ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.4766A>G (p.Tyr1589Cys)

dbSNP: rs1553463119
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000548002 SCV000639631 pathogenic Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2022-08-23 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 1589 of the SCN2A protein (p.Tyr1589Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with benign familial neonatal-infantile seizures (BFNIS) (PMID: 23758435). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 464912). 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"). Experimental studies have shown that this missense change affects SCN2A function (PMID: 23758435).
Center of Genomic medicine, Geneva, University Hospital of Geneva RCV000857242 SCV000999829 likely pathogenic Seizures, benign familial infantile, 3 2018-08-13 criteria provided, single submitter clinical testing
Channelopathy-Associated Epilepsy Research Center RCV002319532 SCV002605495 not provided Complex neurodevelopmental disorder no assertion provided literature only

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