The dystonin/Bpag1 gene encodes several tissue-specific alternatively spliced transcripts that encode cytoskeletal binding proteins. These various isoforms are necessary for maintaining the structural integrity of epithelial, neural, and muscle tissues. Mutations in the dystonin/Bpag1 gene cause dystonia musculorum (dt), a hereditary neuropathy of the mouse characterized by the progressive degeneration of sensory neurons. Several dt mutant alleles exist, most of which have arisen through spontaneous mutations. In this article we demonstrate that the dt locus encodes 107 exons spanning 400 kb. The high frequency of occurrence of spontaneous dt mutants may therefore be a result of the large size of the gene. Analysis of genomic DNA from several dt spontaneous mutant alleles, dt(24J), dt(27J), dt(Alb), and dt(Frk), shows a deletion of the central portion of the gene in dt(Alb) but no large rearrangements or deletions in the other alleles. These other alleles likely have small deletions or rearrangements, or point mutations. To determine the impact of the known and unknown mutations on transcript levels, RT-PCR was performed to detect various coding regions of the dystonin/Bpag1 transcripts in brain and muscle from multiple dt alleles: dt(Tg4), dt(Alb), dt(24J), dt(27J), and dt(Frk). With the exception of dt(Frk), reduced transcript levels were observed for all alleles tested. Such alterations likely result in reduced or absent dystonin/Bpag1 protein levels. Thus, distinct genetic defects lead to a common outcome of reduced transcript expression causing the same phenotype in multiple dt alleles.