Lactose Intolerance Genes

Are you a milk drinker? Does pouring a cold glass of milk sound good? Your genes control whether you are likely to produce lactase as an adult, and it is very easy to check your 23andMe or other genetic data to see if you are likely to enjoy a big glass of milk.

Personally, I had always thought it a bit strange that my husband likes to drink a glass of milk with dinner. It just didn’t appeal to me — at all. I didn’t think ever think about lactose intolerance, though, because I still drink small amounts of milk in my coffee and on cereal. Turns out that I am one of those people who doesn’t produce lactase as an adult. I am relying on bacteria in my gut to break down lactose, so I naturally don’t drink much milk.

Lactose and Lactase:

Lactose, a sugar in milk, is broken down by the enzyme lactase which our bodies produce in the small intestines.

For some people, the production of the lactase enzyme stops when they become adults, driven by a genetic variation near the LCT gene. This means some adults are genetically predisposed to not be able to digest larger quantities of milk.

Population differences: The percentage of the population with genetic variations differs quite a bit among people with different backgrounds. Producing lactase as an adult is the most common genotype for Caucasian populations, while in Asian populations, the majority do not produce lactase as an adult. A theory for this occurrence seems to be an adaptation by Caucasian populations in Europe who relied on dairy products as a source of protein.

For people with European Caucasian ancestry, the main variant to look at is rs4988235. It is located in the MCM6 gene, which influences the LCT gene.  Approximately 90% of Caucasians will have A/A or A/G and still produce lactase to break down milk as an adult. In Asian populations, less than one percent will carry the G allele.

People with African ancestry may find that they carry a different variant (rs145946881) in the MCM6 gene that also causes lactase persistence as an adult.

Bacteria in the gut also break down lactose, so even those who don’t produce lactase can often handle digesting limited amounts of milk.

Genetic Variants for Lactose Intolerance:

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Check your genetic data for rs4988235 (23andMe v4, v5; AncestryDNA):

  • A/A: Still produces lactase as an adult
  • A/G: Still produces lactase as an adult, but less than those with A/A[ref]
  • G/G: No longer produces lactase as an adult

Members: Your genotype for rs4988235 is .


For people of African ancestry, a different variant of the MCM6 gene occurs in about 10-25% of the population and is associated with being able to produce lactase as an adult.

Check your genetic data for rs145946881 (AncestryDNA):

  • C/C: Still produces lactase as an adult[ref]
  • A/C: Still produces lactase as an adult
  • A/A: No longer produces lactase as an adult

Members: Your genotype for rs145946881 is .


Rare mutations: A very small number of people may also have a rare mutation (not covered by 23andMe or AncestryDNA) that causes the lactase gene not to function at all, even in childhood.


Probiotics to the rescue

Quite a few studies have looked at the effect of probiotics on lactose intolerance.  One study from May 2016 found that a specific strain of Lactobacillus acidophilus was significantly effective in reducing the symptoms of lactose intolerance.  There are many types of lactobacillus bacteria available as probiotics and in yogurt or other fermented foods. It is likely that some strains will be much more effective than others in reducing lactose intolerance symptoms for an individual, and it may be worthwhile to try several different types of Lactobacillus probiotics.

Lactase enzyme supplements:

In many countries, you can buy the lactase enzyme in health food stores and take it along with foods containing dairy. Lactose-free dairy products are also available.


Interestingly, a Dutch study showed that while the G/G genotype resulted in adults having a lower dietary calcium intake, it did not correspond to a lower bone density or more fractures.

Recap of your genes

Gene RS ID Risk Allele YOU Notes about the Risk Allele:
LCT rs4988235 G For GG only: no lactase produced as an adult (lactose intolerant)
MCM6 rs145946881 A For AA only: no lactase produced as an adult (African ancestry)


Related Genes and Topics:

Shining Genetic Light on Your Vitamin D Levels
Vitamin D is essential to so many processes in the body! It isn’t actually a vitamin at all, but a prohormone that is synthesized in the skin using cholesterol in a chemical reaction with UVB radiation from the sun. Most people think of vitamin D in regards to bone health because it regulates the uptake of calcium in our intestines, but it also acts in the nucleus of cells to regulate the production of hundreds of different enzymes, influencing health in a multitude of ways.

Do you carry the Hunter-Gatherer or the Farmer Genetic Variant?
Our ancient ancestors lived much differently than we do today. They were hunter-gatherers, living off of fish, meat, and plant foods that they gathered. A huge shift took place when those hunter-gatherers began farming, growing grains, and storing them so that there would be food available all year.

originally published 2/23/15, updated 2/2020

About the Author:
Debbie Moon is the founder of Genetic Lifehacks. Fascinated by the connections between genes, diet, and health, her goal is to help you understand how to apply genetics to your diet and lifestyle decisions. Debbie has a BS in engineering and an MSc in biological sciences from Clemson University. Debbie combines an engineering mindset with a biological systems approach to help you understand how genetic differences impact your optimal health.