A novel but frequent variant in LPA KIV-2 is associated with a pronounced Lp(a) and cardiovascular risk reduction

Abstract

AimsLp(a) concentrations represent a major cardiovascular risk factor and are almost entirely controlled by one single locus (LPA). However, many genetic factors in LPA governing the enormous variance of Lp(a) levels are still unknown. Since up to 70% of the LPA coding sequence are located in a difficult to access hypervariable copy number variation named KIV-2, we hypothesized that it may contain novel functional variants with pronounced effects on Lp(a) concentrations. We performed a large scale mutation analysis in the KIV-2 using an extreme phenotype approach.Methods and ResultsWe compiled an discovery set of 123 samples showing discordance between LPA isoform phenotype and Lp(a) concentrations and controls. Using ultra-deep sequencing, we identified a splice site variant (G4925A) in preferential association with the smaller LPA isoforms. Follow-up in a European general population (n = 2892) revealed an exceptionally high carrier frequency of 22.1% in the general population. The variant explains 20.6% of the Lp(a) variance in carriers of low molecular weight (LMW) apo(a) isoforms (P = 5.75e-38) and reduces Lp(a) concentrations by 31.3 mg/dL. Accordingly the odds ratio for cardiovascular disease was reduced from 1.39 [95% confidence interval (CI): 1.17–1.66, P = 1.89e-04] for wildtype LMW individuals to 1.19 [95%CI: 0.92; 1.56, P = 0.19] in LMW individuals who were additionally positive for G4925A. Functional studies point towards a reduction of splicing efficiency by this novel variant.ConclusionA highly frequent but until now undetected variant in the LPA KIV-2 region is strongly associated with reduced Lp(a) concentrations and reduced cardiovascular risk in LMW individuals.

Investigation of anLPAKIV-2 nonsense mutation in 11,000 individuals: the importance of linkage disequilibrium structure inLPAgenetics

“…We designed an allele-specific triplex TaqMan PCR assay (ast-PCR) amplifying the mutant bases of R21X 19 and the G4925A 13 Supplemental Tables I and II. The assay was run on a 6 384-well ThermoFisher QuantStudio 6 qPCR system.…”

“…The assay was run on a 6 384-well ThermoFisher QuantStudio 6 qPCR system. The R21X assay was validated both against ultra-deep NGS data from Coassin and Schönherr et al, 2019 24 and against a commercial cast-PCR assay (ThermoFisher; as used in 13 ) with a sensitivity of 0.2% mutant fraction (determined according to manufacturer instructions on a NGS-validated sample). For validation, our assay was run on 376 samples from KORA F4, identifying 14 R21X-carriers, which were all confirmed also by the commercial castPCR assay.…”

“…alleles that are identical-by-descent) are associated with a much smaller variation in Lp(a) (typically <2.5-fold 11 ). This indicates that genetic variants exist that regulate the Lp(a) concentrations in addition to isoform size 12,13 . Genome-wide association studies (GWAS) have identified dozens of SNPs distributed over a two megabases region [14][15][16] , but few bona-fide functional variants have been identified 13,[17][18][19] .…”

“…The KIV-2 region encompasses up to 70% of the LPA coding sequence 13 and is therefore an obvious candidate region to search for functional variants affecting Lp(a) concentrations. Very little is known about the impact of sequence variation in the KIV-2 CNV on Lp(a) concentrations because commonly used sequencing and genotyping technologies are not able to resolve variation within this region.…”

“…This revealed hundreds of variants and provided several new putative regulators of Lp(a) levels. For example, the G4925A variant 13 found in 20% of the population is associated with an Lp(a) reduction of up to ≈30 mg/dL and explains a considerable fraction of the individuals presenting low Lp(a) concentrations despite carrying a LMW isoform. This aspect of the relationship between Lp(a) concentrations and apo(a) isoform size is poorly understood so far.…”