rs41380347

goodMag 5.5

This is a intron variant variant in the MCM6 gene.

Key Literature Trait Associations

Lactase Persistence

The G allele at rs41380347 (-13915*G) in the MCM6 intron 13 enhancer region is the primary genetic determinant of lactase persistence in Arab and Middle Eastern populations. Functional assays demonstrated that the -13915*G variant increases enhancer activity driving LCT transcription 4-fold higher than the ancestral T allele. The variant was found at high frequency (>50%) in Saudi Arabian and Bedouin populations (N=1,671 across multiple Middle Eastern and African groups) with complete correlation with lactase persistence phenotype.

Tishkoff SA et al. “Convergent adaptation of human lactase persistence in Africa and Europe.” Nature Genetics (2007)

Allele G

OR —

p —

N 470

Candidate gene study

East African (Tanzanian, Kenyan, Sudanese)

Brass AL et al. “Identification of host proteins required for HIV infection through a functional genomic screen.” Science (new York, N.y.) 319(5865):921-926 (2008)

Allele G

OR —

p 1.0e-10

Large GWAS

Imtiaz F et al. “The T/G 13915 variant upstream of the lactase gene (LCT) is the founder allele of lactase persistence in an urban Saudi population.” Journal of Medical Genetics (2007)

Allele G

OR —

p 1.0e-3

N 432

Candidate gene study

Saudi Arabian

Jones BL et al. “Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep.” American Journal of Human Genetics (2013)

Allele G

OR —

p 3.2e-5

N 422

Candidate gene study

Ethiopian

Anke Liebert et al. “World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection” Human Genetics (2017)

Allele G

OR —

p —

Candidate gene study

multi-ancestry (global)

Alkaraki AK et al. “Lactase persistence in the Jordanian population: Potential effects of the Arabian Peninsula and Sahara's aridification.” Heliyon (2024)

Allele G

OR —

p —

Candidate gene study

Jordanian (Bedouin, farmer, urban)

Lynne C. Olds et al. “−13915*G DNA polymorphism associated with lactase persistence in Africa interacts with Oct-1” Human Genetics (2011)

Allele G

OR —

p —

Candidate gene study

in vitro (cell culture)

Al-Abri AR et al. “Distribution of the lactase persistence-associated variant alleles -13910* T and -13915* G among the people of Oman and Yemen.” Human Biology (2012)

Allele G

OR —

p —

Candidate gene study

Omani and Yemeni Arab

Hassan HY et al. “Genetic diversity of lactase persistence in East African populations.” Bmc Research Notes (2016)

Allele G

OR —

p —

Candidate gene study

East African (12 populations)

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ClinVar annotation

Association

1 submitter4 publications

LACTASE PERSISTENCE

View on ClinVar →

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Research that mentions this SNP (1)

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World-wide distributions of lactase persistence alleles and the complex effects of recombination and selection

AssociationN=2,056Anke Liebert et al.(2017)· Human Genetics

This study examined the worldwide distribution and haplotype structure of five lactase persistence (LP)-associated variants (rs4988235, rs41525747, rs41380347, rs869051967, rs145946881) in the LCT/MCM6 region across 2056 individuals from 52 populations. The research confirmed extended haplotype homozygosity (EHH) for LP alleles consistent with positive selection, but revealed that one ancient ancestral B haplotype also shows marked EHH despite lacking functional LP variants. This extended EHH of the B haplotype corresponds exactly to a region of suppressed recombination, suggesting that recombination patterns rather than selection alone explain some haplotype signatures in this region.

rs41380347

Key Literature Trait Associations

Lactase Persistence

ClinVar annotation

Research that mentions this SNP (1)

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