A Novel de novo TP63 Mutation in Whole Exome Sequencing of a Syrian Family with Oral Cleft and Ectrodactyly

Abstract

Oral clefts and ectrodactyly are common, heterogeneous birth defects. We performed whole exome sequencing (WES) analysis in a Syrian family. The proband presented with both orofacial clefting and ectrodactyly. A paternal side second-degree relative with only an oral cleft was deceased and unavailable for analysis. Variant annotation, Mendelian inconsistencies, and novel variants in known cleft genes were examined. Candidate variants were validated using Sanger sequencing. Twentyeight candidate de novo events were identified, one of which is in a known oral cleft and ectrodactyly gene, TP63 (c.956G>T, p.Arg319Leu), and confirmed by Sanger sequencing. A triallelic SNV was also found in HLA-DRB5, which is similar to and overlaps the known oral cleft gene HLA-DRB1.TP63 mutations are associated with multiple autosomal dominant orofacial clefting and limb malformation disorders. The p.Arg319Leu mutation seen in this patient is de novo but also novel. A known mutation 1bp upstream (rs121908839, c.955C>T, p.Arg319Cys) causes ectrodactyly, providing evidence that mutating this codon is deleterious. It is unclear whether this patient’s mutation is responsible for the entire phenotype. Generation and characterization of tp63 knockout zebrafish showed necrosis and rupture of the head at 3 days postfertilization. The embryonic phenotype could not be rescued by injection of zebrafish or human mRNA. Further functional analysis is needed to determine what proportion of the phenotype is due to this mutation.