Variant Analyses of Candidate Genes in Orofacial Clefts in Multi‐Ethnic Populations

Abstract

Cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) are congenital birth defects where the upper lip and/or palate fail to fuse properly during embryonic facial development. CL/P and CPO fall under the larger category of orofacial clefts (OFCs), which affect ~1.2/1000 live births world-wide and imposes significant social and financial burdens on affected individuals and their families. The etiology of orofacial clefts is complex and likely results from a combination of genetic mutations with environmental covariates. Recent genome wide association studies (GWAS) and whole exome sequencing (WES) for orofacial clefting identified significant genetic associations and variants in several genes. Of these genes, we investigated the role of common and rare variants in the SHH, RORA, MRPL53, ACVR1, and GDF11 genes. We sequenced these five genes in multi-ethnic CL/P and CPO samples in order to find mutations that may provide potential explanations for OFCs missing heritability. In total, 19 variants of interest were found, seven of which were in SHH, one in RORA, three in MRPL53, six in ACVR1, and two in GDF11. Types of mutations found included stop-gained, missense, synonymous, intronic, and splice site variants. Of these 19 variants, 3 novel missense variants were found, one in SHH, one in RORA, and one in GDF11. Rare and novel variants were further analyzed using in-silico predictive tools such as SIFT, Polyphen-2, Provean score, CADD, and HOPE. This study provides evidence that mutations in SHH, RORA, MRPL53, ACVR1, and GDF11 may contribute to risk of OFCs in various populations.