Do you deal with sinus drainage after you eat? Periodic itching and hives? Migraines, irritability, anxiety, brain fog? The weird and seemingly unrelated symptoms of histamine intolerance can drive you nuts trying to figure out the root cause.
Histamine intolerance is caused by an imbalance of too much histamine in the body that isn’t balanced out by your capacity to break it down. Too much histamine can affect many different functions in the body, giving rise to many different symptoms seen in histamine intolerance. The imbalance of histamine can be caused by your body producing too much histamine or by not being able to properly break down histamine from foods. (Or both!)
How well your body breaks down histamine is partly determined by genetics:
- Your genetic data can help you figure out if your genes are contributing to your histamine intolerance.
- Knowing which genetic variants you carry can lead to targeted solutions that are more likely to work for you.
This article goes in-depth on the research into histamine intolerance. I’ll include the genetic variants that impact histamine levels, and then go through solutions and options at the end of the article. Everything is fully referenced, so you can easily dig into the research yourself. This is one article that you may want to bookmark and come back to read again.
What is Histamine Intolerance?
Classified as a biogenic amine, histamine is a molecule that plays many roles in the body. Histamine’s many functions include:
- causes allergic reactions,
- acts within our immune defense system,
- dilates blood vessels (vasodilatation)
- acts as a neurotransmitter
- works as a signaling molecule in the stomach to release acid
While most of us think of histamine only during allergy season, histamine is a vital part of the way your body works.
What are the symptoms of histamine intolerance?
Histamine intolerance symptoms impact many different systems in the body, including[ref]:
- Head: headaches & migraines
- Mood: anxiety, irritability, brain fog
- Stomach: acid reflux, nausea, stomach pain
- Intestines: bloating, diarrhea, constipation
- Heart: heart arrhythmia, dizziness
- Sinuses: drainage, congestion
- Skin: hives, itching, flushing,
- Sleep: insomnia, early waking
People with histamine intolerance usually have several of the symptoms above, but they likely won’t have all of the symptoms.[ref]
Historical note: Too much histamine has been known for decades to cause scombroid poisoning – the type of food poisoning from eating fish that isn’t fresh.[ref]
Here’s a visual overview of what we are going to cover here:
Causes of histamine intolerance:
The two main causes of histamine intolerance are:
- not enough of the enzymes needed to break down histamine (DAO and HMNT)
- too much histamine being produced (gut microbes producing histamine, leaky gut, mast cells degranulating too easily, HDC variants, chronic exposure to allergens).
Breaking down histamine:
There are two ways that your body clears histamine: using the DAO enzyme or the HMNT enzyme.[ref]
- Diamine oxidase (DAO) enzyme: Histamine from foods or bacteria in your gut is broken down, or metabolized, using the DAO (diamine oxidase) enzyme. The DAO enzyme is produced in the villi lining the small intestines and is released to metabolize histamine.[ref]
- Histamine methyltransferase (HMNT) enzyme: The HMNT enzyme works throughout the body, including in the brain, to deactivate and break down histamine created by your cells.[ref]
Diamine Oxidase (DAO) enzyme:
Diamine oxidase is encoded by that AOC1 gene. It is mainly produced in the intestines in order to counteract histamine from foods and histamine created by intestinal bacteria. Foods that contain a lot of histamine include aged cheeses, aged meats, fermented foods, and more.
Certain bacteria in the gut (including those from some probiotics or fermented foods) can also increase histamine levels in the body. People with histamine intolerance show altered gut microbiome composition as well as elevated levels of zonulin, which regulates tight junctions in the intestines (leaky gut).[ref] A recent study of histamine intolerance patience found that they had “a significantly higher abundance of histamine-secreting bacteria…”[ref]
The DAO enzyme is also used by the body to break down other biogenic amines, including tyramine, putrescine, cadaverine, spermidine, and spermine. High levels of other biogenic amines can reduce the ability of DAO to break down histamine.[ref]
Histamine is degraded by DAO into imidazole acetaldehyde, which is then quickly oxidized into imidazole acetic acid.[ref]
The HMNT enzyme is responsible for breaking down histamine in the central nervous system.
