A common nonsense mutation in the repetitive Kringle IV-2 domain of human apolipoprotein(a) results in a truncated protein and low plasma Lp(a)

Abstract

LPA, the gene coding for apolipoprotein(a) [apo(a)], is the major determinant of lipoprotein(a) [Lp(a)] plasma levels, which are associated with risk for coronary heart disease (CHD) and stroke. It is not completely understood how variation in LPA relates to Lp(a) concentrations. One type of variation related to Lp(a) levels is the number of Kringle (K) IV-2 (g.61C>T; GenBank L14005.1) repeats in LPA, but sequence variation may also contribute. Human apo(a) contains from two to >40 nearly identical K IV-2 repeats of genomic size 5.5 kb, which makes it difficult to detect mutations. To elucidate the genetic variation of the apo(a) K IV-2 domain, we isolated a single "nonexpressing" apo(a) allele with 26 K IV-2 repeats, followed by PCR, cloning and sequencing of 96 clones, resulting in an average coverage of each K IV-2 repeat of approximately four-fold. The previously described K IV types 2A and 2B (K IV-2A and K IV-2B) were detected in 74% of the clones. In addition, a new type designated 2C (K IV-2C) was present. A nonsense mutation in the first exon of K IV-2 (g.61C>T) predicted to result in a truncated protein (p.R21X) was found in nine clones on a K IV-2A background. The presence of this mutation was confirmed by analysis of genomic DNA and was shown to represent the rare allele (frequency 0.02) of a SNP. Immunoblot analysis of apo(a) from plasma confirmed the presence of a truncated apo(a) isoform in the index individual and family members. Our data show that SNPs affecting Lp(a) plasma concentrations also exist in the apo(a) K IV-2 domain.

A Polymorphism in the Protease-Like Domain of Apolipoprotein(a) Is Associated With Severe Coronary Artery Disease

“…A number of other polymorphisms in the kringle region and in the 5Ј noncoding region have also been reported to be associated with Lp(a) levels. 23,[25][26][27][28][29][30] We did not find evidence that the association of LPA I4399M with severe CAD was attributable to other variants in the LPA gene. We investigated 18 additional SNPs in the LPA gene that tagged 50 of the 65 SNPs that have allele frequency Ͼ2% in the HapMap CEU population.…”

Structure, function, and genetics of lipoprotein (a)

“…The second exons of all the KIV-2 copies are 100% identical in their nucleotide sequence. The first exons are also identical in their amino acid sequence among each other, but can differ by three synonymous SNPs (41,132) and have been classified accordingly as types A, B, and C. It is noteworthy that the KIV-2 exon 1 type B is completely identical to the first exon of KIV-3, and KIV-2 exons 2 share complete sequence identity with the second exon of KIV-1 (Fig. 2B), which probably has resulted in an erroneous allocation of SNPs in public databases (see below).…”

“…In contrast, a nonsynonymous substitution (p.Arg1508Trp) in KIV-9 (rs140720828), which has a frequency of 8% in Khoi San from South Africa, resulted in by guest, on May 12, 2018 www.jlr.org Downloaded from result in impaired complex formation represent another mechanism resulting in "null alleles" for Lp(a). This nonsense mutation has a frequency of 2% in Europeans (132).…”

Lack of association of rs3798220 with small apolipoprotein(a) isoforms and high lipoprotein(a) levels in East and Southeast Asians

“…Several SNPs at the LPA locus have been identified which are associated with such individual variability of Lp(a) concentrations. For some, this has been related to a causal mechanism [17][18][19].…”