ClinVar Miner

Submissions for variant NM_006920.6(SCN1A):c.264+5G>C (rs794726762)

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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 RCV000180877 SCV000221846 pathogenic Severe myoclonic epilepsy in infancy 2014-12-20 criteria provided, single submitter research
Invitae RCV001212061 SCV001383634 pathogenic Early infantile epileptic encephalopathy with suppression bursts 2019-05-15 criteria provided, single submitter clinical testing This sequence change falls in intron 1 of the SCN1A gene. It does not directly change the encoded amino acid sequence of the SCN1A protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has been observed to be de novo in an individual affected with Dravet syndrome (PMID: 26096185). ClinVar contains an entry for this variant (Variation ID: 189925). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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. This variant disrupts the c.264+2G nucleotide in the SCN1A gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 25669891,17054684). This suggests that this nucleotide is clinically-significant, and that variants that disrupt this position are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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