Gregor Mendel’s studies of inheritance patterns in pea plants helped shape researchers’ understanding of single-gene diseases, which can run in families. Some of the diseases that follow a Mendelian pattern include cystic fibrosis, color blindness, and rare seizure disorders such as phosphatidylinositol glycan class A congenital disorder of glycosylation (PIGA-CDG).
Clement Chow, a geneticist at the University of Utah Health, and his team study the role of genetic variants on disease outcomes, especially in rare diseases. Chow focused on PIGA-CDG when he and his team noticed a family carrying the PIGA mutation where some members remained unaffected by the disease. This finding led them to search for a genetic modifier that might contribute to this observation.
The researchers identified the contactin-2 (CNTN2) gene, which appeared in healthy family members with PIGA mutations. Their findings, published in The American Journal of Human Genetics, revealed that CNTN2 may be a protective genetic modifier in this disease.1 Identifying rare disease modifier genes in families could also aid in developing therapeutic targets.
While PIGA-CDG is caused by a mutation in the PIGA gene on the X chromosome, its expression varies and manifests in different symptoms. There are fewer than 100 reported individuals with the disorder, underscoring a need to better understand PIGA-CDG.
In the studied family, two brothers with PIGA-CDG developed early-onset epilepsy and mild developmental delay. Genetic testing revealed they both inherited the same PIGA variant.2 Notably, their maternal grandfather and a great-uncle also carried the variant but remained asymptomatic. Chow hypothesized that genetic modifiers might play a role in this discrepancy.
Using whole-genome sequencing and pedigree analysis of the family members, the researchers identified candidate modifier genes based on inheritance pattern: protective in healthy genetic carriers and susceptibility in those with PIGA-CDG. The team identified roughly 30 variants for each and then made a shortlist based on the predicted function of the genes involved in glycosylphosphatidylinositol (GPI) anchors.
PIGA encodes for a protein necessary for making GPI anchors, which are essential in attaching proteins to the cell membrane. Without GPI-anchored proteins, cell adhesion, signal transduction, and protection from immune destruction are affected. Based on this criterion, the researchers narrowed their list to three candidate genes.
Using a Drosophila melanogaster eye model, the team tested how the candidate genes influenced PIGA loss in vivo. Since PIGA knockdown significantly reduces eye size, researchers used this trait to assess gene interactions. The predicted protective modifiers were expected to rescue (make the eye bigger), while susceptibility candidates were expected to enhance (make the eye smaller) the PIGA phenotype. Notably, CNTN2, a GPI-anchored protein involved in neuron-glial cell interaction, was a strong protective genetic modifier, rescuing an eye size defect in the flies caused by the loss of PIGA.
The researchers also tested the motor effects of PIGA neuronal knockdown flies–known to have seizures and difficulty moving—such as climbing to the top of a vial. Flies with reduced function for both PIGA and Cont, the fruit fly ortholog to CNTN2, appeared to move more readily and showed reduced severity of seizures.
Based on these findings, the researchers believe that changes to CNTN2 are likely to protect people against the disease. With further investigations between affected families, this finding could eventually lead to a better grasp of understudied rare disorders and the development of therapies for PIGA-CDG.
“If we can use this strategy more broadly, I think we can help address the problem of phenotypic variation in rare disease,” Chow said in a press release. “I am hoping that this will be used as a roadmap moving forward.”
- Thorpe HJ, et al. Identification of CNTN2 as a genetic modifier of PIGA-CDG in a family with incomplete penetrance and in Drosophila. Am J Hum Genet. 2025.
- Bayat A, et al. Lessons learned from 40 novel PIGA patients and a review of the literature. Epilepsia. 2020;61(6):1142-1155.
