ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2046G>T (p.Lys682Asn)

gnomAD frequency: 0.00001  dbSNP: rs756493732
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000260355 SCV000417418 likely benign Seizures, benign familial infantile, 3 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV000476547 SCV000551886 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2022-08-06 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 331728). This variant has not been reported in the literature in individuals affected with SCN2A-related conditions. This variant is present in population databases (rs756493732, gnomAD 0.02%). This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 682 of the SCN2A protein (p.Lys682Asn).
Athena Diagnostics Inc RCV000713070 SCV000843637 uncertain significance not provided 2017-09-15 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000260355 SCV001428679 uncertain significance Seizures, benign familial infantile, 3 2020-01-22 criteria provided, single submitter clinical testing
GeneDx RCV000713070 SCV001789160 uncertain significance not provided 2022-02-27 criteria provided, single submitter clinical testing Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This substitution is predicted to be in the cytoplasmic loop between the first and second homologous domains; Has not been previously published as pathogenic or benign to our knowledge
New York Genome Center RCV000476547 SCV002506682 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2021-05-20 criteria provided, single submitter clinical testing

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