Recent studies show exactly how important HNMT is in controlling brain histamine levels. Genetic variants that change HNMT levels in the brain are linked to an increased risk of neurodegenerative disorders such as Parkinson’s disease. Studies also link HNMT variants to an increased risk of migraines and ADHD.[ref] Rare mutations that inactivate the HNMT enzyme are linked to intellectual disability.[ref]
The HNMT enzyme acts throughout the body. Genetically decreased HNMT is also linked to atopic dermatitis, or eczema.[ref] While DAO can also circulate in the periphery, HNMT is the only enzyme breaking down histamine as a neurotransmitter in the central nervous system.
When histamine is degraded with the help of the HNMT enzyme, it forms N-methylhistamine, which is unable to bind to histamine receptors. Note that a methyl group is needed in the reaction. The N-methylhistamine is then further broken down with the MAO-B enzyme, forming N-methylimidazole acetaldehyde.[ref]
Creation of Histamine:
Histamine is made from of the amino acid histidine. It is an essential amino acid, which means that humans cannot make it in our bodies and must obtain it from diet. Histidine can be used in the body for several different purposes, including the production of histamine.
Histidine decarboxylase (HDC gene) is an enzyme that catalyzes the reaction of histidine into histamine. It does this inside various different cell types, including to create histamine in large amounts in mast cells.
Not enough histamine:
Without enough histidine decarboxylase, animal studies show behavior that resembles Tourette syndrome.
Genetic studies show that people with Tourette’s (vocal and motor tics) may have rare HDC gene mutations as a cause. The loss of histamine in the basal ganglia causes too much dopamine in that region of the brain, resulting in tics.[ref]
Too much histamine and the heart:
Histamine is also essential in the way that the heart muscle functions. Too much histamine here can be detrimental, and people with chronic heart failure have higher average plasma histamine levels. In fact, a genetic variant in the HDC gene that reduces histamine levels is linked to a significantly decreased risk of chronic heart failure.[ref]
Additionally, clinical trials show that blocking the H2 receptor is beneficial for chronic heart failure. Famotidine (Pepcid AC) improved cardiac symptoms and ventricular remodeling. In the heart, histamine increases the force of contraction, and even as far back as 1913, histamine has been known to induce heart arrythmias. [ref][ref]
Histamine receptors explain the different effects of histamine
You may be wondering why one molecule can cause so many different actions in the body…
How can histamine cause headaches and heartburn and hives?
The function of histamine in a certain part of the body depends on the receptor it binds to.
Different histamine receptors are found in different parts of the body:[ref]
- H1 receptors: Found in smooth muscle, endothelial cells (lining the blood vessels), central nervous system, and mast cells. Activating the H1 receptors causes allergy-type symptoms such as itching, swelling, vasodilation, nose running, and skin reactions. H1 receptors are also important in asthma reactions.
- H2 receptors: When histamine activates the H2 receptors in the stomach, acid is released. H2 receptors are also found in the intestinal tract and the walls of blood vessels. Mast cells also have H2 receptors, which, when activated, cause the release of more histamine. In the heart, H2 receptors are important in controlling the rhythm.
- H3 receptors: The central and peripheral nervous systems contain H3 receptors, which act as a feedback loop for histamine levels in the brain. Activating the H3 receptors impacts serotonin, norepinephrine, and acetylcholine release.[ref]
- H4 receptors: These histamine receptors are at the core of the inflammatory response. H4 receptors are found in the bone marrow, basophils (a type of white blood cell), the thymus, small intestine, spleen, colon, and mast cells.[ref]
Three types of histamine receptors are found in the intestines: H1, H2, and H4. Interestingly, a study showed that people with food allergies and IBS had significantly higher levels of H1 and H2 receptors in their intestines.[ref]
Mast cells and histamine release
Mast cells are a type of immune cell that store histamine. They are found in most tissues in the body, especially in the areas of the body exposed to the outside world.
Allergens cause mast cells to burst (degranulate) and release histamine. Large numbers of mast cells are in the skin, bronchial tree mucosa, and intestinal mucosa. Viruses, bacteria, and fungi also activate mast cells.[ref]
Some think that histamine intolerance is a subset of mast cell activation syndrome (MCAS)
Related article: Mast cell activation syndrome
For more in-depth info on mast cells and histamine, check out Research Studies on Mast Cells and Histamine Intolerance, where I dive into all the different ways histamine can affect you.
Shameless Plug: Want to go further with your genetic raw data? Join as a Member!
