LCT rs4988744: Understanding Lactase Persistence Genetics
The rs4988744 variant, often referred to as -13910C>T, is a well-studied genetic marker located in the MCM6 gene that regulates the expression of the neighboring LCT gene. It is strongly associated with lactase persistence, the biological trait that allows adults to continue digesting lactose, the primary sugar found in milk.
What each genotype means
Lactose maldigestion
This genotype is associated with the absence of the lactase-persistence allele, which typically results in a decline in lactase enzyme activity after childhood. Individuals with this genotype may experience symptoms of lactose intolerance after consuming dairy products, though this can vary significantly between individuals.
This is the most common genotype in many global populations, particularly those with low historical reliance on dairy, though it is less common in populations of Northern European descent.
Lactase persistence
This heterozygous genotype is associated with the lactase-persistence phenotype, where the ability to digest lactose continues into adulthood. Because this trait is inherited in a dominant manner, carrying one copy of the T allele is generally sufficient to maintain lactase activity.
This genotype is frequently observed in populations with a long history of pastoralism and dairy consumption, particularly in Europe.
Lactase persistence
This homozygous genotype is strongly associated with the ability to digest lactose into adulthood. Individuals with this genotype maintain high levels of intestinal lactase activity, allowing for the efficient digestion of lactose found in dairy products.
This genotype is common in populations of Northern European ancestry and is found at varying frequencies in other groups with a history of dairy consumption.
What is rs4988744 and Where is it Located?
The variant rs4988744 is a single nucleotide polymorphism (SNP) situated approximately 13,910 base pairs upstream of the LCT gene transcription start site. While it is physically located within the 13th intron of the MCM6 gene, its primary biological function is to act as an enhancer for the LCT gene. This region serves as a regulatory switch that determines whether the body continues to produce the enzyme lactase after the weaning period. In many human populations, the production of lactase naturally declines after childhood, leading to lactose maldigestion. However, specific variants in this regulatory region, including rs4988744, can keep the LCT gene 'switched on' into adulthood. Because this variant is located in a non-coding regulatory region rather than the LCT gene itself, it is a classic example of how genetic changes outside of a protein-coding sequence can have profound effects on human physiology and metabolic traits.
The Role of the LCT Gene
The LCT gene provides the instructions for creating the enzyme lactase. Lactase is essential for breaking down lactose, a complex sugar found in dairy products, into simpler sugars like glucose and galactose that the body can easily absorb. During infancy, almost all humans produce high levels of lactase to digest breast milk. In the majority of the global population, the expression of the LCT gene decreases significantly after weaning, a condition known as lactase non-persistence. When individuals with low lactase levels consume dairy, the undigested lactose passes into the colon, where it is fermented by gut bacteria, potentially causing symptoms like bloating, gas, and diarrhea. The rs4988744 variant is a key genetic factor that influences the transcriptional regulation of LCT, effectively maintaining the enzyme's production in adulthood for those who carry the T allele.
Research Associations and Evidence Strength
The association between rs4988744 and lactase persistence is well-documented, particularly in populations of European descent. Research indicates that the T allele acts in a dominant fashion, meaning that inheriting at least one copy is typically sufficient to maintain lactase activity into adulthood. While the evidence for this variant's role in European populations is robust, it is important to note that it does not account for all cases of lactase persistence worldwide. Other genetic variants have been identified in African, Middle Eastern, and Southern Asian populations that also confer the ability to digest lactose. Therefore, while rs4988744 is a primary marker in some groups, it is not a universal predictor of lactose digestion across all global ancestries. Genetic testing for this variant can provide insight into the biological likelihood of lactase persistence, but it is not a substitute for clinical diagnostic tests, such as a hydrogen breath test, which measure actual physiological response to lactose.
Population Frequency and Global Distribution
The frequency of the rs4988744 T allele varies significantly across different human populations, reflecting a history of gene-culture co-evolution. This variant is highly prevalent in Northern European populations, where the historical practice of dairying provided a selective advantage to those who could digest milk. In contrast, the T allele is rare or absent in many other parts of the world, including large portions of East Asia, sub-Saharan Africa, and the Americas. In these regions, lactase non-persistence is the ancestral and most common state. Because of this uneven distribution, the predictive value of rs4988744 depends heavily on an individual's ancestral background. Researchers continue to study these patterns to better understand how human diets and genetic adaptations have shaped our metabolic health over the last 10,000 years.
What You Can and Cannot Do With This Information
Understanding your genotype for rs4988744 can offer a glimpse into your genetic predisposition for lactase persistence. If you are curious about your own status, this information can help explain why you might or might not experience digestive discomfort after consuming dairy. However, it is crucial to remember that genetics is not destiny. Many factors, including the composition of your gut microbiome and the amount of lactose consumed, influence how you feel after eating dairy. This information should not be used to self-diagnose medical conditions or to make significant changes to your diet without consulting a healthcare professional. If you are experiencing persistent digestive issues, please speak with a doctor or a registered dietitian. They can help you determine if your symptoms are related to lactose intolerance or another underlying health issue, ensuring you receive appropriate guidance tailored to your specific needs.
How common is this variant?
The frequency of the rs4988744 T allele is high in Northern European populations but varies significantly across other global ancestries, where it is often rare or absent.
Frequently asked questions
Is rs4988744 the only gene for lactose intolerance?
No, rs4988744 is just one of several genetic markers associated with lactase persistence. Other variants in the LCT and MCM6 region, as well as factors like gut health, also play a role.
Can I be lactose intolerant even if I have the T allele?
Yes, genetics is only one factor. Other issues like small intestinal bacterial overgrowth or temporary gut inflammation can cause symptoms that mimic lactose intolerance regardless of your genotype.
Does this variant tell me if I have a milk allergy?
No, lactose intolerance is a digestive issue involving the enzyme lactase, while a milk allergy is an immune system reaction to milk proteins. These are two completely different conditions.
Should I get a genetic test for this SNP?
Genetic testing for rs4988744 is available, but it is not necessary for most people. If you have concerns about your digestion, a clinical evaluation by a doctor is more informative than a genetic test alone.
Sources & further reading
Educational information only, last refreshed 9/15/2026. Not medical advice — these associations describe population statistics, not individual predictions.
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Rare variant in the lactase persistence locus marking archaic Eurasian and pastoralist ancestral haplotype variation.
Functional enhancer polymorphism situated upstream of the lactase promoter associated with adult-type lactase persistence in pastoralist populations of Sub-Saharan Africa.
This variant near the LCT gene determines whether you keep producing lactase into adulthood. The genotype associated with lactase persistence means you likely tolerate dairy well.