ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.4547C>T (p.Ser1516Leu)

gnomAD frequency: 0.00003  dbSNP: rs139300715
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000209885 SCV000265507 uncertain significance Severe myoclonic epilepsy in infancy 2021-09-01 criteria provided, single submitter research
GeneDx RCV000494091 SCV000582178 uncertain significance not provided 2022-09-15 criteria provided, single submitter clinical testing Observed in an individual with developmental delay or intellectual disability; however segregation and detailed clinical information was not provided (Hiatt et al., 2018); This substitution is predicted to be in the cytoplasmic loop between the third and fourth homologous domains; 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 variant is associated with the following publications: (PMID: 29655203, 29652076)
Labcorp Genetics (formerly Invitae), Labcorp RCV000702992 SCV000831870 likely benign Early infantile epileptic encephalopathy with suppression bursts 2023-11-17 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004528267 SCV004105789 uncertain significance SCN1A-related disorder 2023-08-09 criteria provided, single submitter clinical testing The SCN1A c.4547C>T variant is predicted to result in the amino acid substitution p.Ser1516Leu. This variant was reported in an individual with an unspecified epilepsy and/or neurodevelopmental disorder (Table S4, Lindy et al. 2018. PubMed ID: 29655203). This variant is reported in 0.013% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-166852557-G-A). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Mayo Clinic Laboratories, Mayo Clinic RCV000494091 SCV004224979 uncertain significance not provided 2022-03-17 criteria provided, single submitter clinical testing PP3

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