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HNMT and Histamine: How Your Genes Affect Histamine Breakdown

The HNMT gene encodes histamine N-methyltransferase, an enzyme that helps break down histamine inside cells, including in the brain. HNMT uses S-adenosylmethionine, also known as SAMe, from the methylation cycle to add a methyl group to histamine. This conversion into N-methylhistamine enables further clearance. Proper HNMT activity helps prevent excessive histamine signaling that can contribute to symptoms such as anxiety, irritability, headaches, sleep disturbance, flushing, or allergy-like reactions.

Because HNMT depends on SAMe, its efficiency is closely tied to the health of the methylation pathway. Low levels of folate, vitamin B12, or choline can reduce SAMe production and slow intracellular histamine clearance. Conversely, good methylation support helps HNMT keep histamine signaling balanced, supporting mood, sleep, immune function, and neurological stability.

How to read your result

This report interprets the rs11558538 variant in HNMT. The effect allele is T. Your genotype will fall into one of three categories below. Use the recommendations to support methylation and histamine balance. PlexusDx does not provide medical advice. This information is educational and not a substitute for professional medical care. Always consult your healthcare provider before making changes to medications, supplements, or diet.

Two effect alleles (TT)

What this means

With the TT genotype you carry two copies of the effect allele and are likely to have reduced HNMT enzyme activity. Slower SAMe-dependent methylation inside cells can lead to diminished intracellular histamine breakdown. When methylation cofactors are adequate you may be fine, but if folate, B12, or choline are low, histamine-related symptoms such as headaches, flushing, insomnia, anxiety, or increased sensitivity to environmental triggers may be more likely.

Practical steps to support HNMT and histamine balance

  • Optimize methylation cofactors: Ensure adequate dietary intake of folate, vitamin B12, and choline. Consider methylated folate and methylcobalamin if recommended by your clinician.
  • Support SAMe production: Foods rich in methionine such as eggs, lean meats, and legumes can help. If supplements are considered, discuss SAMe supplementation with your provider because it can affect mood and medications.
  • Limit high-histamine foods when symptomatic: A short trial reducing aged cheeses, fermented foods, smoked or cured meats, alcohol, and certain fish may reduce symptom burden.
  • Promote gut health: A balanced microbiome supports histamine handling. Include fiber, prebiotic foods, and probiotic strains recommended by your clinician.
  • Address oxidative stress and inflammation: Adequate vitamin C, quercetin, and a diet rich in antioxidants can support histamine tolerance.
  • Track triggers: Keep a symptom and food log to identify patterns and guide targeted interventions with your clinician.
One effect allele (CT)

What this means

With the CT genotype you carry one copy of the effect allele and may have moderately reduced HNMT activity. This can slightly lower intracellular histamine clearance, especially during periods of stress, illness, or when methylation cofactors are low. Many people with one effect allele do not experience major issues if methylation status is good.

Practical steps to support HNMT and histamine balance

  • Keep methylation nutrients steady: Maintain a balanced intake of folate and B12. Consider testing nutrient levels if you have persistent symptoms.
  • Support lifestyle factors: Regular sleep, stress reduction, and moderate exercise help methylation pathways and overall resilience.
  • Monitor histamine load: Be mindful of high-histamine foods when you notice symptoms and reduce intake temporarily to assess benefit.
  • Consider gentle supplementation: Antioxidants such as vitamin C and nutrients that support methylation like betaine or choline may be helpful under clinician guidance.
  • Work with your healthcare provider: If symptoms like chronic headaches, sleep problems, or mood changes persist, discuss targeted testing and interventions.
No effect alleles (CC)

What this means

With the CC genotype you carry two copies of the non-effect allele and are associated with normal HNMT activity. Your HNMT enzyme typically supports efficient SAMe-dependent methylation of histamine, promoting balanced histamine signaling. Even so, methylation cofactors still matter for overall health.

Practical steps to maintain balance

  • Maintain good nutrition: A diet that supplies adequate folate, vitamin B12, choline, and methionine supports optimal methylation and neurotransmitter balance.
  • Adopt healthy habits: Regular sleep, stress management, and a varied diet rich in fruits and vegetables help prevent histamine-related issues.
  • Be aware of other causes: If you develop histamine symptoms, consider other genetic, gastrointestinal, or environmental factors and seek clinical evaluation.

Diet and supplement considerations

Focus on a nutrient-dense eating pattern that supports methylation and lowers excessive histamine exposure when needed.

  • Folate: Leafy greens, legumes, and fortified foods. If you have absorption issues, your clinician may recommend methylfolate.
  • Vitamin B12: Animal proteins, fortified foods, or sublingual/injectable methylcobalamin if deficient.
  • Choline and betaine: Eggs, soy, cruciferous vegetables, and beets support methylation and SAMe regeneration.
  • Methionine and protein: Adequate high quality protein provides methionine, a SAMe precursor.
  • Antioxidants: Vitamin C and flavonoids like quercetin can stabilize histamine and support immune tolerance.
  • Probiotics and gut support: Choose strains that do not increase histamine if you are sensitive. Discuss options with your healthcare provider.

Lifestyle strategies

  • Sleep and stress: Establish consistent sleep and use stress reduction practices such as breathing exercises, meditation, or gentle movement to protect methylation and reduce histamine reactivity.
  • Avoid triggers: Limit alcohol, high-histamine foods, and known personal allergens during symptomatic periods.
  • Regular exercise: Moderate activity supports methylation, mood, and immune regulation.
  • Environmental control: Reduce exposure to molds, strong fragrances, and chemical irritants that can elevate histamine-driven symptoms.

When to talk to your healthcare provider

  • If you have persistent headaches, mood changes, sleep problems, or allergy-like symptoms that affect quality of life.
  • If you are considering starting supplements such as SAMe, high dose methyl donors, or long-term antihistamine use.
  • If you suspect nutrient deficiencies. Blood testing for folate, B12, and related markers can guide safe and effective supplementation.

Limitations and important note

Genetic information helps explain predispositions, not certainties. Environmental factors, diet, medications, and other genes also affect histamine regulation. PlexusDx provides educational information about genetic predispositions only and does not provide medical advice. Always consult your healthcare provider before making changes to treatment, supplements, or lifestyle based on genetic results.