Structural mapping of patient-associatedKCNMA1gene variants

Abstract

KCNMA1 linked channelopathy is a neurological disorder produced by malfunctioning of the BK channel, characterized by seizure, motor abnormalities, and neurodevelopmental disability. Twenty-one KCNMA1 patient-associated variants have been classified as gain-of-function (GOF) or loss of function (LOF) in BK channel activity, and the remaining ~40% are variants of uncertain significance (VUS). To address the physical relationships, this study analyzed KCNMA1 missense variants within the context of BK channel cryoEM structures. Clusters of LOF variants were identified in the pore, within the AC region (RCK1), and near the Ca2+ bowl (RCK2), overlapping with sites of pharmacological or endogenous modulation. However, no clustering relationship was found for GOF variants. Next, variants were analyzed with widely used pathogenicity algorithms. The individual performances of REVEL, Mutpred, MetaLR, and CADD/PHRED were compared for each variant, incorporating them into a weighted summation model (WSM). The WSM component was integrated with BK channel structural parameters in a modular algorithm to generate a 'KCNMA1 meta score' (KMS). KMS performance showed a 7% difference from the highest performing individual algorithm (REVEL). Several functionally uncharacterized variants that showed different predictions between KMS and REVEL were assessed further using electrophysiological recordings of BK currents. Two KMS positive; REVEL negative variants were confirmed pathogenic (M578T and D965V), and one KMS negative; REVEL positive variant was confirmed non pathogenic (D800Y). However, KMS failed to accurately categorize two variants (E656A and K457E). Thus, although incorporation of structural data within the KMS algorithm results in a small performance improvement, its predictive capabilities will be increased as more disease delineated variants are functionally tested, new structural components are available, and novel functional modules are developed.