Rat myelin vacuolation mutation at the Attractin locus (Atrn^mv) is a genomic deletion including the whole exon 1 of the Atrn gene. The precise size and location of the deleted region has not yet been identified because of poor information on genomic organization of the rat Atrn gene. Here, we identified the breakpoints of the Atrn^mv mutation, using a draft sequence of the rat genome. In the Atrn^mv/mv rat, a 6,914-bp genomic region was deleted. Primers flanked 5'- and 3'- breakpoints amplified the Atrn^mv allele but not the wild-type allele. This primer set enables us to distinguish Atrn^mv/+ heterozygous rats from Atrn^+/+ rats, and will contribute to the efficient production of Atrn^mv/mv rats.