Identification of genes affected by disease-associated rare chromosomal rearrangements has led to the cloning of several disease genes. Here we have used a simple approach involving allele-specific RT-PCR-based detection of gene expression to identify a gene affected by a balanced autosome;autosome translocation. We identified a transcribed SNP (tSNP), c.68G-->A, present in a novel untranslated exon of the CLDN14 gene in a male patient with mental retardation who had a balanced t(13;21) chromosomal translocation. We determined an allelic loss of expression of the CLDN14 gene isoform at the 21q22.1 chromosomal breakpoint. Although additional work is necessary to explore a possible function of the novel CLDN14 isoform in brain development and function and the potential pathogenic consequences of its disruption in this patient, the result clearly demonstrates the utility of a tSNP-based detection of allelic loss of gene expression in studies involving chromosomal rearrangements.