An analysis of allelic variation in the ABCA4 gene

PURPOSE. TO assess the allelic variation of the ATP-binding transporter pro tein (ABCA4). METHODS. A combination of single-strand conformation polymorphism (SSCP) an d automated DNA sequencing was used to systematically screen this gene for sequence variations in 374 unrelated probands with a clinical diagnosis of Stargardt disease, 182 patients with age-related macular degeneration (AMD) , and 96 normal subjects. RESULTS. There was no significant difference in the proportion of any singl e variant or class of variant between the control and AMD groups. In contra st, truncating variants, amino acid substitutions, synonymous codon changes , and intronic variants were significantly enriched in patients with Starga rdt disease when compared with their presence in subjects without Stargardt disease (Kruskal-Wallis P < 0.0001 for each variant group). Overall, there were 2480 instances of 213 different variants in the ABCA4 gene, including 589 instances of 97 amino acid substitutions, and 45 instances of 33 trunc ating variants. CONCLUSIONS. Of the 97 amino acid substitutions, 11 occurred at a frequency that made them unlikely to be high-penetrance recessive disease-causing va riants (HPRDCV). After accounting for variants in cis, one or more changes that were compatible with HPRDCV were found on 35% of all Stargardt-associa ted alleles overall. The nucleotide diversity of the ABCA4 coding region, a collective measure of the number and prevalence of polymorphic sites in a region of DNA, was found to be 1.28, a value that is 9 to 400 times greater than that of two other macular disease genes that were examined in a simil ar fashion (VMD2 and EFEMP1).