ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2654C>T (p.Thr885Ile)

dbSNP: rs1699477928
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001314698 SCV001505242 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2022-07-06 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: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1015785). This variant has not been reported in the literature in individuals affected with SCN2A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 885 of the SCN2A protein (p.Thr885Ile).
GeneDx RCV003120548 SCV003798522 pathogenic not provided 2022-08-02 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); 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 within the transmembrane segment S5 of the second homologous domain; This variant is associated with the following publications: (PMID: 31785789)
Revvity Omics, Revvity RCV003120548 SCV003820763 uncertain significance not provided 2021-04-07 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Strasbourg University Hospital RCV002275350 SCV002562863 likely pathogenic Seizure no assertion criteria provided clinical testing

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