Background: Elevated Lp(a) plasma concentrations are determined mainly genetically by the LPA gene locus, but up to 70% of the coding sequence is located in the so-called kringle IV type 2 (KIV-2) copy number variation. This region is not resolved by common genotyping technologies and large epidemiological studies on this region are therefore missing. The Arg21Ter variant (R21X, variant frequency approximately 2%) is a functional variant in this region, but it has never been analyzed in large cohorts and is it unknown whether it is captured by genome-wide association studies. Methods and Results: We developed a highly sensitive allele-specific qPCR assay and genotyped R21X in 10,910 individuals from three populations (GCKD, KORA F3, KORA F4). R21X carriers showed significantly lower mean Lp(a) concentrations (-11.7 mg/dL [-15.5;-7.82], p=3.39e-32). Of particular note, virtually all R21X carriers also carried the splice mutation rs41272114 (D prime=0.957, R2=0.275), as confirmed by pulsed-field gel electrophoresis and long-range haplotyping. This proposes that the R21X mutation arose on the background of the rs41272114 splice variant. Conclusions: We performed the largest epidemiological study on an LPA KIV-2 variant so far. Interestingly, R21X is located on the same haplotype as the splice mutation rs41272114, creating double-null LPA alleles that are inactivated by two independent mutations. The effect of the R21X nonsense mutation can thus not be discerned from the effect of rs41272114 splice site mutation. This emphasizes the importance of assessing the complex LD structure within LPA even for functional variants.

Investigation of an LPA KIV-2 nonsense mutation in 11,000 individuals: the importance of linkage disequilibrium structure in LPA genetics.