Histamine, Sleep, and Circadian Rhythm:
Histamine acts in the brain as a neurotransmitter. It is an alerting neurotransmitter, rising in the morning hours to wake us up. About 50% of the histamine in the brain is from mast cells.[ref]
Benadryl, a commonly used antihistamine, has the side effect of making people sleepy. It is due to the actions of histamine in the brain.
Altering histamine levels in the brain changes sleep:
- In mice, knocking out the histamine receptors in the brain shows that it alters sleep patterns a little bit. Without histamine, mice were slower to wake up. They also had fragmented sleep and decreased non-REM sleep.[ref]
- In another animal study, researchers decreased the number of mast cells in the brain, reducing histamine production. It did not affect the amount of time that the mice slept overall, but it did affect their brain waves in sleep and their ability to bounce back after sleep deprivation.[ref]
In a recent study in people who had suspected histamine intolerance, the researchers found that about 1/4 of the patients had a circadian change in histamine levels that differed from a control group. These patients had significantly reduced DAO enzyme levels during the day and subsequently higher histamine levels.[ref]
Histamine Intolerance Genotype Report
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Membership lets you see your data right in each article and also gives you access to the members’ only information in the Lifehacks sections.
Breakdown of histamine:
DAO (diamine oxidase) is the enzyme produced by the intestines, breaking down histamine from foods. The AOC1 gene codes for the production of the DAO enzyme. Genetic variants in AOC1 can increase or decrease the production of the enzyme.
AOC1 gene: encodes diamine oxidase (DAO):
Check your genetic data for rs10156191 (23andMe v4; AncestryDNA):
- C/C: typical
- C/T: reduced production of DAO, increased risk of migraines due to histamine[ref]
- T/T: reduced production of DAO[ref][ref][ref], increased risk of migraines due to histamine[ref]
Members: Your genotype for rs10156191 is —.
Check your genetic data for rs2052129 (23andMe v5 only):
- G/G: typical (most common genotype)
- G/T: reduced production of DAO, increased risk of migraines due to histamine[ref]
- T/T: reduced production of DAO[ref], increased risk of migraines due to histamine[ref]
Members: Your genotype for rs2052129 is —.
Check your genetic data for rs1049742 (23andMe v4 only):
- C/C: typical
- C/T: reduced production of DAO
- T/T: reduced production of DAO[ref]
Members: Your genotype for rs1049742 is —.
Check your genetic data for rs1049793 H645D (23andMe v4; AncestryDNA(older)):
- C/C: typical, high
- C/G: reduced production of DAO (35% reduction)
- G/G: reduced production of DAO (50% reduction)[ref]
Members: Your genotype for rs1049793 is —.
Check your genetic data for rs2071514 (23andMe v5; AncestryDNA):
- A/A: possibly higher DAO[ref]
- A/G: possibly higher DAO
- G/G: typical
Members: Your genotype for rs2071514 is —.
HNMT genetic variants:
Histamine n-methyltransferase (HMNT) is the enzyme that regulates histamine in the body via converting it from histamine into N-methylhistamine, which can then be eliminated from the body. HNMT is responsible for the elimination of 80% of histamine in the body.[ref]
Check your genetic data for rs1050891 (23andMe v4, v5):
- G/G: typical; lower risk of hyperactivity in ADHD due to food additives[ref]
- A/G: reduced breakdown of histamine compared to G/G
- A/A: reduced breakdown of histamine compared to G/G[ref]
Members: Your genotype for rs1050891 is —.
Check your genetic data for rs11558538 C314T (23andMe results for i3000469, v4; AncestryDNA):
- T/T: reduced HNMT activity[ref][ref] higher histamine levels, increased relative risk of asthma[ref]
- C/T: reduced breakdown of histamine compared to C/C
- C/C: typical[ref]
Members: Your genotype for rs11558538 is — -or- your 23andMe genotype for i3000469 is —.
Check your genetic data for rs2071048 -464(23andMe v4; AncestryDNA):
- T/T: increased risk of asthma (and higher histamine), common variant[ref]
- C/T: typical asthma risk
- C/C: typical asthma risk
Members: Your genotype for rs2071048 is —.
The methylation cycle plays a role in breaking down monoamine neurotransmitters, including histamine. It is also important in creating the methyl groups needed for the HMNT enzyme to work. So looking at your methylation cycle genes can also help with balancing out histamine intolerance.
