rs3135388

A SNP in the HLA-DRA gene on chromosome 6. Its most notable genotype is A;A: 3-6x higher risk of multiple sclerosis

Gene
HLA-DRA
Location
Chr 632,445,274 (GRCh38)
Highest magnitude
2.0Worth knowing
Tested on
23andMe, AncestryDNA
Minor allele frequency
6%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. G;GGoodnormalTypical · 0.091% of people
  2. A;GBad3x higher risk of multiple sclerosisMinor · 1.88% of people
  3. A;AMost notableBad3-6x higher risk of multiple sclerosisWorth knowing · 2.0<1% of people

SNPedia records rs3135388 on the minus strand: (C;C), (C;T), (T;T). Magnitude rates how notable a genotype is from 0 to 10, not how risky it is.

Frequency

Share of each genotype in 11 HapMap populations.

  • AverageG;G 91% A;G 8% A;A <1%
  • European ancestry (Utah)G;G 66% A;G 29% A;A 4%
  • Han Chinese (Beijing)G;G 96% A;G 4% A;A 0%
  • Japanese (Tokyo)G;G 100% A;G 0% A;A 0%
  • Yoruba (Nigeria)G;G 94% A;G 6% A;A 0%
  • African ancestry (Southwest US)G;G 93% A;G 7% A;A 0%
  • Chinese (Denver)G;G 99% A;G <1% A;A 0%
  • Gujarati IndianG;G 96% A;G 4% A;A 0%
  • Luhya (Kenya)G;G 93% A;G 7% A;A 0%
  • Mexican ancestry (Los Angeles)G;G 88% A;G 12% A;A 0%
  • Maasai (Kenya)G;G 96% A;G 5% A;A 0%
  • TuscanG;G 84% A;G 15% A;A 1%

Conditions, medicines and genes

Other HLA-DRA SNPs

All HLA-DRA SNPs

Notes

From SNPedia

Show notes, about 260 words

rs3135388(T) is highly (> 99%) correlated with the HLA-DRB1*1501 allele; the risk allele (T) is associated with a 3 to 6 fold higher risk for developing multiple sclerosis. The risk per allele (or per haplotype) appears additive. It has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and, when linked with DQB1*0602, narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. Note: most publications refer to the risk allele as rs3135388(A), but in dbSNP and SNPedia orientation, it is rs3135388(T). An interesting series of correlations have been woven together to suggest that a possible way to lower the risk of rs3135388(T) carriers developing multiple sclerosis would be to ensure sufficient vitamin D production, presumably through sunlight exposure, during as yet unknown critical periods in development. Association between rs3135388(T) allele and multiple sclerosis also seen in 269 Serbian patients, with an odds ratio of 2 for (T) allele carriers.

G;G

Rs3135388(C;C) is highly correlated with the HLA-DRB1*1501 allele. There is no additional risk of multiple sclerosis associated with the (C;C) genotype.

A;G

Rs3135388(C;T) is highly correlated with the HLA-DRB1*1501 allele. There is a 3x higher risk of multiple sclerosis associated with the (C;T) genotype.

A;A

Rs3135388(T;T) is highly correlated with the HLA-DRB1*1501 allele. There is 3-6x higher risk of multiple sclerosis associated with the (T;T) genotype.

Source and license

Adapted from rs3135388 on SNPedia, using a snapshot taken October 16, 2026. SNPedia content is shared under CC BY-NC-SA 3.0 US, and this page is shared under the same license.

SNPedia is a community-edited wiki. Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice. Magnitude is a community rating of how interesting a genotype is, not a risk score.