Identification of co-segregating RUBCN and KANK1 mutations in a UK amyotrophic lateral sclerosis kindred

Abstract

Bioinformatic analysis of next-generation sequencing data identified novel missense variants in RUBCN (p.Cys517Phe) and KANK1 (p.Pro1332Ala) that co-segregated with amyotrophic lateral sclerosis (ALS) in a United Kingdom kindred and were ultra-rare in European control populations (allele frequency < 0.001%). Likelihood-based segregation analysis demonstrated significant co-segregation with disease, yielding full-likelihood Bayes factor (FLB) scores of 4.6 and 5.5 for RUBCN and KANK1, respectively, exceeding the threshold supporting pathogenicity (FLB [≥] 4.33). Sex-stratified penetrance modelling identified maximal FLB scores of 7.9 for both genes under a model with male and female penetrances of 0.99 and 0.01, respectively. Gene-based burden analysis of deleterious ultra-rare variants in independent ALS case-control cohorts demonstrated exome-wide significant associations with ALS (SKAT-O, p < 1 x 10-9). Functional studies in lymphoblastoid cell lines derived from variant carriers revealed significantly increased apoptosis and dysregulated expression of genes involved in endocytosis, LC3-associated phagocytosis, endoplasmic reticulum stress, and cytoskeletal organisation (p < 0.05). Analysis of spinal cord tissue from ALS cases and controls showed significant upregulation of RUBCN (2.85-fold) and downregulation of KANK1 (0.40-fold) (p < 0.05). Collectively, these findings implicate RUBCN and KANK1 as candidate ALS genes and suggest that disruption of vesicular trafficking, autophagy-related pathways, and cytoskeletal homeostasis may contribute to disease pathogenesis of ALS.