ClinVar Miner

Submissions for variant NM_006920.6(SCN1A):c.965-1G>A (rs794726824)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Bioinformatics, Peking University RCV000180949 SCV000221931 pathogenic Severe myoclonic epilepsy in infancy 2014-12-20 criteria provided, single submitter research
GeneDx RCV000188853 SCV000242483 pathogenic not provided 2014-12-24 criteria provided, single submitter clinical testing c.965-1 G>A: IVS6-1 G>A in intron 6 of the SCN1A gene (NM_001165963.1) The c.965-1 G>A splice site mutation in the SCN1A gene destroys the canonical splice acceptor site in intron 6. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The variant is found in EPILEPSYV2-1 panel(s).
Invitae RCV000551280 SCV000633884 likely pathogenic Early infantile epileptic encephalopathy with suppression bursts 2019-12-16 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 6 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. ClinVar contains an entry for this variant (Variation ID: 189993). 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). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Institute of Human Genetics, University of Leipzig Medical Center RCV000180949 SCV001429466 likely pathogenic Severe myoclonic epilepsy in infancy 2018-06-22 criteria provided, single submitter clinical testing

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