Functional Testing of Human Disease Missense Variants in Caenorhabditis elegans by Targeting COQ2 Variants

Missense variants introduce single amino acid substitutions into proteins that might affect their functions and cause genetic diseases, including kidney disease. The clinical significance of most missense variants in human genes is difficult to determine. We investigated the functional effects of missense variants in highly homologous protein orthologs in humans and the nematode Caenorhabditis elegans.

Ortholog analysis was performed to investigate the utility of C. elegans as a model for assessing the functional consequences of human missense variants, particularly those whose clinical significance remains undetermined. By using CRISPR-Cas9 genome editing, we generated C. elegans coq-2 missense variant mutants that model human missense variants. Phenotypic analyses were conducted to compare pathogenic phenotypes in C. elegans coq-2 missense variant mutants and those of human primary CoQ10 deficiency.

Approximately 250 ortholog pairs were genes reported to be linked to human genetic diseases and approximately half of documented human variants in these genes were missense variants whose clinical significance remains largely undetermined. We chose to characterize undetermined missense variants in COQ2, which encodes coenzyme Q2 polyprenyltransferase (COQ2), as an example to test whether they cause measurable phenotypes when introduced into the orthologous coq-2 in C. elegans. We found marked phenotypes consistent with primary coenzyme Q₁₀ (CoQ10) deficiency in humans, and that the phenotypes were generally rescued by CoQ10 supplementation.

Our findings provide insights into human genetic disease-associated missense variants and demonstrate that C. elegans can be used as a simple, cost-effective in vivo model for testing undetermined missense variants in human disease genes.