Rs1050152

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Orientationplus
Geno Mag Summary
(C;C) 0 normal
(C;T) 2 2.1x increased risk of Crohn's disease
(T;T) 2.1 2.1x increased risk of Crohn's disease
ReferenceGRCh38 38.1/141
Chromosome5
Position132340627
GeneMIR4750, SLC22A4
is asnp
is mentioned by
dbSNPrs1050152
Exacrs1050152
PheGenIrs1050152
nextbiors1050152
hapmaprs1050152
1000 genomesrs1050152
hgdprs1050152
ensemblrs1050152
gopubmedrs1050152
geneviewrs1050152
scholarrs1050152
googlers1050152
pharmgkbrs1050152
gwascentralrs1050152
openSNPrs1050152
23andMers1050152
23andMe allrs1050152
SNP Nexus

SNPshotrs1050152
SNPdbers1050152
MSV3drs1050152
GMAF0.1846
Max Magnitude2.1
? (C;C) (C;T) (T;T) 28
rs1050152, a SNP in the SLC22A4 gene known as L503F, has been associated with an autoimmune disease, in this case, Crohn's disease, odds ratio = 2.1 (CI = 1.31–3.39, p = 0.002), based on a study of 203 cases and 200 controls. The risk allele is rs1050152(T).[PMID 15107849]

A nearby SNP (rs2631367) in the promoter region of the SLC22A5 gene defines a haplotype along with rs3792876, with odds ratio reported as similar for either SNP or the haplotype. Referring to the TC risk haplotype, the population risk attributable to heterozygotes was 19%, and for homozygous haplotype carriers, 27%.[PMID 15107849]



[PMID 21061378] Two independent genetic factors responsible for the associations of the IBD5 locus with Crohn's disease in the Czech population

[PMID 21122496] OCTN1 variant L503F is associated with familial and sporadic inflammatory bowel disease

OMIM604190
Desc
Variant0002
Relatedalso


[PMID 21674708] Two independent genetic factors responsible for the associations of the IBD5 locus with Crohn's disease in the Czech population


[PMID 21695374] Haplotype in the IBD5 region is associated with refractory Crohn's disease in Slovenian patients and modulates expression of the SLC22A5 gene


[PMID 22606245OA-icon.png] Evolutionary Dynamics of Co-Segregating Gene Clusters Associated with Complex Diseases


ClinVar
Risk rs1050152(T;T)
Alt rs1050152(T;T)
Reference rs1050152(C;C)
Significance Non-pathogenic
Disease SLC22A4 POLYMORPHISM
Variation info
Gene SLC22A4 LOC553103
CLNDBN SLC22A4 POLYMORPHISM
Reversed 0
HGVS NC_000005.9:g.131676320C>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000006106.1,



[PMID 15843420OA-icon.png] DLG5 variants do not influence susceptibility to inflammatory bowel disease in the Scottish population.


[PMID 15955786OA-icon.png] Polymorphisms in the DLG5 and OCTN cation transporter genes in Crohn's disease.


[PMID 16796743OA-icon.png] Evidence for the association of the SLC22A4 and SLC22A5 genes with type 1 diabetes: a case control study.


[PMID 17667713] Analysis of candidate genes on chromosomes 5q and 19p in celiac disease.


[PMID 17786191OA-icon.png] rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants.


[PMID 18064451] IL4 in the 5q31 context: association studies of type 1 diabetes and rheumatoid arthritis in the Spanish population.


[PMID 18698678OA-icon.png] Replication of interleukin 23 receptor and autophagy-related 16-like 1 association in adult- and pediatric-onset inflammatory bowel disease in Italy.


[PMID 18715515OA-icon.png] Lack of evidence for association of primary sclerosing cholangitis and primary biliary cirrhosis with risk alleles for Crohn's disease in Polish patients.


[PMID 18756601OA-icon.png] OCTN and CARD15 gene polymorphism in Chinese patients with inflammatory bowel disease.


[PMID 19141711OA-icon.png] Functional genetic variation in the basal promoter of the organic cation/carnitine transporters OCTN1 (SLC22A4) and OCTN2 (SLC22A5).


GET Evidence
SLC22A4-L503F
aa_change Leu503Phe
aa_change_short L503F
impact pharmacogenetic
qualified_impact Insufficiently evaluated pharmacogenetic
overall_frequency 0.303588
summary



[PMID 23474282OA-icon.png] Expression Quantitative Trait Loci Analysis Identifies Associations Between Genotype and Gene Expression in Human Intestine


[PMID 23127916] Polymorphisms in OCTN1 and OCTN2 transporters genes are associated with prolonged time to progression in unresectable gastrointestinal stromal tumours treated with imatinib therapy


[PMID 24415875OA-icon.png] Susceptibility to ulcerative colitis in Hungarian patients determined by gene-gene interactions


[PMID 22875622OA-icon.png] Association between imatinib transporters and metabolizing enzymes genotype and response in newly diagnosed chronic myeloid leukemia patients receiving imatinib therapy.


[PMID 22957492] Pathway analysis of a genome-wide association study of ileal Crohn's disease.