Molecular context of pathogenic variants is associated with phenotype and treatment response in SCN8A-related disorders

Objectives: Genotype-phenotype studies in rare epilepsies typically relate a pathogenic DNA sequence change to clinical outcome, without considering the broader molecular context of a given variant. Here we ask whether clinical heterogeneity in SCN8A-related disorders (SCN8A-RD) is patterned along molecular dimensions that go beyond the specific genetic alteration, to include position in the linear channel topology, proximity to post-translational modification (PTM) and structural sites, and predicted effects on mRNA splicing. Using the International SCN8A Registry, we map these features against seizure, developmental, and treatment-response phenotypes to identify the regions and molecular feature classes with which clinical variability is associated. Methods: We identify "hot-spots" across the coding sequence for seizure types and severity of developmental disability (DD). We then test for enrichment of clinical features near sites related to PTM and protein structure, identify variants that may alter mRNA splicing, and evaluate the interaction between these features and clinical subgroups. Results: We expand on previous work identifying regions of coding DNA sequence that are pathogenic or benign "hot-spots". We show regional enrichment of numerous seizure types and severities of DD. Enrichment analysis of PTM and protein structural sites shows distinct enrichment profiles for developmental, seizure, and medication-response features. Finally, we identify 14 variants that are likely to alter RNA splicing. Significance: We provide a higher-resolution map of pathogenic variation across SCN8A and show that seizure types, developmental severity, and medication response are regionally organized along the coding sequence. Proximity to structural and glycosylation sites distinguishes phenotypic subgroups is associated with differential drug response, including a glycosylation-gabapentin relationship, and 14 missense variants are flagged as likely splice-altering, nominating targets for splice-directed therapy and providing candidates for experimental validation of dual pathogenic mechanisms.