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. Author manuscript; available in PMC: 2021 May 14.
Published in final edited form as: Immunol Cell Biol. 2021 Feb 24;99(5):496–508. doi: 10.1111/imcb.12438

Table 1.

Coding variants associated with genetic risk for T1D. For each coding SNP, chromosomal region, major and minor alleles, risk allele frequency, odds ratio (OR), amino acid (AA) substitution, prediction of functional effect and association with other autoimmune diseases are presented.

Gene Chromosomal
region
T1D associated
coding SNP
Major >
minor
alleles
Risk
allele
Risk allele frequency
T1D OR Ref
for OR
AA
substitution
SIFT/
PolyPhen
predictions
Association with
other
autoimmune
diseases
European African East
Asian
South
Asian
American
PTPN22 1p13.2 rs2476601 G > A A 0.094 0.003 0.000 0.013 0.036 1.81 6 R620W Tolerated/benign RA, CD, JIA, V, MG, UC, CeD
CTLA4 2q33.2 rs231775 A > G G 0.359 0.388 0.637 0.310 0.463 1.20 6 T17A Tolerated/benign RA, CD, UC, JIA
CD226 18q22.2 rs763361 C > T T 0.473 0.737 0.388 0.513 0.452 1.10 89 G307S Tolerated/benign UC, CD, CeD, MS, RA
UBASH3A 21q22.3 rs13048049 G > A G 0.949 0.973 1.000 0.990 0.981 1.19 6 R324Q Tolerated/possibly damaging RA, UC, Ps, MS, CeD
SIRPG 20p13 rs6043409 G > A G 0.660 0.825 0.848 0.858 0.782 1.14 5 A263V Tolerated/benign RA, UC
TYK2 19p13.2 rs34536443 G > C G 0.971 0.999 1.000 0.994 0.980 1.54 6 P1104A Deleterious/probably damaging Ps, RA, MS, CeD, UC, Sj
rs12720356 A > C A 0.908 0.997 1.000 0.989 0.952 1.21 6 I684S Deleterious/possibly damaging UC, CD, Ps, Sj, CeD, MS, AS, RA
SH2B3 12q24.12 rs3184504 C > T T 0.464 0.019 0.003 0.069 0.254 1.27 6 R262W Tolerated/benign CeD, CD, Ps, UC, RA, JIA, MS, Sj
FUT2 19q13.33 rs601338 G > A A 0.441 0.491 0.004 0.283 0.341 1.12 6 W154* Loss of function CD, MS, Ps
IFIH1 2q24.2 rs1990760 T > C T 0.605 0.126 0.187 0.564 0.390 1.14 6 T946A Tolerated/benign UC, Ps, CD, MS, MG
rs35667974 T > C T 0.990 0.999 1.000 0.999 1.000 1.64 6 I923V Tolerated/probably damaging UC, Ps, CD
rs35337543 C > G C 0.981 1.000 1.000 0.998 0.990 1.58 6 Splice donor variant Loss of function UC, Ps
CTSH 15q25.1 rs2289702 C > T C 0.895 0.985 0.929 0.847 0.947 1.26 6 G11R Deleterious/benign -

Minor allele reported in reference to + strand of DNA from European subjects and risk allele frequencies reported from 1000 Genomes Project phase 3 release V3+. T1D OR shown for risk allele from most recent GWAS including the variant. Predictions of impact on protein structure and function shown from SIFT (Sorting Intolerant From Tolerant) and PolyPhen-2 (Polymorphism Phenotyping v2). The “Association with other autoimmune diseases” column includes conditions in which the risk allele for T1D may carry risk or protection for the noted diseases. Disease associations reported from “Immune system” category of PheWAS from ImmunoBase version 0.4.0 (fcf5738). AS, ankylosing spondylitis; CD, Crohn’s disease; CeD, celiac disease; JIA, juvenile idiopathic arthritis; MG, myasthenia gravis; MS, multiple sclerosis; Ps, psoriasis; RA, rheumatoid arthritis; Sj, Sjogren’s syndrome; SNP: single nucleotide polymorphism; T1D: type 1 diabetes; UC, ulcerative colitis; V, vitiligo.