ar-Galactosidase A Gene Rearrangements Causing Fabry Disease

Fabry disease, an inborn error of glycosphingolipid catabolism, results from mutations in theX-linked gene encoding the lysosomal enzyme, a-galactosidase A (EC 3.2.1.22). Six cY-galactosidase A gene rearrangements that cause Fabry disease were investigated to assess the role of Alu repetitive elements and short direct and/ or inverted repeats in the generation of these germinal mutations. The breakpoints of five partial gene deletions and one partial gene duplication were determined by either cloning and sequencing the mutant gene from an affected hemizygote, or by polymerase chain reaction amplifying and sequencing the genomic region containing the novel junction. Although the cr-galactosidase A gene contains 12 Ah repetitive elements (representing -30% of the 12-kilobase (kb) gene or -1 Ah/ 1.0 kb), only one deletion resulted from an Ah-Ah recombination. The remaining five rearrangements involved illegitimate recombinational events between short direct repeats of 2 to 6 base pairs (bp) at the deletion or duplication breakpoints. Of these rearrangements, one had a 3’ short direct repeat within an Ah element, while another was unusual having two deletions of 1.7 kb and 14 bp separated by a 151-bp inverted sequence. These findings suggested that slipped mispairing or intrachromosomal exchanges involving short direct repeats were responsible for the generation of most of these gene rearrangements. There were no inverted repeat sequences or alternating purine-pyrimidine regions which may have predisposed the gene to these rearrangements. Intriguingly, the tetranucleotide CCAG and the trinucleotide CAG (or their respective complements, CTGG and CTG) occurred within or adjacent to the direct repeats at the 5’ breakpoints in three and four of the five CZgalactosidase A gene rearrangements, respectively, suggesting a possible functional role in these illegitimate recombinational events. These studies indicate that short direct repeats are important in the formation of gene rearrangements, even in human genes like (Ygalactosidase A that are rich in Alu repetitive elements.