Structural and Functional Integration of KCNMA1-linked Channelopathy Variants

Abstract

KCNMA1 encodes the pore forming alpha subunit for the voltage- and calcium-gated potassium (BK) channel, associated with a neurological disorder of unknown etiology. Currently, KCNMA1-linked channelopathy variants lack integration between disease and structural datasets, obscuring relationships between variants and known channel functions. To address this, we produced a comprehensive annotation of a human BK channel isoform containing alternative exons at sites 1 and 3 and the NRKEMVYR C-terminus (NM_001271518.2). Protein sequence was annotated with 106 patient variants and 572 tags (structural/functional domains, single nucleotide polymorphisms (SNPs), posttranslational modifications, pharmacological modulation, and others) and contextualized within the cryo-EM structure (PDB ID: 6V38). We hypothesized that pathogenic variants would localize within structurally and functionally defined BK channel modules. We found a cluster of loss-of-function (LOF) variants in at the selectivity filter and in the beginning of RCK1, while gain-of-function (GOF) lack obvious physical proximity. Interestingly, transmembrane segments S3 and S4 and the RCK1-RCK2 linker harbor no patient-associated variants, only a few conservative SNPs. Combing Rare Exome Variant Ensemble Learner REVEL) pathogenicity analysis with structural mapping, we identified residues within the selectivity filter and S6 domains as ‘highly pathogenic’ with scores of 0.95 ± 0.02 and 0.95 ± 0.03 respectively, RCK1 and disordered segments within RCK1 and RCK2 were ‘likely pathogenic’ (0.54 ± 0.17 and 0.54 ± 0.15, respectively), and the extracellular N-terminus and intracellular loops were ‘likely nonpathogenic’ (0.34 ± 0.29 and 0.32 ± 0.08, respectively). Finally, an overlap was observed between LOF variants and antagonistic pharmacological modulators, but no proximity relationship was identified between GOF variants and agonists. Thus, our sequence and structural metadata produced unique views that extend predictions for variant pathogenicity in KCNMA1-linked channelopathy.