rs116855232 — NUDT15 Arg139Cys

The Hidden Pharmacogenetic Risk in Thiopurine Therapy

Thiopurines¹¹ Thiopurines
Azathioprine, mercaptopurine, and thioguanine — immunosuppressants and chemotherapy drugs widely used to treat acute lymphoblastic leukemia, inflammatory bowel disease, autoimmune conditions, and organ transplant rejection are essential medications but carry a narrow therapeutic window²² a narrow therapeutic window
The difference between an effective dose and a toxic dose is small that makes them dangerous without proper dose adjustment. For decades, pharmacogenetic testing focused exclusively on TPMT (thiopurine methyltransferase), the enzyme that breaks down these drugs. But a 2015 breakthrough³³ 2015 breakthrough
Genome-wide association study by Yang et al. in the Journal of Clinical Oncology revealed a second critical gene: NUDT15.

The rs116855232 variant replaces arginine with cysteine at position 139 of the NUDT15 protein (R139C). This single amino acid swap causes the protein to become structurally unstable⁴⁴ structurally unstable
The mutant protein has a 9.4°C lower melting temperature than wild-type, leading to rapid degradation in cells. The result is a near-total loss of enzyme activity — 74% to 100% reduction⁵⁵ 74% to 100% reduction
Measured by Moriyama et al. in functional studies of NUDT15 variants depending on the specific variant. Without functional NUDT15, toxic thiopurine metabolites accumulate in blood cells, causing severe and potentially fatal myelosuppression.

This variant exhibits dramatic ethnic variation. In East Asian populations⁶⁶ East Asian populations
Chinese, Japanese, Korean, Vietnamese ancestry, the T (risk) allele frequency reaches 10%, meaning roughly 1 in 50 individuals are homozygous poor metabolizers. Compare this to European populations, where the variant is nearly absent (0.4% allele frequency), and the clinical significance becomes clear: NUDT15 testing is essential for Asian and Hispanic patients, complementing TPMT testing in populations where TPMT variants are more common.

The Mechanism

NUDT15 (Nudix Hydrolase 15) is a nucleotide diphosphatase⁷⁷ nucleotide diphosphatase
Enzyme that hydrolyzes nucleotide diphosphates to monophosphates with a specific role in thiopurine detoxification⁸⁸ thiopurine detoxification
Converts toxic 6-thioguanine triphosphate (6-TGTP) to inactive 6-thioguanine monophosphate (6-TGMP). When you take azathioprine or mercaptopurine, your body converts these prodrugs into active metabolites including 6-thioguanine nucleotides (6-TGNs)⁹⁹ 6-thioguanine nucleotides (6-TGNs)
These incorporate into DNA and RNA, causing cytotoxic effects that kill rapidly dividing cells. This is therapeutic when targeting cancer cells or overactive immune cells, but becomes dangerous when it affects healthy bone marrow cells.

The R139C substitution disrupts a critical structural element¹⁰¹⁰ structural element
Arginine 139 normally forms stabilizing interactions with Leu131 and Leu134 in the protein core. When cysteine replaces arginine, these interactions weaken, the α2 helix shifts¹¹¹¹ α2 helix shifts
Molecular dynamics simulations show increased fluctuation in the active site region, and the entire protein becomes unstable. Crystal structure studies¹²¹² Crystal structure studies
Enabled by using a small-molecule inhibitor to stabilize the variant protein for X-ray crystallography revealed that R139C protein adopts dual conformations at position 139, lacking the strong electrostatic interactions of wild-type arginine.

Without functional NUDT15, 6-TGTP accumulates to toxic levels¹³¹³ toxic levels
Yang et al. showed TT genotype patients tolerated only 8.3% of planned mercaptopurine dose vs 83.5% in CC genotype. These metabolites incorporate into DNA at excessive rates¹⁴¹⁴ excessive rates
Measured by increased DNA-TG incorporation in NUDT15-deficient cells, triggering DNA damage responses, cell cycle arrest, and apoptosis in bone marrow progenitor cells. The result is severe myelosuppression¹⁵¹⁵ severe myelosuppression
Leukopenia, neutropenia, thrombocytopenia that can be life-threatening if not caught early.

The Evidence

The discovery study¹⁶¹⁶ discovery study
Yang et al. 2015, Journal of Clinical Oncology, genome-wide association study analyzed 657 children with acute lymphoblastic leukemia in the discovery cohort and 371 in the replication cohort. The GWAS revealed two genome-wide significant loci associated with mercaptopurine dose intensity: rs1142345 in TPMT (P = 8.6 × 10⁻⁹) and rs116855232 in NUDT15 (P = 8.8 × 10⁻⁹). Patients homozygous for the NUDT15 variant (TT genotype) tolerated an average of only 8.3% of the planned mercaptopurine dose, compared to 63% for heterozygotes (CT) and 83.5% for wild-type (CC). The T allele was most common in East Asians (10%), followed by Hispanics (7%), rare in Europeans (0.4%), and absent in Africans.

Functional validation¹⁷¹⁷ Functional validation
Moriyama et al. 2016, Nature Genetics performed targeted sequencing of NUDT15 and identified four coding variants (p.Arg139Cys, p.Arg139His, p.Val18Ile, and p.Val18_Val19insGlyVal) that resulted in 74.4–100% loss of nucleotide diphosphatase activity. Biochemical assays showed that NUDT15 inactivates thiopurine metabolites by dephosphorylating them, and deficient enzyme activity leads to accumulation of toxic 6-TGNs with increased incorporation into DNA and RNA.

