Epilepsy-associated Variants of a Single SCN1A Codon exhibit Divergent Functional Properties

ObjectivePathogenic variants in SCN1A, which encodes the voltage gated sodium channel NaV1.1, are associated with multiple epilepsy syndromes exhibiting a range of clinical severity. Loss or gain of function SCN1A variants are reported in different syndromes including Dravet syndrome, which is associated with loss-of-function whereas neonatal/infantile-onset developmental and epileptic encephalopathy (DEE) is associated with gain-of-function. Strategies to predict SCN1A variant pathogenicity and dysfunction have been proposed but are limited by available training data. We investigated the functional properties of four epilepsy-associated SCN1A variants affecting the same codon and sought to correlate channel dysfunction with phenotype. MethodsWhole-cell manual patch-clamp recording was performed on heterologously-expressed NaV1.1 variants. Structural modeling of NaV1.1 variant proteins was conducted using AlphaFold 3. ResultsWe describe an individual with early infantile onset DEE associated with SCN1A-I1347T, and identified three additional cases from the literature or ClinVar with distinct variation of the same codon (I1347N, I1347V, I1347F). Functional studies demonstrated mixed gain and loss of function properties for I1347T, I1347V, and I1347F, but complete loss-of-function for I1347N. Structural models suggest important interactions between isoleucine-1347 and the sixth transmembrane helices of domains 3 and 4 that are disrupted most significantly with asparagine replacement at this position (I1347N). InterpretationPathogenic variants in SCN1A involving the same codon can produce divergent functional effects. Our findings suggest that predicting specific functional effects of SCN1A variants should not rely heavily on position in the protein.