ClinVar Miner

Submissions for variant NM_007254.4(PNKP):c.1186A>G (p.Arg396Gly)

gnomAD frequency: 0.00006  dbSNP: rs563918674
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000648411 SCV000770231 uncertain significance Developmental and epileptic encephalopathy, 12 2022-03-19 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 396 of the PNKP protein (p.Arg396Gly). This variant is present in population databases (rs563918674, gnomAD 0.1%). 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: 538882). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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.
CeGaT Center for Human Genetics Tuebingen RCV000996972 SCV001151990 uncertain significance not provided 2018-09-01 criteria provided, single submitter clinical testing
GeneDx RCV000996972 SCV001998202 uncertain significance not provided 2024-07-03 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on 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)

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