A generalized deficiency of the mitochondrial enzyme, ornithine aminotransferase (OAT) is the inborn error in gyrate atrophy, an autosomal recessive degenerative disease of the choroid and retina of the eye that leads to blindness. Southern analysis, using the OAT cDNA probe, of the OAT gene in a gyrate atrophy patient whose level of OAT protein is markedly decreased indicated the functional gene to be grossly intact. Northern analysis of his OAT mRNA demonstrated only half the normal level of OAT message, suggesting expression of only one of the two alleles of the OAT gene. A functional assay of the expressed OAT mRNA by in vitro translation and immunoprecipitation with anti-human OAT antibody indicated synthesis of an OAT protein from the message. The expressed message was cloned and sequenced and was shown to contain a single base change from C to T, resulting in an amino acid codon change from CAT (histidine) to TAT (tyrosine) at position 319 in the translated OAT protein. The mutant and normal OAT precursors were synthesized using transcriptional expression clones of OAT and in vitro translation of the expressed mRNA and tested in an in vitro mitochondrial transport/processing system. The results indicate that the mutant OAT precursor from the gyrate atrophy patient can be transported to the mitochondria but is minimally processed there, which would lead to degradation of the labile precursor and loss of OAT activity as phenotypically observed.