ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.3880-2A>G

dbSNP: rs794726816
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Bioinformatics, Peking University RCV000180941 SCV000221922 pathogenic Severe myoclonic epilepsy in infancy 2014-12-20 criteria provided, single submitter research
Invitae RCV000707470 SCV000836569 pathogenic Early infantile epileptic encephalopathy with suppression bursts 2018-05-08 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 19 of the SCN1A gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SCN1A-related disease. However, family studies have indicated that this variant was not present in the parents of an individual with clinical features consistent with a SCN1A-related disease, which suggests that it was de novo in that affected individual (Invitae). ClinVar contains an entry for this variant (Variation ID: 189985). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in SCN1A are known to be pathogenic (PMID: 17347258, 18930999). For these reasons, this variant has been classified as Pathogenic.

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