Can your raw DNA file tell you if you are lactose intolerant?
Lactose intolerance is the example everyone reaches for when explaining consumer genetics, because the biology is unusually tidy: one well-understood gene, one famous marker, a clear story about dairy farming and human history.
It is also, for a large share of the world’s population, the clearest example of how a consumer DNA file can get something confidently wrong.
Which genetic marker is linked to lactose intolerance?
rs4988235, on chromosome 2. It sits in a neighbouring gene, MCM6, that regulates LCT — the gene for lactase, the enzyme that breaks down lactose. The ancestral pattern is for lactase production to decline after weaning; a variant here keeps it switched on into adulthood.
That switched-on state is called lactase persistence, and it is the exception rather than the rule in human history. Most adults on Earth produce little lactase. The populations where persistence is common are the ones with long histories of dairying, which is why the trait tracks agricultural history closely.
What do the genotypes at rs4988235 mean?
TT and CT are associated with lactase persistence — continued lactase production into adulthood. CC is associated with the ancestral pattern, where production declines after weaning. One copy of the T allele is generally enough, which is why CT groups with TT rather than sitting between the two.
In your raw file this appears as an ordinary row. Note the strand caution that applies to any manual lookup: depending on how a service reports orientation, the same marker may appear as A/G rather than T/C. The information is identical.
Some services label this “lactose tolerance” and some “lactase persistence”. They mean the same thing, and the second is the more accurate description of what the gene does.
Does this marker work for everyone?
No, and this is the important part. rs4988235 explains lactase persistence in European-descended populations. Several other populations evolved persistence independently through entirely different variants — including in East and West Africa and the Arabian Peninsula — and this marker says nothing about those.
So a person of, say, East African descent can be a lifelong comfortable milk drinker and read as CC at rs4988235. The marker is not wrong; it is answering a different question than the one being asked of it. Their persistence comes from a variant the array very likely does not carry.
This is the single best illustration of a limitation that runs through all consumer genetics. Arrays and the research behind them were built disproportionately around European reference data, and a confident-sounding result from a marker that does not apply to you is worse than no result at all.
Any service reporting this without saying which populations the marker covers is telling a large share of its customers something misleading in a confident voice.
Can the marker disagree with how you actually feel?
Routinely, in both directions. Lactase persistence is about enzyme production, not about symptoms, and several other things cause the same discomfort — irritable bowel syndrome, a milk protein sensitivity, a temporary drop in lactase after a gut infection, or simply the amount of dairy consumed at once.
It also runs the other way. Plenty of people who read as non-persistent tolerate yoghurt and hard cheeses perfectly well, because fermentation and ageing remove much of the lactose. Amount and form matter as much as enzyme status.
If dairy causes you real trouble, the useful next step is a clinician, who can look at the alternatives a marker cannot see. A line in a raw DNA file is not a diagnosis, and a genotype that disagrees with your lived experience does not overrule it.
Is this marker in your raw DNA file?
Almost certainly. rs4988235 is one of the most widely included positions on consumer arrays, so you can search your file for it and read the genotype yourself. Whether that reading means anything for you specifically depends on your ancestry, which is exactly the caveat most reports omit.
Which is the honest summary of this whole topic: the marker is real, the biology is well understood, and the result is only informative for some of the people who receive it. We report coverage alongside the reading for that reason.
How to find a marker in your own file → · What we look at for nutrition →