BHMT Gene and rs3733890: Methylation, Homocysteine, and Health

Last reviewed: May 12, 2026 Last updated: May 12, 2026

Written by: Jay Hastings , CEO of PlexusDx

Jay Hastings is the CEO of PlexusDx, a precision health company focused on genetic testing, blood biomarker insights, and personalized wellness recommendations. He has more than 20 years of experience across healthcare innovation, genomics, laboratory operations, healthcare investing, and strategic finance. His work has included scaling healthcare startups, leading CLIA lab integrations, and helping expand consumer access to precision health tools.

Medically reviewed by: Jayden Lee, PharmD, EMBA

Jayden Lee, PharmD, EMBA, is the PlexusDx Medical Science Liaison with a PharmD and MBA specializing in pharmacogenomics and clinical product development, with a proven ability to bridge the gap between genomic research and practical patient outcomes. Dr. Lee has more than 10 years of professional experience in clinical pharmacy, academia, and research.

This article is part of the PlexusDx Education Hub — your resource for evidence-based guidance on methylation & mthfr. Browse all Methylation & MTHFR education

The BHMT gene, short for betaine-homocysteine methyltransferase, sits at an important junction in the body's methylation and homocysteine-processing machinery. When people ask how a variant like rs3733890 affects health, they are really asking about one of the pathways that keeps homocysteine — an amino acid tied to cardiovascular and neurological health — in a healthy range. This article explains what BHMT does, what rs3733890 represents, and how pathway-level genetic reports can add context.

What the BHMT gene does

BHMT encodes an enzyme that converts homocysteine back into methionine using betaine as a methyl donor. This is one of two routes the body uses to recycle homocysteine; the other depends on folate and vitamin B12 through the MTR and MTHFR pathway. By running an alternative, betaine-fueled route, BHMT provides flexibility — a backup lane that becomes more important when the folate-dependent route is strained. The enzyme is most active in the liver and kidneys.

What rs3733890 represents

rs3733890 is a common single-nucleotide polymorphism in BHMT that produces an amino acid change often described as R239Q. In practical terms, it is a small spelling difference in the gene that can subtly influence enzyme behavior. Research has examined rs3733890 in relation to homocysteine levels and betaine metabolism, with findings that vary across populations. Like most common variants, it represents a tendency rather than a switch — it nudges biology rather than dictating an outcome.

How BHMT connects to methylation health

Methylation is the process of adding methyl groups to DNA, proteins, and other molecules — a reaction essential to gene regulation, neurotransmitter balance, and detoxification. Homocysteine sits at the center of this cycle. When recycling routes work smoothly, homocysteine is kept in check and methionine is regenerated to fuel methylation. BHMT, alongside MTHFR, is one of the genes that shapes how efficiently that recycling happens, which is why methylation-focused reports often look at several of these genes together rather than any one in isolation.

What variation in this pathway can mean

Because BHMT works in concert with folate- and B12-dependent enzymes, no single variant tells the whole story. Someone with a less efficient folate route may lean more on the betaine route, and vice versa. Nutrients matter here too: betaine (also called trimethylglycine), choline, folate, and B vitamins all feed these reactions. This is why practitioners look at genetics, diet, and lab markers such as homocysteine together, rather than reading one gene in a vacuum.

Can PlexusDx reports help?

Genetic reports can add useful context by describing tendencies across methylation-related pathways — a guide, not a guarantee, and never a diagnosis. The Precision Peptide Genetic Test analyzes 14 pathways, 49 peptides, 150+ genetic insights, offering pathway-level education about the biology behind processes such as methylation and homocysteine metabolism. It does not diagnose or treat any condition, and it does not tell you what supplements to take. What it can do is give you and your healthcare provider a clearer picture of your baseline biology to inform a more personalized conversation.

Frequently Asked Questions About the BHMT Gene

What does the BHMT gene do?

BHMT encodes an enzyme that converts homocysteine back into methionine using betaine as a methyl donor, mainly in the liver and kidneys. It provides an alternative route to the folate- and B12-dependent pathway, helping keep homocysteine in a healthy range and supporting the broader methylation cycle.

Is the rs3733890 variant bad?

No — it is a common variant, not a defect. rs3733890 (often described as R239Q) may subtly influence BHMT enzyme activity and homocysteine metabolism, but it represents a tendency rather than a verdict. Its impact depends on your other methylation genes, nutrient intake, and overall health, not on this variant alone.

How does BHMT relate to MTHFR?

BHMT and MTHFR both help recycle homocysteine, but through different routes. MTHFR supports the folate- and B12-dependent pathway, while BHMT uses a betaine-fueled alternative. They work together, so a strain in one route can shift reliance to the other, which is why methylation reports assess several genes at once.

Can a PlexusDx report diagnose a methylation problem?

No. A genetic report describes pathway-level tendencies in methylation and homocysteine processing — it does not diagnose, treat, or manage any condition. It offers educational context you can review with a qualified provider, who may consider genetics alongside diet and lab markers such as homocysteine to guide a personalized approach.

Curious how your genetics fit into the bigger picture? Explore the Precision Peptide Genetic Test for pathway-level insight you can bring to a conversation with your healthcare provider.

The Precision Peptide Genetic Test analyzes how your genes influence peptide-related biological pathways. It does not recommend, prescribe, or determine which peptides you should use, and it does not diagnose, treat, cure, manage, or prevent any medical condition. Consult a qualified healthcare provider before beginning any peptide protocol or making changes to your care.

Medical and Editorial Standards

Medical review process: This article was reviewed for medical accuracy, scientific clarity, evidence alignment, and appropriate discussion of genetics, medications, supplements, biomarkers, and health-related claims.

Sources and evidence: PlexusDx educational content is developed using peer-reviewed research, clinical literature, reputable medical references, and, where applicable, public health or regulatory guidance. References are included at the end of the article when scientific, medical, or health-related claims are discussed.

Commercial transparency: PlexusDx offers genetic testing, blood biomarker testing, personalized supplement recommendations, and related precision wellness services. Product mentions are intended to help readers understand available options and should not be interpreted as medical advice.

Important disclaimer: PlexusDx educational content is for informational purposes only and should not be used as a substitute for professional medical advice, diagnosis, or treatment. Always consult a qualified healthcare provider before making decisions about medications, supplements, genetic testing, lab testing, or health-related care.

This article is part of the PlexusDx Education Hub. Browse all Methylation & MTHFR education