The MTHFR gene codes for an enzyme that is a key player in the folate cycle. It is one source of methyl groups for the methylation cycle. Decreased enzyme activity of MTHFR – combined with a diet lacking in folate or choline – may cause a reduced breakdown of histamine.
Check your genetic data for rs1801133 (23andMe v4, v5; AncestryDNA):
- G/G: typical
- A/G: one copy of MTHFR C677T allele (heterozygous) decreased enzyme function by 40%
- A/A: two copies of MTHFR C677T (homozygous) decreased enzyme function by 70 – 80%
Members: Your genotype for rs1801133 is —.
Check your genetic data for rs1801131 (23andMe v4, v5; AncestryDNA):
- T/T: typical
- G/T: one copy of MTHFR A1298C (heterozygous), slightly decreased enzyme
- G/G: two copies of MTHFR A1298C (homozygous), decreased enzyme by about 20%
Members: Your genotype for rs1801131 is —.
Creation of Histamine:
HDC gene: encodes the histidine decarboxylase enzyme, which is used in the conversion of histidine into histamine
Check your genetic data for rs2073440 (23andMe v4, v5; AncestryDNA):
- T/T: typical
- G/T: Reduced HDC, decreased risk of allergic rhinitis (less histamine), reduced risk of chronic heart failure
- G/G: Reduced HDC, decreased risk of allergic rhinitis (less histamine)[ref] reduced risk of chronic heart failure[ref]
Members: Your genotype for rs2073440 is —.
Check your genetic data for rs267606861 (AncestryDNA only):
- C/C: typical
- A/C: carrier of a pathogenic mutation for Tourettes, reduced HDC (rare)[ref]
Members: Your genotype for rs267606861 is —.
HRH1 gene: histamine receptor 1; this receptor is responsible for the allergy-type symptoms associated with histamine (nose running, eyes watering, itchy skin, airway reactivity)
Check your genetic data for rs901865 (23andMe v4, v5; AncestryDNA):
- C/C: typical
- C/T: increased asthma risk (likely increased HRH1)
- T/T: increased asthma risk (likely increase HRH1)[ref]
Members: Your genotype for rs901865 is —.
HRH2 gene: histamine receptor 2, this receptor is active in the production of stomach acid, the sinus node of the heart, and other places in the body
Check your genetic data for rs2067474 (23andMe v4, v5; AncestryDNA):
- A/A: Decreased HRH2; protective against chronic heart failure[ref],
- protective against gastric cancer[ref], lower risk of gastritis[ref]
- A/G: protective against chronic heart failure, protective against gastric cancer, lower risk of gastritis
- G/G: typical (more common genotype) higher HRH2, higher risk of CHF, gastritis
Members: Your genotype for rs2067474 is —.
HRH4 gene: histamine receptor 4; found throughout the body, including in the brain. Histamine receptors are also important in cancer progression.
Check your genetic data for rs11662595 (23andMe v4, v5; AncestryDNA):
- A/A: typical
- A/G: decreased HRH4 activation (receptor dysfunction), increased risk of progression in non-small cell lung cancer
- G/G: decreased HRH4 activation (receptor dysfunction), increased risk of progression in non-small cell lung cancer[ref]
Members: Your genotype for rs11662595 is —.
Breaking down Tyramine:
The DAO enzyme also breaks down tyramine, another biogenic amine. Many of the same foods that are high in histamine are also high in tyramine.
People who are on MAOIs, a type of antidepressant, are at a higher risk of having problems with breaking down tyramine.
Tyramine is metabolized through three different pathways in the body: MAOA, CYP2D6, and FMO3. Members will see their genotypes below.
If you have variants in all three pathways, please read the full article on tyramine intolerance. This may be exacerbating problems with histamine via using the same DAO enzyme.
