frequency: 0.00015  dbSNP: rs374743798
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000188423 SCV000242036 uncertain significance not provided 2022-11-29 criteria provided, single submitter clinical testing 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)
Invitae RCV000701603 SCV000830413 uncertain significance Developmental and epileptic encephalopathy, 12 2022-09-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 60 of the PNKP protein (p.Arg60Gln). This variant is present in population databases (rs374743798, gnomAD 0.07%). 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: 206381). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.

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