The SNP rs560426 Within ABCA4-ARHGAP29 Locus and the Risk of Nonsyndromic Oral Clefts

• Published in: The Cleft palate-craniofacial journal Vol. 57; no. 6; p. 671
• Main Authors: Wu-Chou, Yah-Huei, Chen, Kuo-Ting Philip, Lu, Yi-Chieh, Lin, Yin-Ting, Chang, Hsien-Fang, Lo, Lun-Jou
• Format: Journal Article
• Language: English
• Published: United States 01.06.2020
• Subjects: Asians; ATP-Binding Cassette Transporters - genetics; Cleft Lip - genetics; Cleft Palate - genetics; Genetic Predisposition to Disease; Genotype; GTPase-Activating Proteins - genetics; Haplotypes; Humans; Polymorphism, Single Nucleotide; SNP association study; chromosome 1p22; nonsyndromic oral clefts; case–parent trio; ABCA4 and ARHGAP29 genes
• ISSN: 1545-1569
• DOI: 10.1177/1055665619899764

Nonsyndromic oral clefts are common birth defect with complex etiology. In the present study, we attempt to further validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. We performed allelic transmission disequilibrium test analysis, on 10 eligible single nucleotide polymorphisms (SNPs) and SNP haplotypes using the Family-Based Association Test. The study sample consisted of 334 case-parent trios of nonsyndromic oral clefts from Taiwanese population, separated into nonsyndromic cleft lip with or without cleft palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups. We found only the SNP rs560426 within the ABCA4 gene showed strong association with NSCPO ( = .03498; Permuted = .05382). No association between other 9 selected SNPs in ABCA4-ARHGAP29 region and the risk of nonsyndromic oral clefts was found. For the haplotype analyses, we found only haplotype T-C (rs570926 and rs3789431) in ABCA4 block 2 showed significant association with nonsyndromic NSCL/P in these Taiwanese trios. We used a family-based analysis in 334 Taiwanese case-parent trios to validate the possible role for ABCA4 and ARHGAP29 in the susceptibility to nonsyndromic oral clefts. This study provides a new evidence for an association between the intron variant rs560426 within ABCA4 and nonsyndromic cleft palate which may contribute their regulatory role in craniofacial development.