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Understanding Choline, FMO3, and What Your Genotype Means for Health

Choline is an essential nutrient that supports brain health, nerve signaling, muscle movement, liver function, cell membrane structure, and the body’s methylation processes, which are important for DNA synthesis and many other biochemical reactions. The FMO3 gene makes an enzyme that helps convert compounds produced from choline in the gut into forms the body can safely eliminate. Variations in FMO3 can influence how choline is routed through metabolic pathways, shifting how your body uses choline-derived compounds such as betaine and methionine.

This article explains how different FMO3 genotypes at the rs2266782 variant can affect choline metabolism and offers practical, evidence-informed suggestions for diet, supplements, lifestyle, and monitoring to help support healthy methylation and overall wellness.

How FMO3 and Choline Connect

  • Choline is used directly in the body and can be converted by gut bacteria into trimethylamine (TMA). FMO3 helps convert TMA into trimethylamine N-oxide (TMAO) for elimination.
  • Choline can also be oxidized to form betaine, which donates methyl groups to form methionine. This methylation pathway supports DNA methylation and other vital reactions.
  • Variants in FMO3 can shift how much choline is funneled toward betaine-to-methionine conversion versus other methylation roles. This is a difference in metabolic routing rather than a disease.

Practical Lifestyle and Diet Recommendations

  • Prioritize choline-rich foods daily: egg yolks, beef liver, salmon and other fatty fish, soybeans and tofu, chicken, cruciferous vegetables (broccoli, Brussels sprouts), and legumes.
  • Balance protein and plant foods to support both choline intake and overall nutrient diversity.
  • Include methyl-donor supporting foods: leafy greens (folate), B-vitamin rich foods (B6, B12), and sources of betaine such as beets and spinach.
  • Stay hydrated and maintain regular physical activity to support metabolism and liver health.
  • Minimize excessive alcohol intake, which can interfere with choline metabolism and liver function.

Supplement Considerations

  • If dietary intake is low, consider a choline supplement (choline bitartrate, choline citrate, or CDP-choline for cognitive support). Recommended dosing should be personalized with a healthcare provider.
  • Consider B-vitamin support for methylation: folate (preferably methylfolate if indicated), vitamin B12, and vitamin B6 as part of a targeted plan if blood tests or symptoms suggest need.
  • Betaine (trimethylglycine) supplements can support methylation in some people but should be used under healthcare supervision, especially if you have cardiovascular risk factors or elevated TMAO concerns.
  • Do not start new supplements without discussing with your healthcare provider, particularly if you are pregnant, breastfeeding, taking medications, or have a medical condition.

Monitoring and Tests to Discuss With Your Provider

  • Basic nutrient labs: serum choline is not commonly measured, but you can check folate, vitamin B12, and homocysteine as indirect markers of methylation status.
  • Liver function tests to monitor liver health if you have risk factors or symptoms.
  • If there are concerns about TMAO, discuss the relevance and potential testing with your clinician. TMAO testing is not standard for most people.
  • Work with your healthcare provider to interpret results in the context of symptoms, diet, medications, and genetic findings.

Genetic Interpretation

2 effect alleles — AA genotype (rs2266782)

If you have the AA genotype, you carry two copies of the effect allele. This genotype is associated with greater conversion of betaine to methionine. In practice, your body may prioritize using betaine-derived methyl groups to produce methionine, which can reduce the amount of choline available for other methylation reactions.

This is not a deficiency but a shift in metabolic routing. To support balanced methylation:

  • Emphasize choline-rich foods: egg yolks, beef liver, salmon, soybeans, chicken, broccoli, and Brussels sprouts.
  • Ensure adequate intake of folate, vitamin B12, and vitamin B6 to support methylation cycles.
  • Consider discussing choline or betaine supplementation with your provider if dietary intake is insufficient or if labs show elevated homocysteine.
  • Maintain liver-supportive lifestyle habits: reduce alcohol, stay active, and prioritize sleep.
1 effect allele — AG genotype (rs2266782)

The AG genotype means you carry one copy of the effect allele. You may have a moderate tendency toward increased betaine-to-methionine conversion, which could modestly shift how choline is used for methylation.

Practical steps to support your choline metabolism include:

  • Include regular servings of choline-containing foods such as eggs, liver, salmon, soy foods, and cruciferous vegetables.
  • Support methylation with folate, B12, and B6 rich foods or supplements when indicated.
  • Monitor homocysteine and B-vitamin status with your healthcare provider if you have symptoms or other risk factors.
  • Adopt general metabolic health habits: balanced diet, regular exercise, and limited alcohol intake.
0 effect alleles — GG genotype (rs2266782)

If you have the GG genotype, you carry two copies of the non-effect allele and are associated with typical FMO3 enzyme activity. Your FMO3 enzyme converts trimethylamine into TMAO as expected, supporting standard choline metabolism. Choline can perform its key roles in brain function, nerve signaling, liver health, and methylation.

Recommendations to maintain healthy choline status:

  • Consume choline-rich foods regularly: egg yolks, beef liver, salmon, soybeans, chicken, broccoli, and Brussels sprouts.
  • Support methylation with diet and B-vitamin intake as needed.
  • Maintain liver and metabolic health through exercise, adequate sleep, and limiting alcohol.

When to Talk to Your Healthcare Provider

  • If you are pregnant, planning pregnancy, or breastfeeding. Choline needs are higher during these times and should be managed with a clinician.
  • If you have symptoms such as persistent fatigue, cognitive changes, liver issues, or abnormal lab results that may relate to methylation or nutrient status.
  • If you are considering higher-dose supplements like betaine or therapeutic methylation support.
  • If you take medications or have medical conditions that can interact with nutrient status or methylation pathways.

PlexusDx provides genetic information to help you better understand how your genes may influence nutrient metabolism and health. This content is educational and not medical advice. Always consult your healthcare provider before making changes to your diet, starting supplements, or making medical decisions. Your provider can integrate genetic results with your medical history, labs, and personal needs to develop a tailored plan.