An intronic mutation in a lariat branchpoint sequence is a direct cause of an inherited human disorder (fish-eye disease).

Abstract

The first step in the splicing of an intron from nuclear precursors of mRNA results in the formation of a lariat structure. A distinct intronic nucleotide sequence, known as the branchpoint region, plays a central role in this process. We here describe a point mutation in such a sequence. Three sisters were shown to suffer from fish-eye disease (FED), a disorder which is caused by mutations in the gene coding for lecithin:cholesterol acyltransferase (LCAT). Sequencing of the LCAT gene of all three probands revealed compound heterozygosity for a missense mutation in exon 4 which is reported to underlie the FED phenotype, and a point mutation located in intron 4 (IVS4:T-22C). By performing in vitro expression of LCAT minigenes and reverse transcriptase PCR on mRNA isolated from leukocytes of the patient, this gene defect was shown to cause a null allele as the result of complete intron retention. In conclusion, we demonstrated that a point mutation in a lariat branchpoint consensus sequence causes a null allele in a patient with FED. In addition, our finding illustrates the importance of this sequence for normal human mRNA processing. Finally, this report provides a widely applicable strategy which ensures fast and effective screening for intronic defects that underlie differential gene expression.

Deletion of a branch-point consensus sequence in the LMX1B gene causes exon skipping in a family with nail patella syndrome

“…9 Such mutations have been found associated with X-linked hydrocephalus, 10 hepatic lipase deficiency, 11 fish-eye disease, 12 congenital contractual arachnodactyly, 13 Sandhoff disease, 14 and Ehlers-Danlos syndrome. 15 These mutations resulted in cryptic splicing, 10,11,14 intron retention 12 and exon skipping. 13,15 That only a handful of such mutations have been identified may reflect the lack of stringency both within the branchpoint consensus, and the flexibility in distance from branchpoint to splice acceptor, that the splicing machinery can tolerate.…”

Characterization of the Effects of Mutations in the Putative Branchpoint Sequence of Intron 4 on the Splicing within the Human Lecithin:cholesterol Acyltransferase Gene

“…6A, bar 2). DISCUSSION We have previously shown that a point mutation in a lariat branchpoint sequence of intron 4 of the LCAT gene (IVS4:T-22C) resulted in the intron retention causing a human inherited disorder, fish-eye disease (25). We have also demonstrated that the thymine residue at the fourth position of the branchpoint sequence in which the natural mutation occurs is crucial for the pre-mRNA splicing (26).…”

“…The retention of intron 4 of human LCAT gene caused by the substitution of the thymine to other nucleotides in the putative branchpoint sequence (25,26) suggested that the mutations of the branchpoint adenosine residue also result in the defective splicing for this particular intron. As shown in Table II, the LCAT cDNA exhibited the highest LCAT activity.…”

“…Mutations in the LCAT gene have been demonstrated to underlie either familial LCAT deficiency or fish-eye disease (FED) (24). We have previously identified a point mutation in intron 4 of the LCAT gene in patients with FED (25). This point mutation resides in a 100% matched branchpoint consensus sequence (CCCTGAC versus YNYTRAY), and it has been shown to result in the complete intron retention.…”

Human genetic variation recognizes functional elements in noncoding sequence

“…There are, however, also clear examples of mutations in noncoding regions, including those within introns, being responsible for diseases (Langford et al 1984;Vijayraghavan et al 1986;Kuivenhoven et al 1996;Webb et al 1996;Yu et al 1999). Additionally, many genome-wide association (GWA) studies have now found associations between intronic variants and diseases such as breast cancer and diabetes (Easton et al 2007;Hunter et al 2007;Scott et al 2007).…”