rs3135391

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

Gene
HLA-DRA
Location
Chr 632,443,210 (GRCh38)
Highest magnitude
3.0Important
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
7%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. G;GGoodnormalTypical · 0.091% of people
  2. A;GBadHLA-DRB1*1501 carrier; higher multiple sclerosis riskWorth knowing · 2.09% of people
  3. A;AMost notableBad3 to 6 fold higher risk for multiple sclerosisImportant · 3.0<1% of people

SNPedia records rs3135391 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 9% 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 93% A;G 7% A;A 0%
  • African ancestry (Southwest US)G;G 88% A;G 12% 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 94% A;G 6% 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 280 words

rs3135391 is highly 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, and is the most significantly associated risk factor for MS. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892470/ PMC2892470 In one study, for example, the odds ratio was reported to be 3.04 (p < 1 x 10e-78). The HLA-DRB1*1501 allele has also been associated with other autoimmune diseases, such as systemic lupus erythematosis (SLE) (see) and possibly narcolepsy. The HLA-DRB1*1501 allele is fairly common; for example, it occurs in 15-30% of individuals of Northern European ancestry. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892470/ PMC2892470 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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892470/ PMC2892470 A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01.

G;G

Rs3135391(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

Rs3135391(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

Rs3135391(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 rs3135391 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.