ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.1247A>G (p.Asn416Ser)

dbSNP: rs2105862220
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University of Leipzig Medical Center RCV001724786 SCV001950116 likely pathogenic Severe myoclonic epilepsy in infancy 2022-02-11 criteria provided, single submitter clinical testing This variant was identified as de novo (maternity and paternity confirmed)._x000D_ Criteria applied: PS2, PM2_SUP, PM5_SUP, PP2, PP3
3billion RCV001724786 SCV005905682 likely pathogenic Severe myoclonic epilepsy in infancy 2023-11-22 criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Missense variant In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.95 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.99 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported to be associated with SCN1A related disorder (ClinVar ID: VCV001297050 /PMID: 31864146). The variant has been previously reported as de novo in a similarly affected individual (PMID: 31864146). A different missense change at the same codon (p.Asn416Lys) has been reported to be associated with SCN1A related disorder (ClinVar ID: VCV000651325 /PMID: 31440721). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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