{{Rsnum
|rsid=6897932
|Gene=IL7R
|Chromosome=5
|position=35874473
|Orientation=plus
|ReferenceAllele=C
|MissenseAllele=T
|GMAF=0.191
|Assembly=GRCh38
|GenomeBuild=38.1
|dbSNPBuild=141
|geno1=(C;C)
|geno2=(C;T)
|geno3=(T;T)
|Gene_s=IL7R
}}{{ population diversity
| geno1=(C;C)
| geno2=(C;T)
| geno3=(T;T)
| CEU | 59.3 | 32.7 | 8.0
| HCB | 70.1 | 22.6 | 7.3
| JPT | 66.1 | 31.2 | 2.7
| YRI | 90.5 | 9.5 | 0.0
| ASW | 80.7 | 15.8 | 3.5
| CHB | 70.1 | 22.6 | 7.3
| CHD | 63.0 | 34.3 | 2.8
| GIH | 72.3 | 26.7 | 1.0
| LWK | 89.9 | 10.1 | 0.0
| MEX | 62.1 | 32.8 | 5.2
| MKK | 80.0 | 18.7 | 1.3
| TSI | 57.8 | 39.2 | 2.9
| HapMapRevision=28
}}The (C) allele of [[rs6897932]], located in the alternatively spliced exon 6 of [[IL7RA]] gene and encoding the amino acid threonine rather than isoleucine at amino acid position 244, is associated with a slight increase (18%) in risk of developing [[multiple sclerosis]]. [PMID 17660817;  Nature Genetics 39, 1083 - 1091 (2007) SG Gregory et al.]

Note that the (C) allele is the most common at this position in all known populations and influences the ratios of the alternative isoforms (membrane bound and soluble) of the gene.

[http://thegenesherpa.blogspot.com/2007/07/ms-genes-and-gwas.html blog post] giving perspective on the significance of this snp

{{PMID|17660817}} a significant risk factor for multiple sclerosis in four independent (overall P = 2.9 x 10(-7)) influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silencer.

[http://content.nejm.org/cgi/content/short/358/7/753 nejm] C allele increasing the risk of multiple sclerosis (odds ratio, approximately 1.2)

{{PMID|18721276}} A replication case-control study involving 599 Spanish patients with [[multiple sclerosis]] yielded a per allele odds ratio of 1.32 per [[rs6897932]](C), (CI: 1.1-1.6, p = 0.0031), and odds per (C;C) genotype vs (T;T) and (C;T) genotypes of  1.5 (CI: 1.18-1.87, p = 0.0007).

{{GWAS Summary
|SNP=rs6897932
|PubMedID=17660530
|Condition=Multiple sclerosis
|Gene=IL7RA
|Risk Allele=C
|pValue=3.00E-007
|OR=1.18
|95CI=1.11-1.26
}}

{{PMID Auto GWAS
|PMID=17554260
|Trait=Type 1 diabetes
|Title=Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes
|RiskAllele=G
|Pval=0.0000079999999999999996
|OR=1.12
|ORtxt=[1.06-1.19]
|OA=1
}}

{{PMID Auto GWAS
|PMID=19525953
|Trait=Multiple sclerosis
|Title=Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci
|RiskAllele=C
|Pval=0.000002
|OR=1.12
|ORtxt=[1.02-1.23]
|OA=1
}}

{{omim
|desc=MULTIPLE SCLEROSIS, SUSCEPTIBILITY TO, 3; MS3
|id=612595
|rsnum=6897932
}}
{{PMID Auto
|PMID=19626041
|Title=Variation in IL7R predisposes to sarcoid inflammation
}}
{{PMID Auto
|PMID=19744146
|Title=IL7RA polymorphisms and chronic inflammatory arthropathies
}}
{{PMID Auto
|PMID=18650830
|Title=Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians
}}

{{PharmGKB
|RSID=rs6897932
|Name_s=
|Gene_s=IL7R
|Feature=
|Evidence=PubMed ID:17660530; Web Resource:http://www.genome.gov/gwastudies/
|Annotation=GWAS Results: Risk alleles for multiple sclerosis identified by a genomewide study (Initial Sample Size: 931 trios, 2,431 controls; Replication Sample Size: 609 trios, 2,322 cases, 2,987 controls; Risk Allele: rs6897932-C).
|Drugs=
|Drug Classes=
|Diseases=Multiple Sclerosis
|Curation Level=Non-Curated
|PharmGKB Accession ID=PA162356686
}}

{{PMID Auto
|PMID=20112030
|Title=Genetic variation in the IL7RA/IL7 pathway increases multiple sclerosis susceptibility
|OA=1
}}

{{PMID Auto
|PMID=20952449
|Title=Evaluation of the established non-MHC multiple sclerosis loci in an Indian population
}}

