HLA-DQ2 : distribution map, subtypes, SNPs, and associated medical conditions


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Here is a map showing the allele frequency of HLA-DQ2. The world's highest frequencies are observed among the Sardinians (59%), the Basques (48%), the Brahui and Balochi of Pakistan (40%), the Moroccans (35%) and the Saudis (35%).



HLA-DQ2 comprises two subtypes DQB1*0201 and DQB1*0202, each divided in about a dozen subclades.

DQB1*0201 has the widest distribution, being found throughout Europe, Siberia, Mongolia, Iran, Saudi Arabia and North Africa. It is the only variant found in northern Europe as well as in Sardinia (all of the 59%).

DQB1*0202 is found in North Africa, southern and western Europe, as well as the Middle East and India. It is absent from northern and eastern Europe, as well as Siberia and Mongolia.

Medical associations

HLA-DQ2 is associated to many autoimmune conditions, but especially Coeliac disease (gluten allergy). 95% of all people with coeliac have HLA-DQ2. Having two copies of DQ2 confer a lifelong risk between 20 and 40% for coeliac disease. Even DQ2 people who do not get coeliac disease have a higher chance of being gluten intolerant. HLA-DQ2 and DQ8 are two of the main risk factors for both gluten intolerance and coeliac.

Unfortunately DQ2 is also one of the most common HLA-DQ type in Eurasia and North Africa. The lowest frequencies in Europe are found among the Saami, the Albanians and the Kosovars.

Other diseases have been linked to DQB1*0201 in association with the allele DQA1*0501. Together these two HLA-DQ form a heterodimer and are known as haplotype DQ2.5. This combination is a risk factor for dermatitis herpetiformis, juvenile diabetes, Lambert-Eaton myasthenic syndrome (LEMS), Sjögren's syndrome, autoimmune hepatitis, Grave's disease and systemic lupus erythematosus (SLE).

The combination of DQA1*0201 and DQB1*0202 defines haplotype DQ2.2, and is found mostly in Mediterranean countries and West Africa, reaching a maximum frequency of about 30% in northern Iberia (and 15% in the British Isles). This haplotype is also associated with a higher risk for coeliac disease.


The SNP's encoding DQB1*0201 are:

- rs2858333 (G means carrier)
- rs4988889 (African subclade, T means carrier - only tested by 23andMe v3)
- rs7745002 (not tested by 23andMe or FTDNA)

I don't know the SNP for DQB1*0202.

Rs2187668 (risk = A) tag SNP for haplotype DQ2.5. It is tested by all versions of 23andMe.

Rs2395182 (risk = G), rs7775228 (risk = C), and rs4713586 (risk = C) create a haplotype tag for DQ2.2. They are tested by 23andMe (except rs4713586) and FTDNA's Family Finder.

Link to prehistoric populations

I have checked 12 ancient genomes from Haak et al 2015, and three of them carried the DQB1*0201 allele(only rs2858333 was tested). They were the Neolithic samples from Alberstedt and Halberstadt, and one Yamna sample (who was homozygous GG).

Three genomes were also positive for haplotype DQ2.5 : Mesolithic Karelia, Neolithic Spain and Neolithic Halberstadt.

As for haplotype DQ2.2, nine out of 12 genomes were positive, including one homozygous (Unetice). The only negative ones were the two Yamna and one LBK. It's not surprising that the Yamna were negative considering that DQ2.2 is virtually absent from eastern and northern Europe today. It is far more surprising that the Mesolithic Karelia and Samara samples carried this allele.
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Interesting, pity 23andMe does not test for all those SNPs. rs2858333 AG, DQB1*0201 carrier, have the CC version for DQ2.5, and have two of the three SNPs listed for DQ2.2

I am quite well.
I find it very odd that a place like Sardinia, with all its Anatolian farmer ancestry, people who invented the farming of cereals, and consumed them for the longest period, should carry a variant for Celiac disease. Perhaps it's their large percentage of WHG?

I don't carry any of the "bad" variants, thank goodness. The older I get the less I like meat, or rather the less meat agrees with me, especially pork products, which I used to love. I'm starting to live on fruits, vegetables, legumes, and things made from grains, like oatmeal, bread, pasta.

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