Search for Chromosomal Instability aiding Variants (CIVa) reveal naturally occurring kinetochore gene variants that perturb chromosome segregation

Chromosomal Instability (CIN) is a hallmark of cancers, and CIN-promoting mutations are not fully known. Here we report 141 Chromosomal Instability aiding Variant (CIVa) candidates by assessing the prevalence of Loss-of-Function (LoF) variants in 135 chromosome segregation genes from over 150,000 humans. Unexpectedly, we observe both heterozygous and homozygous CIVa in Astrin and SKA3, two evolutionarily conserved kinetochore and microtubule-associated proteins essential for chromosome segregation. To stratify harmful versus harmless variants, we combine live-cell microscopy and controlled protein expression. We find the naturally occurring Astrin p.Q1012* variant is harmful as it fails to localise normally, induces chromosome misalignment and promotes chromosome missegregation, in a dominant negative manner. In contrast, the Astrin p.L7Qfs*21 variant generates a shorter isoform that localises and functions normally and the SKA3 p.Q70Kfs*7 variant does not disrupt SKA complex localisation or function, revealing distinct resilience mechanisms that render these variants harmless. Thus, we present a scalable framework to predict and stratify naturally occurring CIVa, and provide insight into resilience mechanisms that compensate for naturally occurring CIVa.