If you have the MTHFR gene and histamine intolerance, you most likely have poor methylation, especially if you are deficient in B vitamins such as folate, vitamin B2, and vitamin B12.
Having the MTHFR gene mutation, additional SNP’s in the methylation pathway, or poor methylation can contribute to histamine intolerance as the primary function of the methylation pathway is to produce the methyl donor called SAMe (also known as s-adenosyl methionine). SAMe is a cofactor for the HNMT enzyme, which metabolizes intracellular histamine inside the cell.
Disclaimer: This site contains affiliate links. As an amazon associate, I earn from qualifying purchases.
Symptoms of poor methylation include histamine intolerance and all the symptoms associated with histamine intolerance. But what is the connection between poor methylation, MTHFR, and histamine intolerance?
The MTHFR gene mutation is 1 of the common SNP’s in the methylation pathway, among others that can decrease the ability of the body to produce SAMe to help with the metabolism of histamine. Someone with SNPs in the MTHFR gene is even more prone to histamine intolerance if there is a deficiency in folate and vitamin B2 from the diet, as these two nutrients are needed for the MTHFR gene to function.
SAMe is a very versatile and precious methyl donor that supports over 200 other functions in the body, including the intracellular metabolism of histamine. A deficiency of SAMe can result in a reduced ability of the HNMT to metabolize histamine, resulting in histamine intolerance symptoms such as asthma, allergies, itchy skin, nasal congestion, headaches, etc.
The MTHFR gene mutation is 1 of the common SNP’s in the methylation pathway, among others that can decrease the ability of the body to produce SAMe to help with the metabolism of histamine.
For the methylation process to work optimally and produce SAMe, B vitamins are required along with magnesium. The primary B vitamins needed for the methylation pathway and production of SAMe are folate (B9), B12, and B2.
Suppose someone has SNP’s in the methylation pathway. In that case, they can be more susceptible to histamine intolerance as having SNP’s in the methylation pathway can cause a decreased ability to produce SAMe.
Vitamin B12 and histamine intolerance
People deficient in vitamin B12 can be prone to histamine intolerance as it is another crucial nutrient required for optimal methylation and production of SAMe.
Vegetarians and vegans often don’t get enough B12, which hinders the body’s methylation pathway and ability to make sufficient SAMe. Eating foods high in magnesium, B12, folate, and B2 is crucial to optimize methylation naturally. Here is the best diet for someone with an MTHFR gene mutation.
Excess inflammation inhibits the ability of many enzymes to function and thus produce SAMe to support histamine metabolism. With chronic inflammation being present in the body and inhibiting methylation, you can see how symptoms of histamine intolerance can present with the root of the problem connected to poor methylation and the production of SAMe.
Inflammation can come from various sources such as inflammatory foods, hidden infections, SIBO, and a leaky gut.
How to reduce inflammation to improve methylation
Utilizing curcumin which has anti-inflammatory properties, can help to calm down inflammation in the body. Adding in anti-inflammatory omega three fish oils can also help to manage inflammation and support optimal methylation. Walnuts, flax seeds, salmon, and chia seeds are other excellent sources of omega 3’s
Optimal Gi contains a blend of 11 herbs and nutrients to help calm down and soothe inflammation that is coming from the gut while promoting the healing of the leaky gut.
Sunflower lecithin for histamine intolerance
Optimal PC, which contains phosphatidylcholine derived from sunflower lecithin, indirectly supports methylation by freeing up the methyl donor SAMe to work elsewhere in the body, such as in the HNMT enzyme. The production of phosphatidylcholine requires SAMe as a cofactor and puts a significant demand on methylation as it uses up a lot of the body’s SAMe. Supplementing with sunflower lecithin frees up SAMe to be available for the HNMT enzyme to metabolize histamine.
B vitamins and histamine intolerance
Optimal multi minus one contains all the b vitamins plus magnesium and zinc to help ensure that all the necessary nutrients are on board so that the methylation pathway can work optimally. Optimal multi minus one does not contain any methylated b vitamins, which many people with histamine intolerance or inflammation may be sensitive to. This multivitamin without the methylated B vitamins is often well tolerated in more sensitive individuals prone to excess inflammation.
As you can see, everything is connected in the body, and getting to the root cause of histamine intolerance can take some detective work. Are you deficient in B vitamins such as vitamin B2, B12, and B9? Is stress causing inflammation and thus slowing down genes in the methylation pathway? What is causing inflammation in the body?
These are some big but worthwhile questions that need to be asked. I highly recommend reading the book Dirty Genes by Doctor Ben Lynch to understand further how our unique genetics can influence our ability to metabolize histamine.
Another primary enzyme that is responsible for metabolizing histamine from food sources is the DAO enzyme. This enzyme is located primarily in the gut to break down extracellular histamine from food.
The best way to initially reduce histamine in the body is to avoid foods high in histamine while providing the body with all the nutrients required by the DAO enzyme, HNMT enzyme, and the methylation pathway to work optimally, and that starts with the diet.
Suppose you would like to do genetic testing. In that case, you can order the Ancestry DNA test kit and upload your raw data to generate your strategene report personalized to you with clinically relevant SNP’s that may be present in the methylation and histamine pathways.
This post is all about what you can expect from your strategene report and genetic testing






Thank you for the article, how can I know if I am sensitive to methylated B vitamins, I am currently taking Homocystex Plus and I have a mutation in the Mthfr gene and histamine intolerance.
Gosh, thats tricky and all I can do is share my experience. For me the methylated B vitamins caused itchy skin in high doses so I switched to a lower dose in a multi vitamin but I began to get itchy skin after eating high histamine foods such as chocolate and sauerkraut which was a new symptom for me so after I while I finally figured out that the only change I had made was taking the multivitamin with the active B vitamins. I stopped and the multivitamin with the active Bs and my histamine symptoms went away. I now will never touch the methylated B vitamins and instead I only use the methyl free multi from seeking health that has other great forms. I learned that when inflammation is present in the body (which I am prone to) many people wont tolerate methylated B vitamins. Inflammation slows down enzymes involved in the methylation pathway yet taking active B vitamins speeds them up. It’s like pushing on the gas and brake at the same time and jams everything up. So my question for you would be, are the methylated B vitamins helping with the purpose of taking them and have your histamine symptoms worsened or improved since taking them?
So what to take in lieu of methyl Bs? I have the DAO mutation and MTHR Mutation? After 3-4 weeks on a multi w/methyl “Pure capulations. Geonomic multi”, I’m experiencing scalp itchiness and some generally as well
Help😳
So I won’t touch methyl B vitamins and instead take methyl free multivitamin from seeking health. Folinic acid acid and adenosycobalamin or hydroxycobalamin are the forms I look for methyl free folate and B12.
This is difficult for beginners finding this out. Just learning what histamine intolerance is??
Yes it can be overwhelming forsure. The concepts and connection I am trying to explain can be difficult to grasp forsure. But histamine intolerance is not super easy as it comes from many sources and metabolized via various pathways. Ben Lynch explains it better in his book Dirty Genes.
Thank you so much for writing this article. I just found out my 18 year old daughter has the MTHFR gene mutation. It’s not something I know a ton about and this articles really helped piece things together in a way I can understand! Looking forward to going through more of your work! Thank you again!
Your welcome! I’s so glad you found the information helpful and easy enough to understand as it is complex. Dr Ben Lynch is another really great resource when it comes to genetics and where I learnt a lot of info from :)