Many structural birth defect patients lack genetic diagnoses because there are many disease genes as yet to be discovered. We applied a gene burden test incorporating de novo predicted-loss-of-function (pLoF) and likely damaging missense variants together with inherited pLoF variants to a collection of congenital heart defect (CHD) and orofacial cleft (OC) parent-offspring trio cohorts (n = 3,835 and 1,844, respectively). We identified 17 novel candidate CHD genes and 10 novel candidate OC genes, of which many were known developmental disorder genes. Shorter genes were more powered in a "de novo only" analysis as compared to analysis including inherited pLoF variants. TFs were enriched among the significant genes; 14 and 8 transcription factor (TF) genes showed significant variant burden for CHD and OC, respectively. In total, 30 affected children had a de novo missense variant in a DNA binding domain of a known CHD, OC, and other developmental disorder TF genes. Our results suggest candidate pathogenic variants in CHD and OC and their potentially pleiotropic effects in other developmental disorders.

The authors have declared no competing interest.

This work was funded by NIH grants R03 HD099358 and R01 HG010501 to M.L.B.

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For CHD, we downloaded de novo variant data from two exome-sequencing studies (Jin et al., Nat. Genet., 2017, 49:1593; Sifrim et al., Nat. Genet., 2016, 48:1060) and one genome-sequencing study (Richter et al., Nat. Genet., 2020, 52:769). We also downloaded the list of rare inherited pLoF variants from Jin et al. For OC, we downloaded genotype data from 4 cohorts from the Gabriella Miller Kids First data portal. Their database of Genotypes and Phenotypes (dbGaP) IDs were phs001168, phs001997, phs001420, and phs002595.

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All data produced in the present work are contained in the manuscript. Code and data for generating the figures is available at https://github.com/BulykLab/CHD-OC-manuscript-figures.