Regulatory Elements in SEM1–DLX5–DLX6 (7q21.3) Locus Contribute to Genetic Control of Coronal Nonsyndromic Craniosynostosis and Bone Density-Related Traits

Purpose The etiopathogenesis of coronal nonsyndromic craniosynostosis (cNCS), a congenital condition defined by premature fusion of one or both coronal sutures, remains largely unknown. Methods We conducted the largest genome-wide association study (GWAS) of cNCS followed by replication, fine mapping, and functional validation of the most significant region using zebrafish animal model. Results GWAS identified six independent genome-wide-significant risk alleles, four on chromosome 7q21.3 SEM1–DLX5–DLX6 locus, and their combination conferred up to seven-fold increased risk of cNCS. The top variants were replicated in an independent cohort and showed pleiotropic effects on brain and facial morphology and bone mineral density. Fine mapping of 7q21.3 identified a craniofacial transcriptional enhancer (eDlx36) within the linkage region of the top variant (rs4727341; odds ratio [95% confidence interval], 0.48[0.39-0.59]; P=1.2E-12) that located in SEM1 intron and enriched in four rare risk variants. In zebrafish, the activity of the transfected human eDlx36 enhancer was observed in the frontonasal prominence and calvaria during skull development and was reduced when the four rare risk variants were introduced into the sequence. Conclusions Our findings support a polygenic nature of cNCS risk and functional role of craniofacial enhancers in cNCS susceptibility with potential broader implications for bone health.