Thiopurine S-methyltransferase (TPMT; Sadenosyl-L-methionine:thiopurine S-methyltransferase, EC 2.1.1.67) activity exhibits genetic polymorphism, with -0.33% of Caucasians and African-Americans inheriting TPMT deficiency as an autosomal recessive trait. To determine the molecular genetic basis for this polymorphism, we cloned the TPMT cDNA from a TPMT-deficient patient who had developed severe hematopoietic toxicity during mercaptopurine therapy. Northern blot analysis of RNA isolated from leukocytes of the deficient patient demonstrated the presence of TPMT mRNAs of comparable size to that in subjects with high TPMT activity. Sequencing of the mutant TPMT cDNA revealed a single point mutation (G238 C), leading to an amino acid substitution at codon 80 (Ala80 Pro). When assessed in a yeast heterologous expression system, this mutation led to a 100-fold reduction in TPMT catalytic activity relative to the wild-type cDNA, despite a comparable level of mRNA expression. A mutation-specific PCR amplification method was developed and used to detect the G238 -> C mutation in genomic DNA of the propositus and her mother. This inactivating mutation in the human TPMT gene provides insights into the genetic basis for this inherited polymorphism in drug metabolism.Thiopurine S-methyltransferase (TPMT; EC 2.1.1.67) is a cytoplasmic enzyme that preferentially catalyzes the Smethylation of aromatic and heterocyclic sulfhydryl compounds, including the anticancer agents 6-mercaptopurine and 6-thioguanine. TPMT activity exhibits genetic polymorphism, with -89% of Caucasians and African-Americans having high TPMT activity, -11% intermediate activity (presumed heterozygotes), and -1 in 300 inheriting TPMT deficiency as an autosomal recessive trait (1, 2). TPMT activity is typically measured in erythrocytes, as the level of TPMT activity in human liver, kidney, and normal lymphocytes has been shown to correlate with that in erythrocytes (3, 4).As part of multiagent chemotherapy for the treatment of acute lymphoblastic leukemia, mercaptopurine typically comprises a large percentage of therapy and is often administered daily throughout 2.5 years of continuation treatment. Mercaptopurine is a prodrug with no intrinsic anticancer activity, requiring intracellular conversion to thioguanine nucleotides, with subsequent incorporation into DNA, as one mechanism of its antiproliferative effects (5). Alternatively, mercaptopurine is metabolized to 6-methylmercaptopurine by TPMT or to 6-thiouric acid by xanthine oxidase. 6-Thiouric acid is an inactive metabolite, whereas 6-methylmercaptopurine nucleotide inhibits phosphoribosyl diphosphate amidotransferase, an enzyme catalyzing the first step in de novo purine synthesis (6, 7). It is not clear whether mercaptopurine's principal mechanism of cytotoxicity is via incorporation of thioguanine nucleotides into DNA and RNA, or via 6-methylmercaptopurine nucleotide inhibition of de novo purine synthesis, or a combination of these effects.Clinical studies in children with acute lymphoblastic l...