Novel Polypyrimidine Variation (IVS46: del T −39…−46) in ABCA1 Causes Exon Skipping and Contributes to HDL Cholesterol Deficiency in a Family With Premature Coronary Disease

Abstract

Abstract-Recent studies have implicated mutations in the ATP-binding cassette transporter A1, ABCA1, as a cause of Tangier disease (TD) and familial hypoalphalipoproteinemia (FHA). We investigated a proband with very low levels of high-density lipoprotein cholesterol (HDL-C, 6 mg/dL) and a history of premature coronary heart disease (CHD). Sequencing of the ABCA1 gene revealed 2 distinct variants. The first mutation was a G5947A substitution (R1851Q).The second mutation was a single-nucleotide deletion of thymidine in a polypyrimidine tract located 33 to 46 bps upstream to the start of exon 47. This mutation does not involve the 3Ј acceptor splice site and is outside the lariat branchpoint sequence (IVS46: del T Ϫ39. . .Ϫ46). Amplification of cDNA obtained in cultured fibroblasts of the proband and affected family member revealed an abnormally spliced cDNA sequence with skipping of exon 47. These variants were not identified in over 400 chromosomes of healthy whites. Compound heterozygotes (nϭ4) exhibited the lowest HDL-C (11Ϯ5 mg/dL) and ApoA-I (35Ϯ15 mg/dL) compared with wild-type (nϭ25) (HDL-C 51Ϯ14 mg/dL; ApoA-I 133Ϯ21 mg/dL) (PϽ0.0005) or subjects affected with either R1851Q (nϭ6) (HDL-C 36Ϯ8; ApoA-I 117Ϯ19) or IVS46: del T Ϫ39. . .Ϫ46 (nϭ5) (HDL-C 31ϩ9; ApoA-I 115ϩ28 (PϽ0.01). These data suggest that polypyrimidine tract variation may represent a novel mechanism for altered splicing and exon skipping that is independent of traditional intronic variants as previously identified in acceptor/donor splice regions or the lariat branchpoint domain.

Cancer-associated missplicing of exon 4 influences the subnuclear distribution of the DNA replication factor CIZ1

“…4A) and is also preceded by a putative branch point adenosine. However, because this is located some way upstream of the 3 0 splice site, and because its expansion suppresses inclusion of exon 4 (see below) rather than enhances it as previously reported for PTs [Chu et al, 1993;Hong et al, 2003], tract i is more likely to be an auxiliary element than a typical PT.…”

“…Furthermore, this occurs exclusively in colorectal cancer cell lines that are deficient in mismatch repair. Variations in pyrimidine repeats that are further upstream from the branch point sequence have also been reported, including intron 46 of the ABCA1 gene [Hong et al, 2003]. Furthermore, in the case of an intronic splicing silencer that regulates skipping of exon IIIb of FGF2, PTB has been shown to play a role [Carstens et al, 2000].…”

Do mutations causing low HDL-C promote increased carotid intima-media thickness?

“…In addition, we studied another pedigree with a previously reported variant in LCAT [I178T] (13). Demographic and CHD risk factor information for each of these kindreds has also been described (7)(8)(9)(10)(11)(12)(13). Affected family members with identified genetic variants and sex-matched and age-related controls underwent carotid β-mode ultrasound as previously described (14).…”

The effect of ABCA1gene polymorphisms on ischaemic stroke risk and relationship with lipid profile

“…ABCA1 gene expression is upregulated in atherosclerotic plaques, further suggesting an association between ABCA1 and atheroma [20]. Reports have suggested a relationship between individual polymorphisms of ABCA1 gene and lipid profiles [21,22]. Furthermore, ABCA1 appears to be required in neuronal tissue for cholesterol efflux to ApoA-I and ApoE.…”