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Orofacial clefts are common developmental disorders that pose significant clinical, economical and psychological problems. We conducted genome-wide association analyses for  cleft palate  only (CPO) and cleft lip with or without palate (CL/P) with ~17 million markers in sub-Saharan Africans. After replication and combined analyses, we identified novel loci for CPO at or near genome-wide significance on chromosomes 2 (near  CTNNA2 ) and 19 (near  SULT2A1 ).  In situ  hybridization of  Sult2a1  in mice showed expression of  SULT2A1  in mesenchymal cells in palate, palatal rugae and palatal epithelium in the fused palate. The previously reported 8q24 was the most significant locus for CL/P in our study, and we replicated several previously reported loci including  PAX7  and  VAX1 .

Genomic analyses in African populations identify novel risk loci for cleft palate