ClinVar Miner

Submissions for variant NM_006922.4(SCN3A):c.5516T>C (p.Leu1839Pro)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV004788632 SCV005399645 uncertain significance Developmental and epileptic encephalopathy, 62 2024-10-11 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as VUS-3A. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with familial focal epilepsy with variable foci 4 (MIM#617935) and developmental and epileptic encephalopathy 62 (DEE; MIM#617938). Although, a single frameshift variant predicted to have a null effect has been reported in an individual with DEE (ClinGen GCEP). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. It has been reported in a single family (PMID: 18242854). (I) 0200 - Variant is predicted to result in a missense amino acid change from leucine to proline. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (v2, v3 and v4). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v4; 1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable missense variants have previous evidence for pathogenicity. (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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