Cystic fibrosis risk variants confer protection against inflammatory bowel disease

Genetic mutations that yield a defective cystic fibrosis (CF) transmembrane regulator (CFTR) protein cause CF, a life-limiting autosomal-recessive Mendelian disorder. A protective role of CFTR loss-of-function mutations in inflammatory bowel disease (IBD) has been suggested, but its evidence has been inconclusive and contradictory. Here, leveraging a large IBD exome sequencing dataset comprising 38,558 cases and 66,945 controls of European ancestry in the discovery stage and a combined total of 42,475 cases and 192,050 controls across diverse ancestry groups in the replication stage, we established a protective role of CF-risk variants against IBD based on the association test of CFTR deltaF508 (p = 8.96E-11) and the gene-based burden test of CF-risk variants (p = 3.9E-07). Furthermore, we assessed variant prioritization methods, including AlphaMissense, using clinically annotated CF-risk variants as the gold standard. Our findings highlight the critical and unmet need for effective variant prioritization in gene-based burden tests.