Physical map of a 1.5 Mb region on 12p11.2 harbouring a synpolydactyly associated chromosomal breakpoint

Synpolydactyly (SPD) is a rare malformation of the distal limbs known to be caused by mutations in HOXD13. We have previously described a complex form of SPD associated with synostoses in three members of a Belgian family whi ch co-segregates with a t(12;22)(p11.2;q13.3) chromosomal translocation. Th e chromosome 12 breakpoint of this translocation maps to 12p11.2 between ma rkers D12S1034 and D12S1596. Here we show that a mutation in the HOXD13 gen e is not responsible for the phenotype, and present a physical map of the r egion around the 12p11.2 breakpoint. Starting from D12S1034 and D12S1596, w e have established a contig approximately 1.5 Mb in length, containing 13 Y AC clones, 16 BAC clones, and 11 cosmid clones. FISH analysis shows that co smid LL12NCO1-149H4 maps across the breakpoint, and Southern blot experimen ts using fragments of this cosmid as probes identify a rearranged BamHI fra gment in the patients carrying the translocation. A search for expressed se quences within the contig have so far revealed one CpG island, seven anonym ous ESTs and three previously characterised genes, DAD-R, KRAG and HT2I, al l of which were found not to be directly disrupted by the translocation. Th e gene represented by EST R72964 was found to be disrupted by the transloca tion. These findings lay the groundwork for further efforts to characterise a gene critical for normal distal limb development that is perturbed by th is translocation.