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rs2230926

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(G;T) 2 1.4x higher risk for rheumatoid arthritis
(T;T) 0 common in complete genomics
ReferenceGRCh38 38.1/141
Chromosome6
Position137874929
GeneTNFAIP3
is asnp
is mentioned by
dbSNPrs2230926
ebirs2230926
HLIrs2230926
Exacrs2230926
Varsomers2230926
Maprs2230926
PheGenIrs2230926
hapmaprs2230926
1000 genomesrs2230926
hgdprs2230926
ensemblrs2230926
gopubmedrs2230926
geneviewrs2230926
scholarrs2230926
googlers2230926
pharmgkbrs2230926
gwascentralrs2230926
openSNPrs2230926
23andMers2230926
23andMe allrs2230926
SNP Nexus

SNPshotrs2230926
SNPdbers2230926
MSV3drs2230926
GWAS Ctlgrs2230926
GMAF0.124
Max Magnitude2

rs2230926, also known as c.380T>G, p.Phe127Cys and F127C, is a SNP in the TNFAIP3 gene on chromosome 6. The tumor necrosis factor alpha-induced protein 3 (TNFAIP3) gene encodes the A20 protein, a key molecule in numerous immunologic and other processes due to it's role in controlling NF-κB activation.

? (G;G) (G;T) (T;T) 28

Meta-analysis found 1.4x risk of rheumatoid arthritis for rs2230926(G;G) [PMID 22402800]

An association was found between Systemic lupus erythematosus (SLE) and rs2230926.[PMID 18677310]

Three independent SNPs in the TNFAIP3 region (rs13192841, rs2230926 and rs6922466) are associated with systemic lupus erythematosus (SLE) among individuals of European ancestry.[PMID 19165919OA-icon.png]

In Sjögren's syndrome patients, the rs2230926(G) allele more than doubles the risk of primary Sjogren's Syndrome-associated Non-Hodgkin Lymphoma, according to a study which replicated the initial report in both UK and French patient cohorts of ~500 patients. The meta-analysis of the UK and French cohorts confirmed the initial finding, with odds ratios of 2.48 (CI: 1.87 - 3.28, p=0.0037) and 2.60, (CI: 1.91 - 3.53, p=0.0031), respectively.[PMID 26338037]

Neighborrs5029939
Distance343
OMIM612378
DescSYSTEMIC LUPUS ERYTHEMATOSUS, SUSCEPTIBILITY TO, 13; SLEB13
Variant
Relatedalso

[PMID 19774492] A single-nucleotide polymorphism of the TNFAIP3 gene is associated with systemic lupus erythematosus in Chinese Han population

GWAS snp
PMID [PMID 19838193]
Trait Systemic lupus erythematosus
Title Genome-wide association study in a Chinese Han population identifies nine new susceptibility loci for systemic lupus erythematosus
Risk Allele C
P-val 1E-17
Odds Ratio 1.72 [1.52-1.94]


[PMID 20112363] The association of a nonsynonymous single-nucleotide polymorphism in TNFAIP3 with systemic lupus erythematosus and rheumatoid arthritis in the Japanese population

GWAS snp
PMID [PMID 20453841]
Trait Rheumatoid arthritis
Title A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility
Risk Allele C
P-val 0.000002
Odds Ratio 1.31 [1.17-1.46]

[PMID 20617138OA-icon.png] Association of TNFAIP3 Polymorphism with Susceptibility to Systemic Lupus Erythematosus in a Japanese Population

[PMID 21208380] The association between BANK1 and TNFAIP3 gene polymorphisms and systemic lupus erythematosus: a meta-analysis

[PMID 19165918OA-icon.png] Genetic variants near TNFAIP3 on 6q23 are associated with systemic lupus erythematosus.

[PMID 19169254OA-icon.png] Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways.

[PMID 19387456OA-icon.png] Meta-analysis and imputation identifies a 109 kb risk haplotype spanning TNFAIP3 associated with lupus nephritis and hematologic manifestations.

[PMID 19417005OA-icon.png] Combined effects of three independent SNPs greatly increase the risk estimate for RA at 6q23.

[PMID 19439038OA-icon.png] Complex genetic association of 6q23 with autoimmune rheumatic conditions.

[PMID 20169177OA-icon.png] Genome-wide association study in Asian populations identifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosus.

[PMID 21326317OA-icon.png] Sequencing of TNFAIP3 and association of variants with multiple autoimmune diseases.

[PMID 22113471OA-icon.png] TNFAIP3 gene polymorphisms are associated with response to TNF blockade in psoriasis.

[PMID 22402800] Associations between TNFAIP3 gene polymorphisms and rheumatoid arthritis: a meta-analysis.


GET Evidence
TNFAIP3-F127C
aa_change Phe127Cys
aa_change_short F127C
impact not reviewed
qualified_impact Insufficiently evaluated not reviewed
overall_frequency 0.142313
summary



GWAS snp
PMID [PMID 23273568OA-icon.png]
Trait Systemic lupus erythematosus
Title Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
Risk Allele G
P-val 1E-13
Odds Ratio 2.71


[PMID 24023622OA-icon.png] Analysis of Gender Differences in Genetic Risk: Association of TNFAIP3 Polymorphism with Male Childhood-Onset Systemic Lupus Erythematosus in the Japanese Population


[PMID 24159176OA-icon.png] Germline and somatic genetic variations of TNFAIP3 in lymphoma complicating primary Sjogren's syndrome


[PMID 23582631] Pathway analysis of genome-wide association studies on rheumatoid arthritis


[PMID 22488580] Brief report: candidate gene study in systemic sclerosis identifies a rare and functional variant of the TNFAIP3 locus as a risk factor for polyautoimmunity.


[PMID 22924496] Associations between TNFAIP3 gene polymorphisms and systemic lupus erythematosus: a meta-analysis.


ClinVar
Risk rs2230926(G;G)
Alt rs2230926(G;G)
Reference rs2230926(T;T)
Significance Untested
Disease not specified
Variation info
Gene TNFAIP3
CLNDBN not specified
Reversed 0
HGVS NC_000006.11:g.138196066T>G
CLNSRC ClinVar
CLNACC RCV000122149.1,



[PMID 25674272OA-icon.png] TNFAIP3 rs2230926 polymorphisms in rheumatoid arthritis of southern Chinese Han population: a case-control study


[PMID 25806576] The polymorphisms of tumor necrosis factor-induced protein 3 gene may contribute to the susceptibility of chronic primary immune thrombocytopenia in Chinese population


[PMID 25337792OA-icon.png] Genetic association study of TNFAIP3, IFIH1, IRF5 polymorphisms with polymyositis/dermatomyositis in Chinese Han population


[PMID 26338037] Germline variation of TNFAIP3 in primary Sjögren's syndrome-associated lymphoma


[PMID 26846592] Single nucleotide polymorphisms of TNFAIP3 are associated with systemic lupus erythematosus in Han Chinese population.