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rs10488631

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(C;C) 3 2x increased risk of developing SLE; 3.2x increased risk of developing primary biliary cirrhosis; and 3.4x increased risk of developing Sjögren's syndrome
(C;T) 2 2x increased risk of developing SLE; 1.6x increased risk of developing primary biliary cirrhosis; and 1.7x increased risk of developing Sjögren's syndrome
(T;T) 1 Normal risk of developing SLE, primary biliary cirrhosis, and Sjögren's syndrome
ReferenceGRCh38 38.1/141
Chromosome7
Position128954129
GeneTNPO3
is asnp
is mentioned by
dbSNPrs10488631
ebirs10488631
HLIrs10488631
Exacrs10488631
Varsomers10488631
Maprs10488631
PheGenIrs10488631
hapmaprs10488631
1000 genomesrs10488631
hgdprs10488631
ensemblrs10488631
gopubmedrs10488631
geneviewrs10488631
scholarrs10488631
googlers10488631
pharmgkbrs10488631
gwascentralrs10488631
openSNPrs10488631
23andMers10488631
23andMe allrs10488631
SNP Nexus

SNPshotrs10488631
SNPdbers10488631
MSV3drs10488631
GWAS Ctlgrs10488631
GMAF0.05418
Max Magnitude3
? (C;C) (C;T) (T;T) 28
rs10488631, a SNP located 3' of the IRF5 gene, has been reported as a possibly causative SNP for systemic lupus erthymatosus (SLE), based on a study of ~700 Swedish patients. The risk allele is rs10488631(C), with a reported odds ratio of 2.07 (CI: 1.63-2.62, p = 9x10e-10).[PMID 18063667]

The C allele is also associated with primary biliary cirrhosis, with each C increasing the odds about 1.6 times. [PMID 20639879OA-icon.png] [PMID 20639880OA-icon.png]

Each C allele increases risk of Sjögren's syndrome by 1.7 times. [PMID 20861858]

[PMID 19092842] SLE rs10488631 and rs7582694

Neighborrs2280714
Distance542
GWAS snp
PMID [PMID 18204098]
Trait Systemic lupus erythematosus
Title Association of systemic lupus erythematosus with C8orf13-BLK and ITGAM-ITGAX
Risk Allele C
P-val 1.9999999999999999E-11
Odds Ratio NR NR
GWAS snp
PMID [PMID 19458352OA-icon.png]
Trait Primary biliary cirrhosis
Title Primary Biliary Cirrhosis Associated with HLA, IL12A, and IL12RB2 Variants
Risk Allele G
P-val 2E-7
Odds Ratio 1.52 [1.30-1.78]
OMIM607218
DescINTERFERON REGULATORY FACTOR 5; IRF5
Variant
Relatedalso
GWAS snp
PMID [PMID 20383147OA-icon.png]
Trait Systemic sclerosis
Title Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus
Risk Allele C
P-val 2E-13
Odds Ratio 1.50 [1.35-1.67]

[PMID 19854706OA-icon.png] Association of IRF5 polymorphisms with activation of the interferon alpha pathway

GWAS snp
PMID [PMID 20453842OA-icon.png]
Trait Rheumatoid arthritis
Title Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk lock
Risk Allele C
P-val 4E-11
Odds Ratio 1.19 [NR]
GWAS snp
PMID [PMID 20639880OA-icon.png]
Trait Primary biliary cirrhosis
Title Genome-wide meta-analyses identify three loci associated with primary biliary cirrhosis
Risk Allele C
P-val 3E-10
Odds Ratio 1.63 [NR]
OMIM612251
Desc
Variant
Relatedalso
GWAS snp
PMID [PMID 21408207OA-icon.png]
Trait
Title Differential Genetic Associations for Systemic Lupus Erythematosus Based on Anti-dsDNA Autoantibody Production
Risk Allele C
P-val 7E-18
Odds Ratio 1.9200 [1.66-2.22]


[PMID 21807777] Preferential Association of Interferon Regulatory Factor 5 Gene Variants with Seronegative Rheumatoid Arthritis in 2 Swedish Case-Control Studies

GWAS snp
PMID [PMID 21779181OA-icon.png]
Trait
Title Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
Risk Allele
P-val 8E-7
Odds Ratio 1.6300 [1.34-1.98]
GWAS snp
PMID [PMID 21750679OA-icon.png]
Trait
Title Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.
Risk Allele C
P-val 4E-7
Odds Ratio 1.3500 [1.20-1.51]


[PMID 22440820OA-icon.png] IRF5 polymorphism predicts prognosis in patients with systemic sclerosis


[PMID 17412832OA-icon.png] Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus.


[PMID 17568788] Opposed independent effects and epistasis in the complex association of IRF5 to SLE.


[PMID 18285424OA-icon.png] Interferon regulatory factor 5 (IRF5) gene variants are associated with multiple sclerosis in three distinct populations.


[PMID 18579578OA-icon.png] A risk haplotype of STAT4 for systemic lupus erythematosus is over-expressed, correlates with anti-dsDNA and shows additive effects with two risk alleles of IRF5.


[PMID 18668568OA-icon.png] Association of the IRF5 risk haplotype with high serum interferon-alpha activity in systemic lupus erythematosus patients.


[PMID 18843782] Different genetic effects of interferon regulatory factor 5 (IRF5) polymorphisms on systemic lupus erythematosus in a Korean population.


[PMID 19109131OA-icon.png] Cutting edge: autoimmune disease risk variant of STAT4 confers increased sensitivity to IFN-alpha in lupus patients in vivo.


[PMID 19838195OA-icon.png] A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.


[PMID 20112383OA-icon.png] Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus.


[PMID 21379322OA-icon.png] Risk alleles for systemic lupus erythematosus in a large case-control collection and associations with clinical subphenotypes.


[PMID 21506939] Replicated association of 17q12-21 with susceptibility of primary biliary cirrhosis in a Japanese cohort.


GET Evidence
rs10488631
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.046875
summary



[PMID 23372721OA-icon.png] The Systemic Lupus Erythematosus IRF5 Risk Haplotype Is Associated with Systemic Sclerosis


[PMID 22328738OA-icon.png] Comprehensive assessment of rheumatoid arthritis susceptibility loci in a large psoriatic arthritis cohort.

GWAS snp
PMID [PMID 24871463OA-icon.png]
Trait Systemic lupus erythematosus
Title GWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
Risk Allele C
P-val 2E-13
Odds Ratio 1.83 [1.684-1.99]


[PMID 26092158] IRF5, PTPN22, CD28, IL2RA, KIF5A, BLK and TNFAIP3 genes polymorphisms and lupus susceptibility in a cohort from the Egypt Delta; relation to other ethnic groups