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Background  Coronary artery disease (CAD) is one of the leading causes of mortality worldwide. It is a multi-factorial disease and several studies have demonstrated that the genetic factors play a major role in CAD. Although variations in cholesteryl ester transfer protein ( CETP ) gene are reported to be associated with CAD, this gene has not been studied in South Indian populations. Hence we evaluated the  CETP  gene variations in CAD patients of South Indian origin.    Methods  We sequenced all the exons, exon-intron boundaries and UTRs of  CETP  in 323 CAD patients along with 300 ethnically and age matched controls. Variations observed in  CETP  were subjected to various statistical analyses.    Results and Discussion  Our analysis revealed a total of 13 variations. Of these, one3’UTRvariant rs1801706 (c.*84G>A) was significantly associated with CAD (genotype association test: OR = 2.16, 95% CI: 1.50–3.10, p = 1.88x10 -5  and allelic association test: OR = 1.92, 95% CI: 1.40–2.63, p = 2.57x10 -5 ). Mutant allele “A” was observed to influence the higher concentration of mRNA (p = 7.09×10 −3 , R 2  = 0.029 and β = 0.2163). Since expression of  CETP  has been shown to be positively correlated with the risk of CAD, higher frequency of “A” allele (patients: 22.69%  vs .controls: 13%) reveals that c.*84G>A is a risk factor for CAD in South Indians.    Conclusions  This is the first report of the  CETP  gene among South Indians CAD patients. Our results suggest that rs1801706 (c.*84G>A) is a risk factor for CAD in South Indian population.

c.*84G>A Mutation in CETP Is Associated with Coronary Artery Disease in South Indians