A 2021 meta-analysis¹⁸¹⁸ 2021 meta-analysis
Zhang et al., Frontiers in Pharmacology, 30 studies examining NUDT15 polymorphisms in Asian populations found that NUDT15 variants conferred an odds ratio of 11.43 (95% CI 7.11–18.35) for early leukopenia and 16.35 (95% CI 10.20–26.22) for early neutropenia. The NUDT15*3 allele (characterized by rs116855232) showed OR 15.31 for early leukopenia and OR 15.85 for early neutropenia. These effect sizes are substantially larger than TPMT variants in the same populations.

Korean cohort studies¹⁹¹⁹ Korean cohort studies
978 patients with Crohn's disease treated with thiopurines showed rs116855232 was significantly associated with leukopenia with an odds ratio of 35.6 (p = 4.88 × 10⁻⁹⁴). European cohorts also showed association: OR 9.50²⁰²⁰ OR 9.50
p = 4.64 × 10⁻⁴ in European IBD patients, though the lower allele frequency means fewer Europeans are affected.

Clinical Implementation

Based on this evidence, CPIC published updated guidelines in 2018²¹²¹ CPIC published updated guidelines in 2018
Clinical Pharmacogenetics Implementation Consortium guideline adding NUDT15 genotype-guided dosing to their existing TPMT recommendations. The guideline classifies NUDT15 phenotypes as normal metabolizer (*1/*1), intermediate metabolizer (*1/*2 or *1/*3 with one loss-of-function allele), or poor metabolizer (*2/*2, *2/*3, or *3/*3 with two loss-of-function alleles). Dosing recommendations for mercaptopurine:

• Poor metabolizers: Initiate at 10% of standard dose (10 mg/m²/day) or consider alternative non-thiopurine therapy for non-malignant conditions
• Intermediate metabolizers: Reduce starting dose to 30–80% of standard if normal starting dose is ≥75 mg/m²/day, with close monitoring for myelosuppression
• Normal metabolizers: Standard dosing with routine monitoring

These recommendations apply to all three thiopurines: mercaptopurine, azathioprine (a prodrug of mercaptopurine), and thioguanine. A 2025 guideline update²²²² A 2025 guideline update
Published January 2025 in Clinical Pharmacology & Therapeutics provides refined recommendations for patients with variants in both TPMT and NUDT15, recognizing that compound intermediate metabolizers²³²³ compound intermediate metabolizers
One variant allele each in TPMT and NUDT15 show additive toxicity and require 20–50% of standard dose depending on baseline dose.

Practical Actions

If you carry one or two copies of the NUDT15 R139C variant, pre-emptive genotyping before starting thiopurine therapy²⁴²⁴ pre-emptive genotyping before starting thiopurine therapy
Joint consensus recommendation from AMP, CPIC, CAP, DPWG, ESPT, and PharmGKB can prevent life-threatening myelosuppression. The NUDT15 poor metabolizer phenotype²⁵²⁵ NUDT15 poor metabolizer phenotype
Homozygous for loss-of-function variants occurs in approximately 1 in 50 East Asians — far more common than TPMT poor metabolizers in Europeans — making this test essential for Asian and Hispanic populations.

For heterozygous carriers (CT genotype), dose reductions of 30–80% are recommended depending on the baseline dose. Full-dose thiopurine therapy poses severe risk in homozygous carriers (TT genotype), who should receive only 10% of standard dose or switch to alternative immunosuppressants for non-cancer indications. Close monitoring of complete blood counts is essential regardless of genotype, with more frequent monitoring for variant carriers.

This variant is also the strongest known risk factor for azathioprine-induced alopecia²⁶²⁶ strongest known risk factor for azathioprine-induced alopecia
Hair loss, a distressing adverse effect in Korean patients with neurological diseases, suggesting systemic effects beyond myelosuppression.

Interactions

NUDT15 and TPMT function in parallel pathways for thiopurine metabolism. TPMT inactivates thiopurines through S-methylation²⁷²⁷ S-methylation
Converting 6-mercaptopurine to 6-methylmercaptopurine, while NUDT15 inactivates the active downstream metabolite 6-TGTP by dephosphorylating it to 6-TGMP. When both enzymes are impaired — for example, a patient who is heterozygous for both TPMT rs1142345 (TPMT*3B)²⁸²⁸ TPMT rs1142345 (TPMT*3B)
Major TPMT loss-of-function variant common in Europeans and NUDT15 rs116855232 — the combined effect is greater than either alone²⁹²⁹ greater than either alone
Additive toxicity requiring more aggressive dose reductions.

A 2024 multiethnic study³⁰³⁰ 2024 multiethnic study
1,863 children with ALL across diverse ancestries found that compound TPMT/NUDT15 intermediate metabolizers (1.2% of the cohort, predominantly Hispanic) tolerated a median mercaptopurine dose of only 25.7 mg/m²/day — significantly lower than single-gene intermediate metabolizers. These patients required more substantial dose reductions to avoid toxicity while maintaining therapeutic efficacy.

Other pharmacogenetic factors that influence thiopurine toxicity include ITPA variants³¹³¹ ITPA variants
Inosine triphosphatase deficiency leads to accumulation of 6-thio-ITP, though ITPA's effect size is smaller than NUDT15 or TPMT. The combined consideration of NUDT15, TPMT, and potentially ITPA genotypes enables truly personalized thiopurine dosing.

For patients on thiopurines who also take allopurinol³²³² allopurinol
Xanthine oxidase inhibitor used to treat gout, dose reduction to 25% of standard is required regardless of NUDT15 genotype, as allopurinol blocks an alternative thiopurine inactivation pathway, dramatically increasing 6-TGN levels.