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Abstract Background Chromosomal abnormalities affecting human chromosome 15q11-q13 underlie multiple genomic disorders caused by deletion, duplication and triplication of intervals in this region. These events are mediated by highly homologous segments of DNA, or duplicons, that facilitate mispairing and unequal cross-over in meiosis. The gene encoding an amyloid precursor protein-binding protein (<it>APBA2</it>) was previously mapped to the distal portion of the interval commonly deleted in Prader-Willi and Angelman syndromes and duplicated in cases of autism. Results We show that this gene actually maps to a more telomeric location and is partially duplicated within the broader region. Two highly homologous copies of an interval containing a large 5' exon and downstream sequence are located ~5 Mb distal to the intact locus. The duplicated copies, containing the first coding exon of <it>APBA2</it>, can be distinguished by single nucleotide sequence differences and are transcriptionally inactive. Adjacent to <it>APBA2 </it>maps a gene termed KIAA0574. The protein encoded by this gene is weakly homologous to a protein termed X123 that in turn maps adjacent to <it>APBA1 </it>on 9q21.12; <it>APBA1 </it>is highly homologous to <it>APBA2 </it>in the C-terminal region and is distinguished from <it>APBA2 </it>by the N-terminal region encoded by this duplicated exon. Conclusion The duplication of <it>APBA2 </it>sequences in this region adds to a complex picture of different low copy repeats present across this region and elsewhere on the chromosome.</p

Partial duplication of the APBA2 gene in chromosome 15q13 corresponds to duplicon structures