Thiopurine S-methyltransferase is encoded by the TPMT gene. It performs an important function in metabolizing the commonly used thiopurine medication family including azathioprine, 6-mercaptopurine, and 6-thioguanine (Dean & Kane, Mercaptopurine Therapy and TPMT and NUDT15 Genotype, 2020). Thiopurine drugs are used to treat conditions like acute lymphoblastic leukemia, autoimmune disorders, and organ transplant rejection (Relling, et al., 2018). Inherited variations of the TPMT gene result in differences in enzyme activity levels among individuals. Reduced TPMT enzyme activity can lower the metabolic inactivation of thiopurines, which allows thioguanine nucleotides (TGNs), active cytotoxic metabolites, to build up (Dean, Azathioprine Therapy and TPMT and NUDT15 Genotype, 2020). An overaccumulation of TGNs raises a patient’s risk for developing severe bone marrow suppression, a serious adverse drug reaction (Relling, et al., 2018). It is important to develop an understanding of TPMT genetic variation in order to customize thiopurine therapy for individual patients.

Variant alleles of TPMT have been identified that result in altered enzyme activity relative to the reference allele, TPMT*1. The TPMT*1 allele is considered the reference sequence associated with normal enzyme function when specific defining variants are not present. Alleles associated with no enzyme function are TPMT*3A, TPMT*3C, and TPMT*4 (Relling, et al., 2018). The TPMT*3A allele is the most frequent non-functional variant among people of European ancestry, whereas TPMT*3C is found more commonly in East Asian populations (Relling, et al., 2018). Other alleles result in decreased enzyme function, including TPMT*2 and TPMT*8 (Relling, et al., 2018). There are nearly 30 total documented variant alleles and the rest contribute to the spectrum of TPMT activity levels in the population.

TPMT variant alleles are designated using the standard star allele nomenclature (*) widely adopted for pharmacogenes (Dean, Azathioprine Therapy and TPMT and NUDT15 Genotype, 2020). The reference allele associated with normal function is named TPMT*1. Other alleles are assigned consecutive numbers and are defined by one or more specific DNA sequence differences relative to the 1 allele. These sequence differences precisely documented using standard HGVS nomenclature, like 460G>A for a nucleotide change or Ala154Thr for the resulting protein change. Lettered suffixes denote sub-alleles within a group, like TPMT*3A, TPMT*3B, and TPMT*3C, which contain different combinations of defining variants. The Pharmacogene Variation (PharmVar) Consortium standardizes the allele definitions, ensuring consistent communication in research and clinical settings.

TPMT alleles are grouped into functional categories reflecting their impact on the enzyme’s metabolic capacity: Normal Function (NF), Decreased Function (DF), or No Function (NF) (Relling et al., 2019). TPMT*1 is the standard NF allele; TPMT*2 and TPMT*8 are examples of DF alleles; TPMT*3A, TPMT*3C, TPMT*4, and TPMT*5 are established NF alleles (Relling et al., 2019; Dean, 2025). An individual inherits two TPMT alleles, forming their diplotype, which determines their overall predicted metabolic phenotype (Relling, et al., 2018). The Normal Metabolizer (NM) phenotype arises from possessing two NF alleles and corresponds to typical enzyme activity. The Intermediate Metabolizer (IM) phenotype generally results from carrying one NF allele and one NF or DF allele and is associated with reduced enzyme activity. The Poor Metabolizer (PM) phenotype occurs in individuals with two NF alleles and leads to low or completely absent enzyme activity.

The clinical consequence of TPMT variation related to thiopurines is mainly described by the differential risk of severe myelosuppression (Relling, et al., 2018). A common method to assess the risk phenotypically is the TPMT enzyme activity assay performed using a patient’s red blood cells (Relling, et al., 2018). The test directly quantifies the functional capability of the TPMT enzyme within those cells. The assay typically measures the formation rate of methylated thiopurine metabolites when cell lysate is incubated with a thiopurine substrate (Dean, Azathioprine Therapy and TPMT and NUDT15 Genotype, 2020). Activity levels are noted in standard units, often related to hemoglobin content or packed red blood cell volume. Measured low enzyme activity points to impaired thiopurine metabolism and predicts increased susceptibility to drug-induced toxicity at standard doses.

Research has consistently shown a strong concordance between a person’s TPMT genotype and their measured TPMT erythrocyte enzyme activity. Individuals identified through genotyping as PM demonstrate very low or negligible enzyme activity levels in the red blood cell assay (Relling, et al., 2018). Those genotyped as IM exhibit intermediate enzyme activity values, falling right between PM and NM levels. Patients with NM genotypes show enzyme activity within the expected normal or high range. The genotype-phenotype relationship directly informs drug response. A lower activity in PMs and IMs causes higher TGN accumulation, explaining their increased risk for myelosuppression compared to NMs on standard thiopurine doses. Clinical guidelines utilize this correlation to recommend genotype-based thiopurine dose adjustments, often advising reduced doses for PMs and IMs or selection of alternative medications (Relling, et al., 2018).

References

Dean, L. (2020). Azathioprine Therapy and TPMT and NUDT15 Genotype. Medical Genetics Summaries [Internet], https://www.ncbi.nlm.nih.gov/books/NBK100661/.

Dean, L., & Kane, M. (2020). Mercaptopurine Therapy and TPMT and NUDT15 Genotype. Medical Genetics Summaries [Internet], https://www.ncbi.nlm.nih.gov/books/NBK100660/.

Relling, M., Schwab, M., Whirl-Carrillo, M., Suarez-Kurtz, G., Pui, C.-H., Stein, C., . . . Yang, J. (2018). Clinical Pharmacogenetics Implementation Consortium Guideline for Thiopurine Dosing Based on TPMT and NUDT15 Genotypes: 2018 Update. Clinical Pharmacology and Therapeutics, https://ascpt.onlinelibrary.wiley.com/doi/10.1002/cpt.1304.