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Analyze Your Genetic Variants For Choline Deficiency

Choline deficiency - An Introduction

What is choline?

Choline is an essential, water-soluble, vitamin-like substance that is required for maintaining the structure, integrity, and signaling functions of the cell membranes, for neurotransmission and lipid transportation.

It also acts as a source of methyl groups and is essential for fetal development during pregnancy.

Though choline can be synthesized in the body, you need to acquire some through your diet as well, in order to avoid deficiency.

The choline requirement varies with age.

According to the National Nutrition Research Institute of North Carolina, only a mere 10% of the population has sufficient intake of choline, while the others are deficient.

Inadequate choline in the body can lead to many problems, including cardiovascular diseases, neuro-psychiatric diseases such as Alzheimer’s and schizophrenia, and degenerative diseases like osteoporosis.

Functions of choline

Choline is an essential component in the diet for the primary reason that it performs many crucial roles in the body. 

  • Our cell structure, especially the cell membrane, is made up of lipids. Choline forms an integral part of this structure and plays a role in maintaining the integrity of the cell membrane.
  • Choline plays a crucial role in fat and cholesterol metabolism. It is involved in the removal of cholesterol from the liver. A deficiency of choline leads to the accumulation of fats and cholesterol in the liver.
  • Choline, along with other vitamins, is required for DNA synthesis.
  • It is also an essential part of the nervous system as it forms an integral part of the neurotransmitter acetylcholine.

What are the symptoms of choline deficiency? 

The symptoms of choline deficiency include:

  • Fatigue
  • Muscle aches
  • Decreased energy levels
  • Mood changes
  • Nerve damage
  • Fatty liver

Choline deficiency:  What’s the genetic link?

Gene 1: MTHFD1

The rs2236225 is an SNP found in the MTHFD1 gene on chromosome number 14.

It is involved in folate metabolism.

Choline requirements are altered in polymorphisms of the MTHFD1 or methylenetetrahydrofolate dehydrogenase 1 gene.

A study done in Canada showed that the mutation in the MTHFD1 could increase the risk of heart defects.

Caucasian mothers with rs2236225 (C, T) and rs2236225 (T, T) alleles were at an increased risk (of about 1.5-1.7 times) of having children compared to mothers with no (T) alleles.

However, one must be cautious while reading results as the studies have statistical uncertainties.

C/TPossible increased risk of birth defects
T/TAbout 1.5x risk for Caucasian mothers to give birth to NTD children

Gene 2:  PEMT

A part of the choline requirement of the body can be satisfied by the synthesis of phosphatidylcholine that is catalyzed by PEMT or phosphatidylethanolamine N-methyltransferase in the liver.

The polymorphisms may alter choline requirements in the PEMT gene.

The SNP rs12325817 in the promoter region of the PEMT gene, a large percentage of carriers of the C allele developed organ dysfunction when on a low choline diet.

Also, sexual differences were observed in the effect of PEMT gene rs12325817, and it is possible that the SNP alters the estrogen responsiveness of the promoter.

Unusual estrogen regulation of PEMT gene results in choline deficiency-associated liver dysfunction.

Effect on women with the following allele combination in SNP rs12325817.

The presence of C allele puts one at risk of developing organ dysfunction.

rs12325817PEMTC/CChances of organ dysfunction
C/GMore susceptible to choline deficiency and fatty liver
G/GFewer chances of organ dysfunction


Source: Wikipedia

What causes acetylcholine deficiency?

The neurotransmitter acetylcholine is synthesized from choline.

So, a deficiency of choline leads to a lack of acetylcholine.

Though our body can synthesize its choline, we need to eat choline-rich foods to maintain its optimum levels in the body.

So, inadequate dietary intake of choline is the biggest reason for the deficiency of choline and acetylcholine.


The ideal requirement of choline for everyone varies with age.

Adult men should be able to consume 550mg per day, and adult women need to consume 425mg per day.

The choline needs for women increase during pregnancy to 450mg per day and even more during breastfeeding to 550mg per day.

Does acetylcholine affect mood?

Acetylcholine system plays an essential role in mood swings and also contributes to mental conditions like depression.

It was found that brains of depressed individuals tend to have higher concentrations of acetylcholine. 

The relationship between mood changes due to the withdrawal of smoking and acetylcholine has been the basis for studying its effect on mood changes.

Does choline cause anxiety?

Choline deficiency has many different effects on our body.

It improves brain functioning, memory, cognitive function, learning, and memory.

However, a deficiency of the substance can lead to effects such as depression, anxiety, mood disorder, and Alzheimer’s.

Does choline help with weight loss? 

Yes, choline helps with weight loss. In competitive sports events, individuals are expected to gain and lose weight in a short time.

Choline supplementation helps in these situations when the athlete has to lose weight rapidly.

The reason for this is that choline plays a vital role in fat metabolism.

Dietary sources of choline

The dietary sources of choline include:

  • Beef:  68 grams of beef contains 290 mg of choline
  • Eggs: A single egg can provide 20-25% of your daily required amount of choline
  • Salmon: 110 gms that contains about 62.7 mg of choline
  • Chicken liver: 68 gms contains 222mg choline
  • Cod: 85 gms contains 248 mg  choline
  • Cauliflower: A ½ cup of cauliflower contains 24.2 mg choline
  • Soyabean oil: 15 ml contains 47.3 mg choline
  • Broccoli: 118ml contains 31.3 mg choline

Vegetables that are rich in choline are:

  • Broccoli
  • Cauliflower 
  • Brussel sprouts
  • Swiss Chard
  • Asparagus
  • Collard Greens

Some fruits that contain choline are:

  • Clementines
  • Rhubarb
  • Mulberries
  • Melon 
  • Grape Fruit
  • Blackberries
  • Oranges
  • Avocado
  • Strawberries

Health risk associated with choline deficiency

The inadequate consumption of choline can lead to high homocysteine and all the risks associated with hyperhomocysteinemia.


There are certain groups of people who are at an increased risk of choline deficiency. These include:

  • Individuals who consume large quantities of alcohol
  • Postmenopausal women
  • Pregnant women
  • Athletes who are performing endurance sports

What are the effects of excess choline in the body?

While it is essential to maintain an adequate amount of choline in the body at all times, an excessive amount of choline can be harmful too.

The harmful effects of excess choline include:

  • Sweating
  • Diarrhea
  • Nausea
  • Vomiting
  • Reduced blood pressure
  • Fishy body odor
  • Fatigue

However, one can take a few precautions to avoid excessive choline intake.

A word of caution

Before taking choline supplements, it is highly recommended to read the quantity of choline and if in doubt, seek the advice of your doctor.

Do you have your DNA raw data from 23andMe, AncestryDNA, FTDNA, MyHeritage?

Upload your DNA raw data to Xcode Life. Our Gene Nutrition Report analyses choline needs, gluten sensitivity, lactose intolerance, vitamin needs, and 33 more such categories.

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