Identification of CNTN2 as a genetic modifier of PIGA-CDG in a family with incomplete penetrance and in Drosophila.

Loss-of-function mutations in the X chromosome gene PIGA lead to phosphatidylinositol glycan class A congenital disorder of glycosylation (PIGA-CDG), an ultra-rare 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 carry PIGA c.395C>G (p.Ser132Cys), an ultra-rare variant predicted to be damaging. Strikingly, the maternal grandfather and a great uncle also carry the same PIGA variant, but neither presents with symptoms associated with PIGA-CDG. We hypothesized that genetic modifiers might contribute to this reduced penetrance. Using whole-genome sequencing and pedigree analysis, we identified possible susceptibility variants found in the probands and not in the carriers and possible protective variants found in the carriers and not in the probands. Candidate genetic modifier variants included heterozygous, damaging variants in three genes involved directly in glycosylphosphatidylinositol (GPI)-anchor biosynthesis and additional variants in other glycosylation pathways or encoding GPI-anchored proteins. Using a Drosophila eye-based model, we tested modifiers identified through genome sequencing. Loss of CNTN2, a predicted protective modifier that encodes a GPI-anchored protein responsible for neuron/glial interactions, rescues loss of PIGA in the eye-based model, as we predict in the family. Further testing found that the loss of CNTN2 also rescues PIGA-CDG-specific phenotypes, including seizures and climbing defects in Drosophila neurological models of PIGA-CDG. Using pedigree information, genome sequencing, and in vivo testing, we identified CNTN2 as a strong candidate modifier that could explain the incomplete penetrance in this family. Identifying and studying rare disease modifier genes in families may lead to therapeutic targets.