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Functional investigation of an undescribed missense variant in the SCN1A gene in a patient with Dravet syndrome

Pathogenic variants in the SCN1A gene are associated with a spectrum of epileptic disorders ranging in severity from familial febrile seizures to Dravet syndrome. Large proportions of reported pathogenic variants in SCN1A are annotated as missense variants and are often classified as variants of uncertain significance when no functional data are available. Although loss-of-function variants are associated with a more severe phenotype in SCN1A, the molecular mechanism of single nucleotide variants is often not clear, and genotype-phenotype correlations in SCN1A-related epilepsy remain uncertain.

The variants located in the coding regions of a gene are known to disrupt splicing both through activation of cryptic splice sites in exons and through changes in exon cis-regulatory sequences. This study described a novel case of a patient with Dravet syndrome caused by an undescribed missense variant c.4852G>A (p.Gly1618Ser) in the SCN1A gene. Using an in vitro system with midigene expression it was demonstrated that this variant was splice-affecting, leading to the two 2 isoforms formation. The first major event is an activation of the cryptic exon donor splicing site, resulting in a 5-nucleotide shortening of exon 28 of the SCN1A gene. This results in a frame shift and the formation of a premature stop codon p.(Gly1618Cysfs*6). The second minor event is an exon 28 skip, which also results in a frame shift and the stop codon formation (p.(Asn1528Valfs*7)). In both cases, there is a deletion of almost the entire domain IV of the Nav1.1 protein, including the pore-forming region, which is critical for the normal functioning of the protein at the protein level. To our knowledge, this is the first report on the functional investigation of a missense variant affecting splicing in Dravet syndrome

Peter Sparber, Svetlana Mikhailova, Varvara Galkina, Yulia Itkis and  Mikhail Skoblov Functional investigation of an undescribed missense variant affecting splicing in a patient with Dravet syndrome. Front. Neurol. doi: 10.3389/fneur.2021.761892