What Is Thiopurine Methyltransferase & Why Is It Important?

Thiopurine methyltransferase, usually called TPMT, is an enzyme your body uses to break down a class of medications known as thiopurines, drugs prescribed for conditions ranging from inflammatory bowel disease to childhood leukemia and organ transplant rejection. TPMT matters because people inherit different levels of it, and those differences can mean the gap between a drug working safely and causing dangerous, sometimes life-threatening side effects. Understanding your TPMT status before starting one of these medications is now considered a cornerstone of pharmacogenomics, the practice of tailoring drug choices and doses to a person’s genetic makeup.

What TPMT Actually Does

TPMT is a cytosolic enzyme that catalyzes a chemical reaction called S-methylation of sulfur-containing compounds, including the thiopurine drugs mercaptopurine, azathioprine, and thioguanine.¹ In plain terms, it takes an active drug molecule and attaches a methyl group to it, which deactivates the molecule and makes it easier for your body to clear. The methyl group comes from a donor molecule called S-adenosyl-L-methionine, a common biological workhorse your cells use in many methylation reactions.²

TPMT is not the only pathway that handles thiopurines. When you take a drug like mercaptopurine, three competing routes process it simultaneously: one converts it into active metabolites called 6-thioguanine nucleotides (6-TGN), which are the molecules that actually suppress your immune system or kill cancer cells; the second is TPMT, which methylates the drug and shunts it away from that active pathway; and the third breaks it down into an inactive waste product via xanthine oxidase.³ The balance among these three routes determines how much active drug ends up in your cells. If TPMT is sluggish or absent, more of the drug pours down the 6-TGN pathway, and active metabolite levels can climb to toxic concentrations.

Why People Have Different Levels of TPMT

TPMT activity varies because of inherited differences in the gene that encodes it. Since researchers first identified these genetic polymorphisms, many sequence variants that reduce enzyme activity have been catalogued and formally named by a nomenclature committee.⁴ The variants most commonly studied and most clinically relevant are TPMT*2, *3A, *3B, *3C, and *4.⁵ Mutant versions of the TPMT protein are broken down faster inside cells, which is why people who carry these variants end up with less working enzyme.¹

In broad terms, the population breaks into three groups. Roughly 90% of people carry two normal copies of the gene and have full TPMT activity. About 10% carry one normal copy and one variant, giving them intermediate activity. And roughly 1 in 300 people carry two variant copies, leaving them with very little or no TPMT activity at all. That last group faces the greatest danger from standard thiopurine doses.

The Danger of Low TPMT Activity

The most serious risk is myelosuppression, a shutdown of bone marrow that slashes production of white blood cells, red blood cells, and platelets. Without enough white cells, ordinary infections can become fatal. TPMT polymorphisms have been clearly linked to this increased myelosuppression risk, which is why genotyping before treatment has become standard practice in many centers.⁵

A study of patients with Crohn’s disease who developed severe myelosuppression on azathioprine illustrates the pattern vividly. Among 41 patients with bone marrow toxicity, about 10% had two mutant TPMT alleles, 17% had one, and 73% had no known mutation. But the speed of toxicity told a clearer story: patients with two mutant copies developed bone marrow failure within six weeks of starting the drug, while those with one mutant copy took anywhere from one to 18 months, and those with a normal genotype ranged from two weeks to over seven years.⁶ That rapid onset in patients with the lowest TPMT activity underscores why catching the deficiency before the first dose matters so much.

Which Diseases Require Thiopurines

TPMT testing is relevant anywhere thiopurine drugs are used, and those drugs show up across a surprisingly wide range of medicine. In gastroenterology, azathioprine and mercaptopurine are mainstays for maintaining remission in ulcerative colitis and Crohn’s disease, including in pediatric patients.⁷ In oncology, mercaptopurine and thioguanine are critical components of chemotherapy regimens for acute lymphoblastic leukemia, one of the most common childhood cancers.⁸ In transplant medicine, azathioprine helps prevent organ rejection. And in rheumatology and dermatology, azathioprine is prescribed for autoimmune conditions like lupus, rheumatoid arthritis, and severe eczema. Regardless of the underlying disease, the same TPMT-related toxicity risk applies whenever one of these drugs is on the table.

