In genes clinically associated with CHD we observed compound heterozygous variants inherited in trans in ZFPM2, NSD1, NOTCH1, VCAN, and MYH6 and rare homozygous variants in MYH6. Variation was observed in 9 additional genes including compound heterozygous variants in ADAM17, CHRD, IFT140, PTPRJ, and RYR1 and rare homozygous variants in ATE1, and the presence of heart defects in mouse knockout models for these loci supports their association with human cardiac malformations. This evidence concerns the gene IFT140 and coronary artery disorder.