rs4988235 — LCT -13910C>T

LCT - Lactase Persistence and Dairy Tolerance

The ability to digest lactose (milk sugar) in adulthood is one of the most well-known examples of recent human evolution. Most mammals, including most humans historically, lose the ability to produce lactase enzyme after weaning. But populations that domesticated dairy cattle independently evolved mutations that keep the LCT gene active into adulthood.

The Mechanism

The rs4988235 variant is located upstream of the LCT gene in an enhancer element ¹¹ An enhancer is a distant regulatory DNA sequence that can increase a gene's expression even from thousands of base pairs away within the MCM6 gene on chromosome 2. The A allele (T on the coding strand, hence the "-13910C>T" name) maintains LCT gene expression throughout life by keeping the enhancer active. The G allele (ancestral C) allows the enhancer to be silenced after early childhood, leading to progressive loss of lactase production.

Evolutionary History

Lactase persistence evolved independently at least five times in human history, in pastoral populations across Europe, East Africa, the Arabian Peninsula, and Central Asia. The European variant (rs4988235) arose approximately 7,500 years ago and spread rapidly through the population, representing one of the strongest known examples of positive selection²² strongest known examples of positive selection
Bersaglieri T et al. Genetic Signatures of Strong Recent Positive Selection at the Lactase Gene. Am J Hum Genet, 2004 in the human genome ³³ Positive selection means carriers had a survival or reproductive advantage, causing the variant to increase rapidly in frequency - likely because dairy provided a reliable, calorie-dense food source and a safe alternative to potentially contaminated water.

Dramatic Population Differences

The frequency of the persistence allele (A) varies enormously by ancestry: 57% in Europeans (where dairy farming originated), but only 0.3% in East Asians, 12% in Africans, and 15% in South Asians. This makes rs4988235 one of the most population-stratified variants in the human genome. In Northern Europe specifically, the frequency reaches 70-90%, while in parts of East Asia it is virtually absent.

Lactose Intolerance in Practice

About 65-70% of the global adult population is lactose non-persistent (GG genotype), though this varies enormously by ancestry. Symptoms of lactose intolerance (bloating, gas, cramps, diarrhea) typically appear 30 minutes to 2 hours after consuming lactose-containing foods.

Living with Lactose Non-Persistence

If you are GG, you are not necessarily completely intolerant. ⁴⁴ Colonic bacteria can partially ferment undigested lactose, and tolerance often depends on dose, gut transit time, and microbiome composition Many lactose non-persistent individuals can tolerate small amounts of lactose, fermented dairy (yogurt, kefir), and aged hard cheeses (which have very little lactose). Lactase enzyme supplements taken before dairy consumption can also help. The severity of intolerance varies widely between individuals.