Alternative splice sites and transcript variations of CACNA1H---A human T-calcium channel gene candidate for idiopathic generalized epilepsies

Highly alternatively spliced genes may provide complicated paradigms for phenotypic expression and complex targets for disease mutations. Functional changes created by missense mutations may differentially affect variant proteins, while missense, silent and non-coding mutations may alter developmental regulation of splice variant expression. CACNA1H is a human gene encoding Cav3.2 low voltage-activated, T-type calcium channels associated with bursting behavior in neurons, and has been linked to more than 30 mutations predisposing to Childhood Absence Epilepsy (CAE) and other Idiopathic Generalized Epilepsies (IGEs). Normal physiology and missense mutations have been previously evaluated for a single splice form of Cav3.2 expressed in transformed cell lines. We here show that CACNA1H is alternatively spliced at 12-14 sites capable of generating both functional and non-functional transcripts. Variable cytoplasmic and extracellular protein domains point to likely differences in gating behavior, sensitivity to neuromodulation and interactions with extracellular matrix. Biophysical profiles of selected physiological Cav3.2 variants reveal marked differences in kinetics and steady state gating parameters most likely to affect membrane firing. These were comparable to or larger than changes reported for previously studied mutations. Missense CAE and IGE mutations were clustered near segments associated with anomalous splicing. Missense and silent mutations were found to destroy, create or change the regulatory specificity of predicted exonic splicing enhancer (ESE) sequences that may control splicing regulation. We discuss a paradigm for CACNA1H expression of Cav3.2 subunits that may influence future basic and clinical studies.