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Choline, the PEMT Gene, and Why It Matters for Liver and Brain Health

Choline is an essential nutrient used to build cell membranes, support brain function, and help the liver process and transport fats. We obtain choline from foods such as eggs, meat, fish, soy, and certain vegetables, and our bodies can also make some choline internally. A key enzyme in that internal pathway is produced by the PEMT gene. Variations in PEMT can change how well the enzyme works, which affects internal choline production and may influence liver fat handling and overall metabolic health.

How PEMT affects choline and liver function

The PEMT enzyme converts certain compounds into phosphatidylcholine, a form of choline that is essential for packaging and exporting fats from the liver. When PEMT activity is reduced, the liver can struggle to export fat efficiently, increasing the risk that fat will accumulate. This can contribute to non-alcoholic fatty liver disease even in people who are lean. Because of this, people with reduced PEMT activity often rely more on dietary choline to meet their needs.

What you can do to support choline balance and liver health

  • Eat choline-rich foods regularly: Prioritize egg yolks, beef liver, salmon, chicken, soybeans, and cruciferous vegetables (broccoli, Brussels sprouts). Combining sources across meals helps meet daily needs.
  • Consider targeted supplements if needed: If dietary intake is low or if you have a PEMT variant that reduces internal production, supplements such as choline bitartrate, CDP-choline (citicoline), or phosphatidylcholine can be helpful. Betaine (trimethylglycine) also supports methylation pathways related to choline metabolism. Start with recommended doses on product labels and discuss with your healthcare provider.
  • Support liver health with lifestyle: Maintain a balanced diet, keep a healthy body weight, engage in regular physical activity, limit excess alcohol, prioritize sleep, and manage stress. These habits reduce liver inflammation and improve metabolic resilience.
  • Monitor relevant labs: Periodic liver function tests (ALT, AST, GGT), fasting lipid panel, and assessment of nutrient status (including folate, B12, and possibly choline if available) can provide useful information for managing risk.
  • Special situations: Pregnancy increases choline needs for fetal brain development. If pregnant or planning pregnancy, discuss choline intake with your healthcare provider to ensure adequate intake and appropriate supplementation.

Genetic Interpretations for PEMT rs7946

Two effect alleles (TT) — Reduced PEMT activity

Your TT genotype is associated with decreased PEMT enzyme activity. That means your liver makes less choline internally and relies more on dietary choline. With reduced internal choline production your liver may be more prone to accumulating fat, which can increase the risk of non-alcoholic fatty liver disease even if you are lean.

Practical recommendations

  • Prioritize daily choline-rich foods: egg yolks, beef liver (infrequently due to vitamin A), salmon, chicken, soybeans, and cruciferous vegetables.
  • Consider a choline supplement if dietary intake is insufficient. Options include choline bitartrate, phosphatidylcholine, or CDP-choline. Typical supplemental doses range from 250 mg to 550 mg/day for many adults, though needs vary. Discuss dose with your healthcare provider.
  • Betaine supplements or foods rich in betaine (beets, spinach, wheat bran) may support methylation and choline-related pathways.
  • Check liver enzymes and a fasting lipid profile periodically to monitor liver health and metabolic risk.
  • If pregnant or planning pregnancy, consult your healthcare provider about tailored choline targets and prenatal supplementation.
  • Continue healthy habits: regular exercise, maintain a balanced diet, limit alcohol, and manage stress.
One effect allele (CT) — Likely reduced PEMT activity

Your CT genotype is associated with likely decreased PEMT activity. You may produce somewhat less choline internally and will rely more on dietary intake to meet needs. This profile can also be linked to increased risk of fat accumulation in the liver, particularly in lean individuals.

Practical recommendations

  • Make choline-rich foods a regular part of meals: egg yolks, salmon, chicken, soy products, and cruciferous vegetables.
  • If dietary intake is low, consider a moderate choline supplement. Discuss the type and dose with your healthcare provider to match your individual needs.
  • Support methylation and liver pathways with adequate folate and vitamin B12 through diet or supplementation when appropriate.
  • Monitor liver health with routine blood tests such as ALT, AST, and a fasting lipid panel when recommended by your provider.
  • Maintain an active lifestyle, manage sleep and stress, and limit excessive alcohol to protect liver function.
No effect alleles (CC) — Typical PEMT activity

Your CC genotype is associated with normal PEMT enzyme activity. Your liver is likely able to produce choline efficiently, supporting normal phosphatidylcholine production, cell membrane integrity, brain function, and fat transport out of the liver.

Practical recommendations

  • Continue eating a balanced diet that includes choline sources: eggs, salmon, chicken, soybeans, and cruciferous vegetables.
  • Most people with typical PEMT activity do not require routine choline supplements if dietary intake is adequate, but supplements remain an option if intake is low or in special circumstances such as pregnancy.
  • Follow general liver-friendly lifestyle habits: regular exercise, weight management, moderate alcohol use, good sleep, and stress reduction.
  • Consider routine labs as recommended by your healthcare provider to monitor liver enzymes and metabolic health.

Choosing supplements and doses

If you and your healthcare provider decide supplementation is appropriate, common formulations include choline bitartrate, phosphatidylcholine, and CDP-choline. Betaine may be used as an adjunct to support methylation. Typical supplemental ranges vary; many adults take 250 mg to 550 mg of choline daily from supplements, but individual needs depend on diet, genetic profile, sex, pregnancy status, and overall health. Start with a conservative dose and adjust under medical guidance.

When to check in with a healthcare provider

  • If you have elevated liver enzymes or symptoms such as unexplained fatigue, abdominal discomfort, or changes in appetite.
  • If you are pregnant, planning pregnancy, or breastfeeding — choline needs increase and personalized guidance is important.
  • If you are considering high-dose supplements, have existing liver disease, or take medications that affect liver function.

PlexusDx provides educational information about genetic predispositions and how genetics may influence nutrient needs and health risks. This content is not medical advice. Always consult your healthcare provider before making changes to diet, starting supplements, or making clinical decisions based on genetic information.