HLA-A3: distribution map, subtypes, SNPs and associated medical conditions


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Here is a map showing the allele frequency of HLA-A3, which is divided in two subtypes : A3:01 and A3:02. The former is mostly found in Europe, with lower frequencies across the Middle East, Central Asia (Uygurs), India and even isolated parts of Africa (Cameroon). The latter peaks in Georgia and is found mostly in the Middle East, North Africa and South Asia.

The relatively high frequency of A3 in Andalusia, Turkey, Israel, Georgia and Armenia results from the cumulative presence of A3:01 and A3:02 alleles.

The world's highest frequencies of HLA-A3*01 are observed among the Saami (25-30%) of northern Norway and Sweden and the Finns (25%), followed by the Northwest Russians, Scandinavians, Germans, Belgians, East English, but also Czechs, Austrians, Slovenes, Croatians and Bosnians.

Overall the distribution of A3:01 appears to correspond fairly well with the proportion of Mesolithic European, and particularly Nordic/Germanic ancestry. It correlates relatively well with the distribution of Y-DNA haplogroups I1 and I2a2, and I2a1b in the Dinaric Alps.


Medical conditions

HLA-A3 is a secondary risk factor for myasthenia gravis and lower CD8+ levels in hemochromatosis patients.


You can verify if you carry the HLA-A3 type by checking the SNP's rs9380122 (G means carrier). It is tested by 23andMe and FTDNA's FamilyFinder.

Link to prehistoric populations

I have checked these SNP's in over 50 prehistoric genomes from the Palaeolithic to the Iron Age. HLA-A3 was positive in the following genomes:

- Palaeolithic Kostenki from southern Russia (homozygous GG).

- Alberstedt genome from Neolithic Germany. This is probably a sign that Neolithic farmers in the region had mixed with the indigenous Mesolithic population related to Y-haplogroup I1 (as indeed I1 has been found in the LBK culture).

However this SNP was missing from many genomes, including all those from Scandinavia.
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