Disease-associated Kv1.3 Variants are Energy Compromised with Impaired Nascent Chain Folding

Nascent proteins fold in a stepwise manner during all stages of biogenesis. This progression is particularly complex for ion channels composed of multiple biogenic and functional domains and subunits. The human Kv1.3 ion channel, encoded by KCNA3, is expressed in neuronal and immune cells. Its dysregulation produces chronic inflammatory disease and autoimmune disorders, which affect many in the US population, especially women. Using the unbiased ‘genome-first’ approach with integrated patient biobank databases, we identified KCNA3 gene variants associated with human disease and examined their impact on Kv1.3 channel biogenesis. Our tertiary and quaternary folding assays and all-atom molecular dynamics simulations show that KCNA3 gene variants in T1, the channel’s intersubunit recognition domain, manifest early-stage T1 folding defects, energetic instabilities, and conformational distortion of subunits concomitant with tertiary unwinding. These findings identify molecular mechanisms by which patient-associated variants influence channel assembly, potentially contributing to diverse clinical phenotypes underlying human disease.