Identification ofCNTN2as a genetic modifier of PIGA-CDG through pedigree analysis of a family with incomplete penetrance and functional testing inDrosophila

Abstract

AbstractLoss of function mutations in the X-linkedPIGAgene lead to PIGA-CDG, an ultra-rare congenital disorder of glycosylation (CDG), typically presenting with seizures, hypotonia, and neurodevelopmental delay. We identified two brothers (probands) with PIGA-CDG, presenting with epilepsy and mild developmental delay. Both probands carryPIGAS132C, an ultra-rare variant predicted to be damaging. Strikingly, the maternal grandfather and a great-uncle also carryPIGAS132C, but neither presents with symptoms associated with PIGA-CDG. We hypothesized genetic modifiers may contribute to this reduced penetrance. Using whole genome sequencing and pedigree analysis, we identified possible susceptibility variants found in the probands and not in carriers and possible protective variants found in the carriers and not in the probands. Candidate variants included heterozygous, damaging variants in three genes also involved directly in GPI-anchor biosynthesis and a few genes involved in other glycosylation pathways or encoding GPI-anchored proteins. We functionally tested the predicted modifiers using aDrosophilaeye-based model of PIGA-CDG. We found that loss ofCNTN2, a predicted protective modifier, rescues loss ofPIGAinDrosophilaeye-based model, like what we predict in the family. Further testing found that loss ofCNTN2also rescues patient-relevant phenotypes, including seizures and climbing defects inDrosophilaneurological models of PIGA-CDG. By using pedigree information, genome sequencing, andin vivotesting, we identifiedCNTN2as a strong candidate modifier that could explain the incomplete penetrance in this family. Identifying and studying rare disease modifier genes in human pedigrees may lead to pathways and targets that may be developed into therapies.