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TPMT protein levels

TPMT · rs1800462

Where this position leads

Condition: Celiac Disease

Drug: Thiopurines

rs1800462 Condition: Celiac Disease Celiac Disease Condition Drug: Thiopurines Thiopurines Drug rs1800462 rs1800462 TPMT

What the study found

Who was studied 47,745 European ancestry individuals.

The effect Each copy of the G allele shifted the measure 0.875 lower (95% confidence interval 0.76-0.99); p = 9 × 10−57.

How common The G allele had a frequency of about 0% in the people studied.

Where it sits Chromosome 6, band 6p22.3 — a missense change in TPMT.

What ClinVar records

Classification drug response for Thiopurine S-methyltransferase deficiency; no assertion criteria provided (0 of 4 stars, 1 submitter), last evaluated 1999-02-01. ClinVar record 12721 NM_000367.2(TPMT):c.238G>C (p.Ala80Pro)

What this is ClinVar's aggregate record for this position (as of its 2026-10-19 release), not a result about you. A classification describes the variant against the condition named, as laboratories submitted it. Whether a person carries this variant, and what that would mean for them, is a question for a clinical test and a genetic counsellor.

What each result means

C/C No copy of the version the research linked to TPMT protein levels. This is the starting point the study compared everyone against.
C/G One copy of the version the research linked to TPMT protein levels. That is a smaller link than two copies.
G/G Two copies of the version the research linked to TPMT protein levels. That is the strongest link of the three results. A link in a study is not a diagnosis.
Source
A scalable variational inference approach for increased mixed-model association power
Loya H, Kalantzis G, Cooper F, Palamara PF
Nature genetics · 2025 · PMID 39789286 · open access

Questions about rs1800462

What is rs1800462?

rs1800462 is a single position in the genome, in or near the TPMT gene. Published research associates it with tpmt protein levels. A single variant does not decide an outcome — it shifts a probability, and for most common variants the shift is small.

What conditions is rs1800462 linked to?

On MyGeneLog this position is linked to Celiac Disease. The research behind each link, and its sources, are set out on that condition page.

Does rs1800462 affect how medicines work?

TPMT carries pharmacogenomic findings for Thiopurines. That is educational information, not a prescription or a dosing guide. Any decision to start, stop or change a medicine belongs with the clinician or pharmacist managing your treatment.

Does having rs1800462 mean I will get this?

No. Common variants like this one move a probability slightly and, on their own, rarely decide anything about one person. Nothing on this page is a diagnosis, and health decisions should be made with a clinician who can see your whole picture.

Where does the information about rs1800462 come from?

GWAS Catalog, Nature genetics 2025, PMID:39789286. Every variant on MyGeneLog comes from public primary sources and is published with its citation and the date it was checked.

Quoting this page

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TPMT protein levels (rs1800462). MyGeneLog™. https://www.mygenelog.com/variants/rs1800462

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