|Gene||RS ID||Risk Allele||Your Genotype||Notes About Risk Allele|
|FMO3||rs2266780||G||--||Mild decrease in FMO3|
|FMO3||rs2266782||A||--||Mild decrease in FMO4|
|FMO3||rs909530||T||--||Mild decrease in FMO5|
|FMO3||rs909531||C||--||Mild decrease in FMO6|
|FMO3||rs28363581||C||--||Decreased FMO3 (rare|
|FMO3||rs3832024||D||--||Decreased FMO3 (rare|
|FMO3||rs61753344||T||--||Decreased FMO3 (rare|
|CYP2D6||rs3892097||T||--||Decreased or non-functioning CYP2D6 enzyme|
|CYP2D6||rs5030655||D||--||Decreased or non-functioning CYP2D6 enzyme|
|CYP2D6||rs1065852||A||--||Decreased or non-functioning CYP2D6 enzyme|
|CYP2D6||rs16947||A||--||Decreased or non-functioning CYP2D6 enzyme|
|CYP2D6||rs5030867||G||--||Decreased or non-functioning CYP2D6 enzyme|
|CYP2D6||rs5030656||D||--||Decreased or non-functioning CYP2D6 enzyme|
|CYP2D6||rs28371706||A||--||Decreased or non-functioning CYP2D6 enzyme|
Lifehacks for histamine intolerance:
Below are the research-backed solutions for histamine intolerance. You may need to try several different ‘lifehacks’ to see which works best for you.
A Low-histamine diet, at least initially:
A low-histamine diet restricts foods that contain high levels of histamine or that cause the body to release histamine. To experiment with a low-histamine diet, eliminate all of the higher histamine foods for a period of time to see how your body responds.
In general, foods that are fermented or aged are higher in histamine. A quick overview of high histamine foods includes processed meats, cheeses (except farmers cheese), fish and seafood that isn’t completely fresh, spinach, chocolate, tomatoes, strawberries, wine, sake, and more.
If you are considering a low histamine diet, I find this histamine food list to be the most thorough: Complete list of foods that are high in histamine (pdf).
What does a low-histamine diet do?
- Decreasing the amount of histamine you take into your body will lower the overall amount of histamine circulating in your body.
- Research studies show that a low histamine diet helps with chronic urticaria (itchiness, hives), migraines, stomach problems, and asthma.[ref][ref]
Should you maintain a low histamine diet long-term?
Trying a low-histamine diet for a period of time can give you a lot of insight into how histamine affects your body, but it may not be a diet you want to continue long-term. A low-histamine diet restricts many healthy foods that you may enjoy, such as spinach, strawberries, and avocados.
Use a low histamine diet as a tool to learn which histamine-containing foods bother you the most. It can also be a short-term way of getting histamine responses under control.
Low FODMAPs diet: histamine and gut problems
Interestingly, a randomized controlled study for people diagnosed with IBS found that a low FODMAPs diet reduced symptoms and reduced histamine levels. It could mean that a FODMAPs diet works because IBS is related to histamine intolerance – or – could mean that the people diagnosed with IBS were really dealing with gut-related histamine symptoms.[ref] Additionally, the low FODMAPs diet may be helping to decrease intestinal barrier permeability.
A low FODMAPs diet cuts out a lot of high histamine foods, so it could reduce histamine levels through eating fewer foods high in histamine. On the other hand, a low FODMAPs diet impacts the gut microbiome and histamine-producing bacteria. Animal studies also link IBS to mast cell activation in the colon, so changing the gut microbiome with a FODMAPs diet may also impact colonic mast cells.[ref]
Learn more about what is included in a low FODMAPs diet: Starting a Low FODMAPs diet
Vitamins & Natural Supplements for Histamine Intolerance:
Related Articles and Topics:
Mast cells: MCAS, genetics, and solutions
Mast Cell Activation Syndrome, or MCAS, is a recently recognized disease involving mast cells that misbehave in various ways. Symptoms of MCAS can include abdominal pain, nausea, itching, flushing, hives, headaches, heart palpitations, anxiety, brain fog, and anaphylaxis. Dive into the research into mast cells, genetics, and solutions.
Notes about Histamine and Mast Cells
A compilation of notes and reference studies on the functioning of mast cells and histamine receptors.
Tyramine: The Cheese Effect and Your Genes
Tyramine is another biogenic amine, found in a lot of the same foods as histamine. An inability to break down tyramine can cause a variety of symptoms.
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Originally published April, 2015.
Debbie Moon is the founder of Genetic Lifehacks. Fascinated by the connections between genes, diet, and health, her goal is to help you understand how to apply genetics to your diet and lifestyle decisions. Debbie has a BS in engineering and also an MSc in biological sciences from Clemson University. Debbie combines an engineering mindset with a biological systems approach to help you understand how genetic differences impact your optimal health.