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The t(4;9)(B3;E3.2)12Gso reciprocal translocation is an autosomal recessive mouse mutation involving chromosome 4, band B3 (Mmu4B3) and chromosome 9, band E3.2 (Mmu9E3.2). The most striking phenotype of the 12Gso homozygote involves axial skeleton deformities, resulting in significant shortening of body length, scoliosis, displaced hips and kinky tails. Homozygous animals are significantly smaller than normal littermates and frequently exhibit early lethality, as many of the mutants perish by 1 day postnatal, and many others do not survive the three weeks to weaning age. Homozygous 12Gso mice also develop an unusual bone marrow defect that closely resembles leukemia. The penetrance of the mutation is variable with significant dependence on genetic background. Fluorescent in situ hybridization and reverse transcription polymerase chain reaction were used to localize the chromosome 4 breakpoint to a 600 base pair region intrinsic to ATP-binding cassette 1 (Abca1), a gene that encodes a large transmembrane protein involved in cholesterol efflux. The disruption of Abca1 results in a truncated transcript. Aberrant expression of genes associated with lipid metabolism has been detected in 12Gso homozygotes, and previous data by others describing the effects of Abca1 null mutations in humans and mice indicate the likely involvement of this gene in the early lethality of 12Gso homozygotes. Using polymerase chain reaction (PCR)-based methods, we have cloned and sequenced DNA surrounding the 9;4 chromosome junction in 12Gso/12Gso DNA. The chromosome 9 breakpoint maps to a relatively gene-poor region, lying in the intergenic region between an uncharacterized T-box gene, Tbx18, and a ras-like EST, Rock1. Both genes represent potential candidates for the skeletal anomalies present in 12Gso homozygotes. These studies lay a firm foundation for future studies with the unique model offered by the 12Gso mouse, aimed at identification of novel genes and previously unknown pathways required for skeletal development and associated with leukemia susceptibility in humans and mice.