Lactose Intolerance: The genetics of not producing lactase

Are you a milk drinker? Does pouring a cold glass of milk sounds good? Your genes control whether you are likely to produce lactase as an adult, and it is 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 don’t go overboard on drinking milk.

Getting into the science:
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 an adult, driven by a genetic variation near the LCT gene. This means that some adults are genetically predisposed to not be able to digest larger quantities of milk.

The percentage of the population with the 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. This is thought to be an adaptation by Caucasian populations in Europe who relied on dairy products as a source of protein.

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

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

Genes Involved in Lactose Production

If your genotype is GG on rs4988235, you will not produce lactase and will probably not be able to handle larger quantities of milk as an adult. From talking with other people about this, it seems that those with GG naturally limit their intake of milk.

Check your 23andMe results for rs4988235 (v.4, v.5 of 23andMe; AncestryDNA):
AA: Still produces lactase as an adult
AG: Still produces lactase as an adult (probably less than those with AA – study)
GG: No longer produces lactase as an adult

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

For people of African origin, a different variant of the MCM6 gene is found in about 10-15% of the population and is associated with being able to produce lactase as an adult.

Check your 23andMe results for rs145946881 (v.4, v.5 of 23andMe; AncestryDNA):
CC: Still produces lactase as an adult [study]
AC: Still produces lactase as an adult
AA: No longer produces lactase as an adult

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.

If you are interested in digging deeper into the types and numbers of lactose-consuming bacteria in your gut, you could do a microbiome test from uBiome or another company.

More to read:


originally published 2/23/15, updated 10/17

8 Replies to “Lactose Intolerance: The genetics of not producing lactase”

    1. Hi Luigi,
      I’m not sure how your 23andMe data for rs2988235 has CC. I just double checked and the only two options with 23andMe are A and G.

      Are you perhaps using genetics data from a different source? 23andMe only reports on the forward or plus DNA strand orientation. My articles that link to 23andMe also give the data in that orientation, but if you look at studies or on dbSNP, you will find that for rs2988235 it is usually given in the reverse or minus strand orientation (thus giving a C or T as an option).

  1. Hello Debbie thanks for your help. I solved the mistery I was reading the data through Promethease. 23andMe for some reason still uses GRCh37 and not GRCh38 so the alleles need to be flipped and the CC becomes GG. I do not know why they do not update it.

    1. Glad you are able to figure out the difference here.
      Actually, the different reference genome (GRCh37 vs. GRCh38) isn’t what causes the allele to need to be flipped here. It is defined on the minus strand for both reference genomes. The need to ‘flip’ the alleles is due to 23andMe (AncestryDNA, as well as anyone else doing the same type of ) always using the plus strand while the SNP is defined relative to the minus strand.
      The different reference genomes will come into play if you download the 23andMe raw data file and look at the position along the chromosome. That will be different for GRCh37 vs. GRCh38.
      Thanks for your comment.

  2. Sorry Dabbie I do not understand. So what should I do to correct the errors that can appear in your reports compared to 23andMe?

    1. There is no error in the article. If you click the link in the article to go to 23andMe, it matches to the data as listed on 23andMe. You said that you are using your Promethease report instead. Promethease switches the 23andMe data to match their reporting.
      In general, whether you are looking at research studies, Promethease, or other sources, if you need to convert from the forward strand (23andMe orientation) to the reverse strand, just remember that C=G and T=A.

  3. Just curious if ancestry dna results can be used. I haven’t used 23 and me and would like to use the data I already have.

    1. Hi Cheryl,
      Yes, you can use AncestryDNA for the lactose genes. There isn’t a way to look up your gene information on the website, though. You will need to download the raw data file. Then you could try opening it as a text file and do a ‘find’ for the rs id number, or you can import it into Excel and search for it there. Here is how to download the file from and import it into Excel:
      Hope this helps!

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