New genetic variants in the CCR5 gene and the distribution of known polymorphisms in Omani population

• Published in: International journal of immunogenetics Vol. 41; no. 1; pp. 20 - 28
• Main Authors: Al-Mahruqi, S. H., Zadjali, F., Koh, C. Y., Balkhair, A., Said, E. A., Al-Balushi, M. S., Hasson, S. S., Al-Jabri, A. A.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.02.2014
• Subjects: 5' Untranslated Regions; Adult; Alleles; Binding Sites; Computational Biology - methods; Gene Frequency; Genetic Predisposition to Disease; Haplotypes; HIV Infections - genetics; Human immunodeficiency virus 1; Humans; INDEL Mutation; Linkage Disequilibrium; Mutation; Oman; Physical Chromosome Mapping; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Promoter Regions, Genetic; Receptors, CCR2 - genetics; Receptors, CCR5 - genetics; Transcription Factors - metabolism; Oman
• ISSN: 1744-3121; 1744-313X
• DOI: 10.1111/iji.12081

Summary C–C motif chemokine receptor‐5 (CCR5) is a pro‐inflammatory receptor that binds to chemokines and facilitates the entry of the R5 strain of HIV‐1. A number of polymorphisms were identified within the promoter and coding regions of the CCR5 gene, some of which have been found to affect the protein expression and thus receptor function. Although several CCR5 polymorphisms were shown to vary widely in their distribution among different ethnic populations, there has been no study addressing the potential variants of the CCR5 gene in the Omani population. The aim of this study was to identify the polymorphic sites that exist within the CCR5 gene in Omanis. Blood samples were collected from 89 Omani adult individuals, and genomic DNA was amplified by polymerase chain reaction and sequenced to identify the polymorphic sites. The distribution of the detected variants was examined and compared with the previously published data. Four new indels were detected of 32 variable positions, −2973A/–, −2894A/–, −2827TA/– and −2769T/–, and all were located in the 5′UTR. Furthermore, two new mutations, −2248G/A and +658A/G, were observed for the first time; the −2248G/A was detected in the intron 1 region in one subject and +658A/G in the coding region of the CCR5 in another subject. In silico analysis showed that the novel variations in the 5′UTR may have effects on the transcription factor binding sites. Therefore, this study demonstrates the presence of two new SNPs and four novel indels in the CCR5 gene in the Omani population. Our findings support the wide spectrum of genetic diversity reported within the CCR5 gene region among different ethnic groups.