In silico prediction of the impact of genomic variations in the small conductance calcium activated potassium channel SK3 structure and function

Lucia Padilla^1,2Coral Del Val³Daria Neidre^1,2Agustín S Kokenge^1,2Juan E Martinez^2,3Antonio Lucio Teixeira^1,3Igor Zwir³Gabriel A. de Erausquin^1,2*

• ¹Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, Joe R. & Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States
• ²Laboratory of Brain Development, Modulation and Repair, Joe & Teresa Long School of Medicine, University of Texas Health San Antonio, San Antonio, Texas, United States
• ³Department of Computer Science and Artificial Intelligence, ETS of Computer and Telecommunications Engineering, University of Granada, Granada, Spain

The small-conductance calcium-activated potassium channel SK3, encoded by the KCNN3 gene, plays a critical role in regulating dopaminergic neuron (DN) firing patterns by modulating afterhyperpolarization currents. SK3 dysfunction has been implicated in neuropsychiatric and neurodegenerative disorders. We analyzed structural and functional consequences of KCNN3 splicing and genetic variation. Alternative splicing variants of the KCNN3 gene were retrieved from the Ensembl database and aligned using T-Coffee, manually inspected and curated. Protein domains were identified with Pfam 35.0, SMART 9.0, and InterPro 98.0, and visualized. An AlphaFold2 model of SK3 full-length protein (UniProt: Q9UGI6) used as reference and structural models of its splicing variants were predicted with ColabFold. Functional domains (S1-S6 transmembrane helices, H5 pore loop, and calmodulin-binding) were defined and superimposed onto the AlphaFold2 reference. Domain integrity was assessed based on completeness of all expected residue indices within each functional region. SNPs and CNVs across all coding KCNN3 splicing variants were analyzed, classified, and filtered to isolate pathogenic variants prioritizing non-synonymous amino acid substitutions. Differential variant impacts across splicing isoforms were assessed by mapping variant positions to individual transcript protein sequences and used to predict functional consequences. Two long and two short splicing variants are known. Short variants lack the motif required for potassium channels. Pathogenic variants result from missense mutations resulting in amino acid substitutions. In all cases, the consequential effects depend on the specific location and role of the amino acid being changed.