Sequence and functional changes in a putative enhancer region upstream of the apolipoprotein(a) gene

Two enhancer regions upstream of the apolipoprotein(a) (apo(a)) gene were amplified and sequenced from subjects who were known to express abnormally high or low amounts of lipoprotein(a) (Lp(a)). No base changes were found in the DHII region situated 28 kb from the apo(a) gene. Three common base substitutions were found in the DHIII region about 20 kb from the gene. One, an A to G change at position -1230, increased the activity of reporter-gene constructs approximately 2.5-fold. The other two, a C to A change at -1617 and a G to T change at -1712, decreased reporter activity by 30 and 40%, respectively. The sites at -1230 and -1617 were in linkage disequilibrium with each other and also with a polymorphic site near the DHII enhancer and sites in the apo(a) promoter and gene. The rarer G variant at -1230 was associated with smaller alleles. After correcting for the effect of allele size, values of Lp(a) concentration for alleles associated with the G variant at -1230 were 70% higher than those associated with the more common A variant. In contrast, the corrected values for alleles associated with the rare T variant at -1712 were 40% lower than those associated with the common G variant. Thus, overall the changes observed in this enhancer could influence apo(a) gene transcription up to 4-fold and could provide a significant contribution to the variation in Lp(a) concentrations in plasma.