Testing Before Treatment

There are two main ways to assess TPMT status: genotyping, which reads the DNA to look for known variant alleles, and phenotyping, which directly measures enzyme activity in a blood sample. Both approaches work, but they have slightly different strengths. A systematic review of 17 studies found that genotyping had sensitivity ranging from 55% to 100% and specificity from 94% to 100%, while phenotyping had sensitivity from 92% to 100% and specificity from 86% to 98%.⁹

In practical terms, genotyping is better at confirming that someone definitely has a variant, because its specificity is very high. But it can miss rare or novel mutations that are not on the standard test panel, which is why its sensitivity can dip. Phenotyping, on the other hand, catches anyone with low enzyme activity regardless of the cause, but it can be thrown off by recent blood transfusions, concurrent medications, or lab variability. A study comparing a newer whole-blood phenotype assay with the standard red-cell method found 97% concordance with genotyping results for both, though distinguishing between low-activity and intermediate-activity groups was harder, with concordance dropping to 79%.¹⁰ Many centers now run both tests for the most complete picture.

A pediatric comparison of Sanger sequencing and standard genotyping found that every patient who underwent sequencing would have been accurately phenotyped by the simpler genotyping method, with no significant difference in allele, genotype, or phenotype frequencies between the two techniques.¹¹ That is reassuring for hospitals that use the less expensive genotyping approach rather than full sequencing.

How Test Results Change Your Dose

Clinical guidelines from the Clinical Pharmacogenetics Implementation Consortium (CPIC) provide specific dosing recommendations based on TPMT genotype. The most recent update calls for adjusting starting doses of mercaptopurine, thioguanine, and azathioprine according to both TPMT and NUDT15 genotypes, including for individuals who carry variants in both genes.¹² In general terms, people with normal TPMT activity start at the standard dose, people with intermediate activity start at a reduced dose (often around half), and people with very low or absent activity are either given a dramatically reduced dose with intensive monitoring or switched to a different drug entirely.

The real-world payoff of following these guidelines is striking. A study of patients receiving azathioprine or mercaptopurine for autoimmune diseases found that myelotoxicity occurred in only 2% of patients who were genotyped before treatment, compared to more than 21% of those who were genotyped only after problems developed. Among patients with intermediate TPMT activity whose doctors followed the dose-reduction recommendation, the rate of bone marrow toxicity was 13%, compared to 87% when the recommendation was ignored. Healthcare costs were more than three-fold higher in intermediate metabolizers compared to normal metabolizers, and preemptive genotyping with physician adherence brought costs back in line with the normal-activity group.¹³

NUDT15 and Why TPMT Is Not the Whole Story

TPMT was the first pharmacogenomic marker linked to thiopurine toxicity, but it is not the only one. A second gene, NUDT15, also affects how thiopurines are handled, and variants in it can cause the same kind of myelosuppression. NUDT15 variants are particularly common in people of East Asian ancestry: the frequency of variant NUDT15 haplotypes reaches about 29% in East Asian populations, compared with roughly 21% in Latin American populations, 13% in South Asian populations, and under 2% in non-Finnish European populations.¹⁴ This is why updated CPIC guidelines now recommend testing for both TPMT and NUDT15 before starting thiopurines.¹²

Knowing about NUDT15 matters especially if you are of East Asian descent, because TPMT-only testing would miss a major source of toxicity risk. A patient could have perfectly normal TPMT and still develop devastating bone marrow failure due to a NUDT15 variant. Testing both genes together gives the most complete safety picture.

Population Differences in TPMT Variants

The specific TPMT variants that circulate in a population differ depending on ancestry. The TPMT*3A allele, which carries two amino acid changes, is the most common reduced-function variant among Europeans (minor allele frequency around 3.8%) and Latinos (about 4.3%). In contrast, TPMT*3C, which carries only one of those amino acid changes, is the dominant variant in African populations (minor allele frequency around 4.8%).¹⁵ TPMT deficiencies overall are most prevalent in Sub-Saharan Africa.¹⁶

In South Indian populations, a study found that TPMT*3C was the only variant detected, at a frequency of 1.2%, while *2, *3A, *3B, and *8 were not found at all. The TPMT distribution in this population differed significantly from other groups worldwide.¹⁷ These differences are not academic curiosities. Standard genotyping panels were largely designed around European variant frequencies, so a test that checks only for *3A might miss the most relevant variant in a patient of African or South Asian descent. Knowing which alleles to look for in which populations helps laboratories pick the right tests.

Drug Interactions That Mimic Low TPMT

Your TPMT genotype is not the only thing that determines how much enzyme activity you effectively have. Certain commonly prescribed medications can inhibit TPMT, lowering its activity and pushing more drug down the toxic pathway even if your genes are normal. This is especially relevant for patients with inflammatory bowel disease, who often take aminosalicylate drugs like sulfasalazine or mesalamine alongside their thiopurines.

