The results of genetic linkage studies for autism have suggested that a susceptibility locus for the disease is located on the long arm of chromosome 7 (7q). Two unrelated autistic individuals were identified with translocations mapping within the region of linkage. The first translocation, t(7;13)(q31.3;q21) has been mapped to a region just proximal to CFTR. We have identified a novel gene, named RAY1 (or FAM4A1) that is directly interrupted at this breakpoint. This gene contains 16 exons, with evidence of alternative splicing, and spans at least 220 Kb. Mutation screening of all exons was performed on a screening set of 27 unrelated autistic individuals, but no phenotype- specific variants were identified. Apparent homologues of RAY1 have also been identified in mouse, rat, pig, chicken, fruit fly and nematode. Mammalian homologues are over 90% identical. We have also identified several novel, non-coding transcripts in this region. The second translocation, t(5;7)(q15:q31.32), has been localized to a BAC clone just distal to CFTR, and efforts are now underway to identify coding regions within this BAC cone.