Distinguishing syndromic and nonsyndromic cleft palate through analysis of protein-altering de novo variants in 818 trios.

De novo variants (DNs) are sporadically occurring variants found in an offspring but absent in both parents. DNs most commonly arise in the germline and are not under selective pressure; therefore, they may be enriched for disease-causing alleles. In fact, DNs have been implicated in multiple rare genetic disorders. Cleft palate (CP) is a craniofacial congenital anomaly occurring in ∼1 in 1,700 live births. Genome-wide association studies have found fewer than a dozen CP-specific loci, while exome and targeted sequencing studies in family-based and case-control cohorts often lack statistical power to conclusively identify causal variants. We therefore hypothesized that CP probands would be enriched for protein-altering DNs, which may explain the relative dearth in discovery. A complicating factor in understanding CP, however, is its phenotypically heterogeneous nature. As such, we aggregated sequence data for 818 trios with CP representing a combination of subtypes and isolated and syndromic presentations. We identified global enrichment of protein-altering DNs (1.48, p = 1.28 × 10-28) and exome-wide-significant (p < 1.3 × 10-6) gene-specific enrichment for SATB2, MEIS2, COL2A1, ZC4H2, EFTUD2, KAT6B, and ANKRD11. We found a statistically significant higher enrichment of protein-altering DNs in syndromic (1.70, p = 6.95 × 10-26) versus nonsyndromic (1.31, p = 8.51 × 10-8) probands but no differences between subtypes. We explored differences in gene-specific enrichment, finding some unique to syndromic probands (ZC4H2) or nonsyndromic probands (IRF6), as well as some shared between groups (SATB2). Altogether, we show that DNs are a contributor to CP risk and that combined analysis can enhance our ability to find genetic associations that would otherwise be undetected.