Is lactose intolerance genetic?

Genetic guide · Updated June 2026

23andMe & raw DNA

The genetics: one switch, the LCT gene

As babies, we all make lactase — the enzyme that breaks down lactose, the sugar in milk. The lactase enzyme is produced by the LCT gene. In most mammals, lactase production switches off after weaning.

In humans, whether it stays on is controlled by a variant just upstream of LCT, in the neighbouring MCM6 gene: rs4988235 (also written as the -13910 C/T variant).

• A T allele keeps lactase switched on for life → lactase persistence (you tolerate lactose).
• Two C alleles (CC) → lactase production declines after childhood → lactase non-persistence (primary lactose intolerance).

It's essentially a one-variant trait, which is why it's one of the clearest genotype-to-trait links in all of consumer genetics.

Primary vs secondary: not all lactose intolerance is genetic

This matters: the gene explains primary lactose intolerance — the gradual, lifelong kind driven by your DNA. There's also secondary lactose intolerance, caused by temporary damage to the gut lining (after a stomach bug, from coeliac disease, etc.). Secondary intolerance is not genetic and often resolves once the gut heals. So a "tolerant" genotype doesn't rule out a temporary bout.

Why it varies so much by ancestry

The lactase-persistence variant is a famous example of recent human evolution. It spread in populations with a long history of dairy farming — so persistence is common in Northern Europeans and some African and Middle Eastern pastoralist groups, and much rarer in East Asian populations, where lactose intolerance is simply the norm. None of it is "abnormal" — it's just which ancestral diet your genes are tuned for.

How to check your lactose gene

1. Download your raw data (or from AncestryDNA / MyHeritage).
2. Search it for rs4988235 and read your genotype — a T means likely tolerant, CC means likely non-persistent.
3. Or use our free DNA explorer — it checks this marker in your browser, nothing uploaded.

One caveat: strand orientation varies between files, so the letters may appear as A/G instead of T/C — good tools handle that automatically.

The bottom line

Primary lactose intolerance is genetic and comes down to one variant near LCT — but symptoms also depend on dose, gut health, and the secondary (non-genetic) kind. Knowing your genotype explains the tendency, not the whole story. For everything else hiding in your file, see our guide to analyzing 23andMe raw data, or browse the rest of the Quanome blog.

Frequently asked questions

Is lactose intolerance genetic?

For most adults, yes — 'primary' lactose intolerance is determined by a variant near the LCT gene (rs4988235) that controls whether you keep producing lactase into adulthood. 'Secondary' lactose intolerance, caused by temporary gut damage from illness, is not genetic.

Which gene causes lactose intolerance?

The lactase enzyme is made by the LCT gene, but the on/off switch is a variant in the nearby MCM6 gene — rs4988235 (also called -13910 C/T). The T allele keeps lactase active (lactose tolerance); two C alleles mean lactase declines after childhood (intolerance).

How do I check my lactose-intolerance gene in raw DNA?

Search your 23andMe or AncestryDNA raw file for rs4988235 and read your genotype, or use a tool that looks it up. Carrying a T allele is associated with lactase persistence; CC is associated with non-persistence.

Why is lactose tolerance more common in some populations?

The lactase-persistence variant spread in populations with a long history of dairying — it's common in Northern Europeans and some African and Middle Eastern groups, and much rarer in East Asian populations, where lactose intolerance is the norm.