Laboratory studies using blood from IBD patients showed that sulfasalazine was a particularly potent TPMT inhibitor, with concentrations needed to block the enzyme roughly 10 to 20 times lower than for 5-aminosalicylate or its acetylated metabolite. The inhibition was consistent regardless of whether the patient’s baseline TPMT activity was very high, normal, or intermediate.¹⁸ The practical implication is that adding sulfasalazine to someone already on azathioprine could functionally push them into a lower TPMT activity category, increasing the risk of myelosuppression. Doctors need to account for these interactions, not just the genetic results on paper.

Thiopurine Shunting and the Role of Allopurinol

Not everyone with problems on thiopurines has low TPMT. There is a separate phenomenon called thiopurine shunting, where an unusual proportion of the drug gets funneled toward methylated metabolites rather than the desired active metabolites, even when TPMT activity measures as normal. These patients end up with high levels of 6-methylmercaptopurine (6-MMP), which can damage the liver, and low levels of the therapeutically useful 6-TGN. Research suggests that high TPMT enzyme activity alone does not fully explain this preferential 6-MMP production, and other as-yet-unidentified mechanisms are likely involved.¹⁹

A workaround that has gained traction, particularly in gastroenterology, involves adding allopurinol (a drug traditionally used for gout) alongside a reduced dose of the thiopurine. Allopurinol blocks xanthine oxidase, one of those three competing metabolic pathways, which redirects the drug toward the active 6-TGN pathway. A case report from transplant medicine illustrates this strategy: a renal transplant recipient developed liver toxicity from excessive 6-MMP production despite normal TPMT activity, and the addition of allopurinol corrected the metabolic imbalance.²⁰ While this approach is well-established in IBD clinics, its use in transplant settings and during pregnancy remains limited, and clinicians in those fields are still building the evidence base.

Skin Cancer Risk on Thiopurines

Beyond bone marrow toxicity, long-term thiopurine use carries a moderately elevated risk of non-melanoma skin cancers, and the risk appears to grow with longer duration of treatment. A large retrospective cohort of ulcerative colitis patients found that the adjusted hazard ratio for non-melanoma skin cancer while on thiopurines was about 2.1 compared with unexposed patients. The incidence rate climbed with each year of use, rising from roughly 5.8 per 1,000 person-years in the first year to 13.6 per 1,000 person-years in the fifth. After stopping thiopurines, the risk trended back down.²¹

A meta-analysis confirmed that thiopurines increase overall skin cancer risk in IBD patients by about 80%, driven by non-melanoma skin cancers, while no statistically significant increase was found for melanoma.²² A separate systematic review echoed the finding that the risk appears proportional to how long the drugs are taken.²³ For patients on long-term thiopurines, dermatologists typically recommend annual full-body skin checks, daily sunscreen, and prompt evaluation of any new or changing skin lesions.

Thiopurines in Pregnancy

One question that comes up frequently for women of childbearing age with IBD, autoimmune conditions, or organ transplants is whether thiopurines are safe during pregnancy. The accumulated evidence supports the safety of mercaptopurine and azathioprine during pregnancy and breastfeeding.²⁴ Maintaining disease remission during pregnancy is important because disease flares can themselves harm both parent and fetus, so stopping a drug that is keeping the disease quiet is not automatically the safer choice.

That said, TPMT status and metabolite monitoring remain just as important during pregnancy. The transplant case described earlier highlighted the value of recognizing thiopurine shunting before conception, so that the azathioprine-plus-allopurinol combination could be optimized ahead of time.²⁰ Pre-pregnancy planning that includes TPMT genotyping and metabolite checks allows doctors to settle on a safe, effective regimen before the additional complexity of pregnancy comes into play.

Evolutionary Conservation of TPMT

An interesting wrinkle from a comparative biology standpoint is how conserved the TPMT gene is across species. When researchers compared TPMT amino acid sequences across more than 20 mammalian and non-mammalian vertebrate species, they found that most of the positions where human variant alleles cause amino acid changes are highly conserved throughout vertebrate evolution.²⁵ In other words, nature has been protecting those particular amino acids for hundreds of millions of years, which strongly implies they are functionally important. The mutations that reduce TPMT activity in humans are not occurring at random, structurally forgettable positions; they are hitting spots that evolution deemed worth preserving. This helps explain why those mutations have such outsized consequences for drug metabolism rather than causing merely subtle changes in enzyme efficiency.