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From SNPedia

Geno Mag Summary
(C;C) 2.5 likely to be lactose intolerant as an adult
(C;T) 1.1 likely to be able to digest milk as an adult
(T;T) 1.1 can digest milk
ReferenceGRCh38 38.1/141
is asnp
is mentioned by
dbSNP (classic)rs4988235
1000 genomesrs4988235
GWAS Ctlgrs4988235
Max Magnitude2.5
? (C;C) (C;T) (T;T) 28

Also known as "C/T(-13910)" or just 13910T, and located in the MCM6 gene but with influence on the lactase LCT gene, rs4988235 is one of two SNPs that is associated with the primary haplotype associated with hypolactasia, more commonly known as lactose intolerance in European populations. [PMID 11788828], [PMID 15114531OA-icon.png]

In these populations, the rs4988235(T) allele is both the more common allele and the one associated with lactase persistence; individuals who are rs4988235(C;C) are likely to be lactose intolerant.

Note that while lactose intolerance is usually reported only for rs4988235(C;C) homozygotes, at least one publication finds that lactase enzyme activity actually forms a continuum across the three rs4988235 genotypes, being lowest in C/C homozygotes, intermediate in T/C heterozygotes, and highest in T/T homozygotes. It is therefore likely the heterozygotes may also experience symptoms of lactose intolerance at times (depending on age and amount of lactose).[PMID 25625576OA-icon.png]

In populations of sub-Saharan Africans, though, the rs4988235(T) allele is so rare that it's unlikely to be predictive of lactase persistence, and other SNPs are predictive instead. [PMID 15106124, PMID 17159977]

[PMID 20225268] The T-13910C polymorphism in the lactase phlorizin hydrolase gene is associated with differences in serum calcium levels and calcium intake

[PMID 20447925OA-icon.png] Can lactase persistence genotype be used to reassess the relationship between renal cell carcinoma and milk drinking? Potentials and problems in the application of Mendelian randomization

[PMID 22572735] Lactase persistence may have an independent origin in Tibetan populations from Tibet, China

[PMID 17436249OA-icon.png] Measuring European population stratification with microarray genotype data.

[PMID 18194137] Adult-type hypolactasia is not a predisposing factor for the early functional and structural changes of atherosclerosis: the Cardiovascular Risk in Young Finns Study.

[PMID 18462498OA-icon.png] Genetic polymorphisms in PTPN22, PADI-4, and CTLA-4 and risk for rheumatoid arthritis in two longitudinal cohort studies: evidence of gene-environment interactions with heavy cigarette smoking.

[PMID 18602983OA-icon.png] Heterogeneity in gene loci associated with type 2 diabetes on human chromosome 20q13.1.

[PMID 18605960] Genetic testing for adult-type hypolactasia in Italian families.

[PMID 18797476OA-icon.png] Lactase persistence-related genetic variant: population substructure and health outcomes.

[PMID 18974842OA-icon.png] Gender differences in genetic risk profiles for cardiovascular disease.

[PMID 19138442] Genetic lactase non-persistence, consumption of milk products and intakes of milk nutrients in Finns from childhood to young adulthood.

[PMID 19265028OA-icon.png] Geographical structure and differential natural selection among North European populations.

[PMID 19326473OA-icon.png] Natriuretic peptide system gene variants are associated with ventricular dysfunction after coronary artery bypass grafting.

[PMID 19687126OA-icon.png] A non-synonymous variant in ADH1B is strongly associated with prenatal alcohol use in a European sample of pregnant women.

[PMID 19943975OA-icon.png] Polymorphism in the oxytocin promoter region in patients with lactase non-persistence is not related to symptoms.

[PMID 20015952OA-icon.png] European lactase persistence genotype shows evidence of association with increase in body mass index.

[PMID 20031626OA-icon.png] Variation in the 4q25 chromosomal locus predicts atrial fibrillation after coronary artery bypass graft surgery.

[PMID 20109229OA-icon.png] Haplotype allelic classes for detecting ongoing positive selection.

[PMID 20616999OA-icon.png] Usefulness of Mendelian randomization in observational epidemiology.

[PMID 21152447] Adult-type hypolactasia and lactose malabsorption in Poland.

[PMID 21193851OA-icon.png] Association of the LCT-13910C>T polymorphism with obesity and its modulation by dairy products in a Mediterranean population.

[PMID 21235777OA-icon.png] Lactase persistence genotypes and malaria susceptibility in Fulani of Mali.

[PMID 22965418OA-icon.png] Genetic variation in the lactase gene, dairy product intake and risk for prostate cancer in the European prospective investigation into cancer and nutrition

[PMID 23252911] The lactase persistence -13910C>T polymorphism shows indication of association with abdominal obesity among Portuguese children.

[PMID 22948027OA-icon.png] Stronger signal of recent selection for lactase persistence in Maasai than in Europeans.

[PMID 23028602OA-icon.png] Lactase persistence and lipid pathway selection in the Maasai.

[PMID 23029545OA-icon.png] Several different lactase persistence associated alleles and high diversity of the lactase gene in the admixed Brazilian population.

[PMID 23479116OA-icon.png] Associations of the lactase persistence allele and lactose intake with body composition among multiethnic children.

[PMID 23647908] The lactase persistence genotype is associated with body mass index and dairy consumption in the D.E.S.I.R. study.

[PMID 25505833OA-icon.png] The lactase persistence genotype is a protective factor for the metabolic syndrome

Risk rs4988235(G;G) Rs4988235(T;T)
Alt rs4988235(G;G) Rs4988235(T;T)
Reference Rs4988235(C;C)
Significance Other
Disease Lactase persistence
Variation info
Gene MCM6
CLNDBN Lactase persistence
Reversed 1
HGVS NC_000002.11:g.136608646G>A
CLNSRC OMIM Allelic Variant
CLNACC RCV000008124.2,

[PMID 29063188OA-icon.png] World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection.

[PMID 30728219OA-icon.png] Dairy Product Intake and Risk of Type 2 Diabetes in EPIC-InterAct: A Mendelian Randomization Study.