rs1050891 — HNMT 3'UTR variant

HNMT - The Tissue Histamine Pathway

Histamine N-methyltransferase (HNMT) is the second major enzyme for degrading histamine in your body. While DAO works in the gut to intercept dietary histamine, HNMT operates inside cells throughout your body - particularly in the brain, liver, kidneys, and bronchial epithelium. It is the dominant pathway for clearing histamine from tissues and the central nervous system.

The Mechanism

HNMT works by transferring a methyl group from S-adenosylmethionine ¹¹ SAM is the body's universal methyl donor, used in hundreds of biochemical reactions (SAM) onto histamine, converting it to N-methylhistamine, which is then further broken down and excreted. The rs1050891 variant is located in the 3' untranslated region ²² The 3'UTR is a regulatory region of mRNA that affects how much protein is produced without changing the protein itself (UTR) of the HNMT gene, which influences mRNA stability and translation efficiency. The G allele reduces HNMT protein production, leading to slower histamine clearance in tissues.

The Methylation Connection

Because HNMT requires SAM as a methyl donor, its function is directly tied to your methylation capacity. If you also carry MTHFR variants (rs1801133 or rs1801131) that reduce methylfolate production, your HNMT may be further compromised by limited methyl group availability. ³³ When SAM is scarce, HNMT must compete with dozens of other methyltransferases for the available supply This creates a meaningful interaction between the methylation and histamine pathways.

The Double Hit Scenario

The most clinically significant situation arises when someone has impaired function in both DAO and HNMT pathways. DAO handles dietary histamine in the gut; HNMT handles endogenous and residual histamine in tissues. If both pathways are compromised, histamine can accumulate from multiple sources simultaneously, leading to more pronounced and persistent symptoms.

Practical Implications

Supporting HNMT function means supporting methylation: adequate B12, folate ⁴⁴ Methylfolate (5-MTHF) is the active form that bypasses the MTHFR enzyme step entirely (ideally as methylfolate if you have MTHFR variants), and riboflavin. If you have both HNMT and DAO variants, a comprehensive approach addressing both diet (low histamine) and methylation support (B vitamins) may be necessary.