Lack of evidence for a significant association between nonsyndromic cleft lip with or without cleft palate and the retinoic acid receptor alpha gene in the Japanese population

Nonsyndromic cleft lip with or without cleft palate (NSCLP) is one of the most common craniofacial malformations. Both genetic and environmental factors are thought to be involved in the pathogenesis. The retinoic acid receptor α (RARA) is one of the candidate genes for the pathogenesis of NSCLP. An association between a Pst I restriction fragment length polymorphism or D17S579 microsatellite marker polymorphism of the RARA gene and NSCLP was previously suggested, but no nucleotide change that may influence the gene expression or the protein sequence has been reported to date. To investigate the possible association between the RARA gene and NSCLP in Japanese patients, we performed a transmission disequilibrium test (TDT) using three microsatellite markers at the RARA locus in 48 parent-offspring trios. The allele-wise TDT did not show evidence of an association between the RARA gene and NSCLP. We also screened nucleotide changes in eight patients with family histories using exonby-exon direct sequencing. We found a novel nucleotide change (1161C>T) that is located in exon 1 of the RARA gene in one patient whose father also had the disease. Because the 1161C>T was inherited from the patient's healthy mother, the mutation was not considered to be responsible for NSCLP. We then screened all probands for the nucleotide changes in the promoter region of the RARA gene using denaturing high-performance liquid chromatography. A novel nucleotide length polymorphism of a thymidine tract was identified in three patients. No association between this polymorphism and NSCLP was observed. Our findings suggest that the RARA gene variations do not contribute to the development of NSCLP in the Japanese population.