ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.5623C>T (p.Leu1875Phe)

dbSNP: rs1553463764
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519669 SCV000619597 uncertain significance not provided 2020-03-02 criteria provided, single submitter clinical testing Not observed in large population cohorts (Lek et al., 2016); Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); 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 substitution is predicted to be within the C-terminal cytoplasmic domain
Athena Diagnostics Inc RCV000519669 SCV001476048 uncertain significance not provided 2019-10-08 criteria provided, single submitter clinical testing
Invitae RCV001339444 SCV001533187 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2021-04-01 criteria provided, single submitter clinical testing This sequence change replaces leucine with phenylalanine at codon 1875 of the SCN2A protein (p.Leu1875Phe). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and phenylalanine. 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: "Probably Damaging"; Align-GVGD: "Class C15"). This variant has not been reported in the literature in individuals with SCN2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 450962). This variant is not present in population databases (ExAC no frequency).
GenomeConnect - Simons Searchlight RCV001265276 SCV001443393 pathogenic Complex neurodevelopmental disorder 2016-05-10 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2016-05-10 and interpreted as Pathogenic. Variant was initially reported on 2016-02-08 by GTR ID of laboratory name Center for Genomics and Transcriptomics . The reporting laboratory might also submit to ClinVar.

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