Abstracts

Rationale: Genetic variants affecting the four voltage-gated sodium channel encoding genes SCN1A, SCN2A, SCN3A and SCN8A are associated with 1-2% of patients with neurodevelopmental disorders (NDDs). The underlying biology how variants in these genes cause a heterogeneous group of NDDs is not understood limiting therapeutics strategies and drug development.  Methods: We report on the largest cohort to date including >520 patients with neurodevelopmental disorders positive for either rare single nucleotide or large copy number variants in the four selected genes. We perform a range of novel genotype-phenotype analyses and correlate our observations with self-generated large scale single cell human cortex RNA sequencing data and public RNA tissue sequencing studies at different developmental stages. In addition, we in silico transferred patient and control variants (from the gnomAD database) across the different channels and performed local enrichment analyses to prediction gain and loss of function sensitive sites of the proteins. We subsequently validated the predictions using >40 patch clamp experiments.  Results: We show that for missense variant carrying patients the age of seizure onset follows gene expression order of SCN2A, SCN8A and SCN1A. Missense and truncating variants as well as full deletions all cause infantile onset epilepsy “Dravet syndrome” in >95% of SCN1A variant carriers. Missense variants in SCN2A, SCN8A near or in the pore are associated with early onset epilepsies whereas truncating variants and deletions are associated with developmental disorders with or without later onset seizures, predominantly autism. We bioinformatically predict and molecular validate across all four channels that gain-of-function (GoF) sensitive sites are near the pore region whereas loss-of-function sensitive regions are extracellular located. Full gene duplications of SCN2A and SCN8A mimic the early onset epilepsy phenotypes associated with GoF missense variants in the same genes. The contrasting disease biology of SCN1A vs. SCN2A, SCN8A can be explained by higher expression ratios at inhibitory vs. excitatory neurons.  Conclusions: In summary, we present a novel model explaining the heterogeneity of sodium channel associated neurodevelopmental disorders. The novel developed model and ability to predict functional consequences of variants set the foundation of precision medicine in sodium disorder pathologies, have direct consequences in clinical practice and will facilitate drug development.  Funding: DL and EPP recieve funding from the Dravet Foundation