TPMT and NUDT15

Thiopurine drug therapy is used to treat autoimmune diseases, inflammatory bowel disease, acute lymphoblastic leukemia, and to prevent rejection after solid organ transplant. ¹

The inactivation of thiopurine drugs is catalyzed in part by thiopurine methyltransferase (TPMT) and nudix hydrolase 15 (NUDT15). 1

Bayoumy AB, Crouwel F, Chanda N, et al. Advances in thiopurine drug delivery: the current state-of-the-art. Eur J Drug Metab Pharmacokinet. 2021;46(6):743-758.

, 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

, 3

Pratt VM, Cavallari LH, Fulmer ML, et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051-1063.

Variants in the TPMT and/or NUDT15 genes are associated with an accumulation of cytotoxic metabolites leading to increased risk of drug-related toxicity with standard doses of thiopurine drugs, 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

, 3

Pratt VM, Cavallari LH, Fulmer ML, et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051-1063.

and the effects on thiopurine catabolism can be additive.

This Test Fact Sheet focuses on genetic testing for TPMT and NUDT15 variants, which can be performed before or during thiopurine therapy. The enzyme activity phenotype of TPMT can be measured directly before drug administration. After the initiation of therapy, concentrations of thiopurines and metabolites can be measured to optimize thiopurine therapy dosing. For more information about these tests, refer to the Thiopurine Methyltransferase, RBC and Thiopurine Metabolites in Red Blood Cells Test Fact Sheets.

For more information on pharmacogenetic testing, refer to the ARUP Consult Germline Pharmacogenetics - PGx topic.

Disease Overview

Thiopurine drugs include azathioprine, mercaptopurine, and thioguanine. ¹

, 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

These are inactive prodrugs that must be metabolized to 6-thioguanine nucleotides (6-TGNs) to function. 1

Bayoumy AB, Crouwel F, Chanda N, et al. Advances in thiopurine drug delivery: the current state-of-the-art. Eur J Drug Metab Pharmacokinet. 2021;46(6):743-758.

, 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

 The primary metabolic route for inactivation of thiopurine drugs is catalyzed by TPMT. 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

TPMT can be inhibited by common drugs, including NSAIDs, diuretics, and ulcerative colitis treatments such as mesalamine.

When TPMT activity is low, more 6-mercaptopurine (6-MP) may be converted into active (cytotoxic) 6-TGN, which accumulates in the body. ²

Excess 6-TGN in bone marrow (BM) inhibits purine synthesis, which in turn inhibits cell proliferation and contributes to excessive myelosuppression. 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

Specific TPMT variants (seen with higher frequency among individuals of African and European descent) have been associated with TPMT deficiency of varying severity. 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

, 3

Pratt VM, Cavallari LH, Fulmer ML, et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051-1063.

In individuals with no or very low TPMT activity, severe myelosuppression occurs with conventional thiopurine doses. 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

, 3

Pratt VM, Cavallari LH, Fulmer ML, et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051-1063.

Thirty to sixty percent of individuals with intermediate TPMT activity experience moderate to severe myelosuppression with conventional thiopurine doses. 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

, 3

Pratt VM, Cavallari LH, Fulmer ML, et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051-1063.

NUDT15 catalyzes the conversion of cytotoxic 6-TG triphosphate metabolites to the less toxic 6-TG monophosphate. ²

NUDT15 variants (seen with higher frequency among individuals of Asian and Hispanic descent) reduce enzyme activity and contribute to excessive myelosuppression. 2

Relling MV, Schwab M, Whirl-Carrillo M, et al. Clinical Pharmacogenetics Implementation Consortium guideline for thiopurine dosing based on TPMT and NUDT15 genotypes: 2018 update. Clin Pharmacol Ther. 2019;105(5):1095-1105.

, 3

Pratt VM, Cavallari LH, Fulmer ML, et al. TPMT and NUDT15 genotyping recommendations: a joint consensus recommendation of the Association for Molecular Pathology, Clinical Pharmacogenetics Implementation Consortium, College of American Pathologists, Dutch Pharmacogenetics Working Group of the Royal Dutch Pharmacists Association, European Society for Pharmacogenomics and Personalized Therapy, and Pharmacogenomics Knowledgebase. J Mol Diagn. 2022;24(10):1051-1063.

Thiopurine dosing should rely on disease-specific guidelines and the degree of myelosuppression. ²

Genetics

Genes

TPMT, NUDT15

Inheritance

TPMT: Autosomal codominant ²

NUDT15: Autosomal codominant

Test Interpretation

Variants Tested

Gene (Transcript)	Alleles	Predicted Allele Function
TPMT (NM_000367)	TPMT*2: rs1800462, c.238G>C	No function
	TPMT*3A: rs1800460, c.460G>A; rs1142345, c.719A>G	No function
	TPMT*3B: rs1800460, c.460G>A	No function
	TPMT*3C: rs1142345, c.719A>G	No function
	TPMT*4: rs1800584, c.626-1G>A	No function
	TPMT*11: rs72552738, c.395G>A	No function
	TPMT*29: rs267607275, c.2T>C	No function
	TPMT*42: rs759836180, c.95dupA	Possible no function
NUDT15 (NM_018283)	NUDT15*2 or *3: rs116855232, c.415C>T	No function
	NUDT15*4: rs147390019, c.416G>A	Uncertain function
	NUDT15*14: rs777311140, c.80-81insCGGG	Possible no function

Allele frequencies and phenotype predictions are available at PharmVar ⁴

or PharmGKB. 5

PharmGKB. Last updated 2024; accessed Nov 2024.

Sensitivity/Specificity

Analytic sensitivity/specificity: 99%

Results

Metabolizer status is reported separately for each gene analyzed.

Metabolizer Status	Interpretation
Intermediate	Possible susceptibility to dose-related toxicity from standard doses of thiopurine drugs
Possible intermediate	Susceptibility to dose-related toxicity from standard doses of thiopurine drugs
Poor	Probable susceptibility to dose-related toxicity from standard doses of thiopurine drugs
Normal	Standard doses of thiopurine drugs are likely appropriate
Indeterminate	Genotype cannot help determine susceptibility to dose-related toxicity when using thiopurines

Limitations

• Only targeted TPMT and NUDT15 variants will be detected by this test.
• Diagnostic errors can occur due to rare sequence variations.
• Genotyping in individuals who have received an allogeneic stem cell or bone marrow transplant will reflect donor status and is not recommended.
• Because the complex TPMT*3A allele contains the variants found in the *3B and *3C alleles, genotyping cannot distinguish the *1/*3A genotype (intermediate TPMT activity) from the rare *3B/*3C genotype (no or low TPMT activity); the *1/*3A genotype is assumed when both *3B and *3C are detected.
• Thiopurine drug metabolism and risk for adverse reactions to thiopurines may be affected by genetic and nongenetic factors that are not evaluated by this test.
• This test does not assess for TPMT allele variants associated with ultrahigh enzyme activity.
• Genotyping does not replace the need for therapeutic drug monitoring and clinical observation.