rs419788

A SNP in the NELFE gene on chromosome 6. Its most notable genotype is T;T: 2.3x risk for lupus

Gene
NELFE
Location
Chr 631,961,022 (GRCh38)
Highest magnitude
1.5Minor
Tested on
23andMe, AncestryDNA, FamilyTreeDNA
Minor allele frequency
22%

Genotypes

Plus strand, as in 23andMe and AncestryDNA files.

  1. T;TMost notableBad2.3x risk for lupusMinor · 1.54% of people
  2. C;TBad2.0x risk for lupusMinor · 1.228% of people
  3. C;CGoodaverageTypical · 0.068% of people

SNPedia records rs419788 on the minus strand: (A;A), (A;G), (G;G). 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.

  • AverageT;T 4% C;T 28% C;C 68%
  • European ancestry (Utah)T;T 10% C;T 38% C;C 52%
  • Han Chinese (Beijing)T;T 10% C;T 45% C;C 45%
  • Japanese (Tokyo)T;T 14% C;T 48% C;C 38%
  • Yoruba (Nigeria)T;T <1% C;T 14% C;C 85%
  • African ancestry (Southwest US)T;T 2% C;T 11% C;C 88%
  • Chinese (Denver)T;T 6% C;T 50% C;C 45%
  • Gujarati IndianT;T 1% C;T 22% C;C 77%
  • Luhya (Kenya)T;T 0% C;T 8% C;C 92%
  • Mexican ancestry (Los Angeles)T;T 2% C;T 40% C;C 59%
  • Maasai (Kenya)T;T <1% C;T 7% C;C 92%
  • TuscanT;T 3% C;T 27% C;C 71%

Conditions, medicines and genes

Notes

From SNPedia

Notes

rs419788, a SNP in an intron of the SKIV2L gene in the MHC class III region, has been associated with lupus in a large study of UK patients. In dbSNP orientation, the risk allele is rs419788(A), and the risk is dose-dependent (i.e. rs419788(A;A) individuals are at higher risk than rs419788(A;G) individuals]. The reported odds ratio is 2.0 (CI: 1.6 - 2.6, permuted p < 0.0001).

Source and license

Adapted from rs419788 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 Its entries can be incomplete, out of date or wrong, and nothing here is a diagnosis or medical advice.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.