Loss-of-function variants in ciliary genes confer high risk for tetralogy of Fallot

Tetralogy of Fallot (TOF), the most common severe cyanotic congenital heart disease, has unclear genetic causes. Through next-generation sequencing in 131 patients with nonsyndromic TOF, we identified an increased burden of rare deleterious variants in ciliary genes and cilium pathway and observed a multigenic inheritance pattern, with an odds ratio (OR) of 1.672 [95% confidence interval (CI), 1.120 to 2.547; P = 0.0104] for more than two deleterious variants and a cumulative OR of 3.158 (95% CI, 1.381 to 6.371; P = 0.0038) for six variants. Functional validation in single- and double-heterozygous mouse models carrying these variants recapitulated TOF-like phenotypes and impaired normal cilia structure and function, particularly disrupting Hedgehog signaling in cardiomyocytes, and down-regulating key transcription factors Gata4 and Nkx2-5. Together, our study provides compelling evidence linking ciliary gene variants to a heightened risk of TOF in Han Chinese, offering valuable genetic insights into the etiology and pathogenesis of nonsyndromic TOF and supporting a multigenic inheritance model for the disease.