Propionic acidemia is an inborn error of metabolism resulting from a deficiency of propionyl-CoA carboxylase activity. The alpha- and beta-subunits of the enzyme are encoded by the PCCA and PCCB genes, respectively. Using direct sequencing and restriction digests of amplified reverse transcripts and genomic DNA, we have identified two mutations of the PCCB gene in a propionic acidemia patient from the pccC complementation subgroup (the PCCB gene contains the major complementation group pccBC and subgroups pccB and pccC). One of the proband alleles contains an inframe 3-bp deletion inherited from the father which results in the deletion of an isoleucine residue in the beta-subunit of the enzyme. The other mutant allele, inherited from the mother, has a 14-bp deletion and an addition of 12 bp of new sequence at the same site as the father's allele. The inserted sequence is a partial duplication of a sequence just upstream of the mutation site. The net result of this mutation generates a frameshift and a downstream stop codon. Examination of fibroblast mRNA from the patient showed that it consists essentially of the father's sequence, making it effectively the only expressed allele for the beta-protein. A survey of additional patient cell lines revealed the insertion/deletion rearrangement in three additional patients, two from the pccBC group and one unclassified. The 3-bp deletion allele was unique to the proband. The identification of two distinct alleles occurring at the same site in the PCCB gene underscores the importance of this site in enzyme function or integrity.