Gene Number: 3938

Location: 2q21.3

Key Functions: Lactose digestion, intestinal nutrient absorption, gastrointestinal health, evolutionary adaptation

LCT (lactase) encodes the enzyme lactase–phlorizin hydrolase (LPH), which is found on the surface of cells lining the small intestine. Its primary job is to break down lactose, the main sugar in milk, into the simpler sugars glucose and galactose, which the body can absorb and use for energy. This function is especially vital during infancy, when milk is the primary source of nutrition.

In most mammals—and in many humans—lactase activity declines after weaning, a normal process known as lactase non-persistence. When lactase levels drop, undigested lactose passes into the colon, where bacteria ferment it, producing gas and leading to the familiar symptoms of lactose intolerance such as bloating, cramping, and diarrhea. However, some people continue to produce lactase into adulthood—a trait called lactase persistence—thanks to genetic changes that keep the LCT gene switched on.

This persistence is controlled not by LCT itself, but by regulatory variants in a nearby gene, MCM6, which acts as an enhancer of LCT expression. The most studied variant, −13910C>T (rs4988235), is common in Northern Europeans and allows continued lactase production throughout life. Other populations, such as some East African and Middle Eastern pastoralist groups, have developed different mutations that serve the same purpose—making lactase persistence one of the best examples of gene–culture coevolution in humans.

The trait likely evolved because dairy provided a valuable source of calories, hydration, and calcium in early agricultural societies. Populations that relied heavily on milk as a staple food had a clear evolutionary advantage if they could digest lactose, leading to strong positive selection for these mutations. Today, lactose intolerance remains the global norm, affecting up to 90% of adults in East Asia and much of Africa, but only around 5–10% in Northern Europe.

Modern research also shows that LCT variants can shape the gut microbiome. People with lower lactase activity often harbor more lactose-fermenting bacteria, such as Bifidobacterium, which can partially compensate for reduced enzyme activity. This dynamic illustrates how genetics and the microbiome interact to influence digestion and overall gut health.

In rare cases, congenital lactase deficiency occurs due to mutations in LCT itself, leading to severe lactose intolerance from birth. More commonly, lactase deficiency is secondary, resulting from intestinal injury, infection, or inflammation that damages the intestinal lining.

In summary, LCT is a fascinating example of how human genetics, diet, and evolution are intertwined. Whether one enjoys milk freely or avoids it, the story of LCT reflects a remarkable chapter in human adaptation—showing how our genes have evolved alongside our cultural practices to shape the way we eat, digest, and live.