{{PharmGKB
|RSID=rs6897932
|Name_s=IL7R: T244I
|Gene_s=IL7R
|Feature=
|Evidence=PubMed ID:17660530
|Annotation=This nonsynonymous coding SNP in exon 6 of IL7R showed highly significant evidence of association with multiple sclerosis.
|Drugs=
|Drug Classes=
|Diseases=Multiple Sclerosis
|Curation Level=Curated
|PharmGKB Accession ID=PA161925604
}}

{{PharmGKB
|RSID=rs6897932
|Name_s=
|Gene_s=IL7R
|Feature=
|Evidence=PubMed ID:17660816
|Annotation=In a case-control study of Nordic populations, rs6897932 was the most strongly associated of several SNPs associated with risk of multiple sclerosis.
|Drugs=
|Drug Classes=
|Diseases=Multiple Sclerosis
|Curation Level=Curated
|PharmGKB Accession ID=PA162356124
}}

{{PMID Auto
|PMID=21287555
|Title=The interleukin-7 receptor ? chain contributes to altered homeostasis of regulatory T cells in multiple sclerosis
}}

{{PMID Auto
|PMID=21543551
|Title=Relevance of IL7R genotype and mRNA expression in Dutch patients with multiple sclerosis
}}

{{PMID Auto
|PMID=22363405
|Title=Sample Reproducibility of Genetic Association Using Different Multimarker TDTs in Genome-Wide Association Studies: Characterization and a New Approach
|OA=1
}}

{{PMID Auto
|PMID=17915034
|Title=Finding disease candidate genes by liquid association.
|OA=1
}}

{{PMID Auto
|PMID=18354419
|Title=IL2RA and IL7RA genes confer susceptibility for multiple sclerosis in two independent European populations.
}}

{{PMID Auto
|PMID=18461312
|Title=The immunogenetics of multiple sclerosis.
}}

{{PMID Auto
|PMID=18490360
|Title=The complex genetics of multiple sclerosis: pitfalls and prospects.
|OA=1
}}

{{PMID Auto
|PMID=18563381
|Title=Study of the association between the CAPSL-IL7R locus and type 1 diabetes.
}}

{{PMID Auto
|PMID=18565446
|Title=Refining genetic associations in multiple sclerosis.
|OA=1
}}

{{PMID Auto
|PMID=18853133
|Title=Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.
|OA=1
}}

{{PMID Auto
|PMID=19073967
|Title=Shared and distinct genetic variants in type 1 diabetes and celiac disease.
|OA=1
}}

{{PMID Auto
|PMID=19221116
|Title=Use of a genetic isolate to identify rare disease variants: C7 on 5p associated with MS.
|OA=1
}}

{{PMID Auto
|PMID=19231135
|Title=Variation in the IL7RA and IL2RA genes in German multiple sclerosis patients.
}}

{{PMID Auto
|PMID=19293837
|Title=Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor.
|OA=1
}}

{{PMID Auto
|PMID=19359276
|Title=Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.
|OA=1
}}

{{PMID Auto
|PMID=19468064
|Title=Parasites represent a major selective force for interleukin genes and shape the genetic predisposition to autoimmune conditions.
|OA=1
}}

{{PMID Auto
|PMID=19546505
|Title=IL-21 drives secondary autoimmunity in patients with multiple sclerosis, following therapeutic lymphocyte depletion with alemtuzumab (Campath-1H).
|OA=1
}}

{{PMID Auto
|PMID=19626040
|Title=Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis.
|OA=1
}}

{{PMID Auto
|PMID=19956108
|Title=Analysis of 55 autoimmune disease and type II diabetes loci: further confirmation of chromosomes 4q27, 12q13.2 and 12q24.13 as type I diabetes loci, and support for a new locus, 12q13.3-q14.1.
|OA=1
}}

{{PMID Auto
|PMID=20007504
|Title=Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci.
|OA=1
}}

{{PMID Auto
|PMID=20072139
|Title=Association of the AFF3 gene and IL2/IL21 gene region with juvenile idiopathic arthritis.
|OA=1
}}

{{PMID Auto
|PMID=20182566
|Title=The genetic aspects of multiple sclerosis.
|OA=1
}}

{{PMID Auto
|PMID=20194581
|Title=Interleukin 7 receptor alpha polymorphism rs6897932 and susceptibility to multiple sclerosis in the Western Balkans.
}}

{{PMID Auto
|PMID=20368992
|Title=Multiple sclerosis susceptibility-associated SNPs do not influence disease severity measures in a cohort of Australian MS patients.
|OA=1
}}

{{PMID Auto
|PMID=20405052
|Title=The effect of single nucleotide polymorphisms from genome wide association studies in multiple sclerosis on gene expression.
|OA=1
}}

{{PMID Auto
|PMID=21161391
|Title=Association between the IL7R T244I polymorphism and multiple sclerosis: a meta-analysis.
}}

{{PMID Auto
|PMID=21244681
|Title=Thymic stromal lymphopoietin (TSLP) is associated with allergic rhinitis in children with asthma.
|OA=1
}}

{{PMID Auto
|PMID=21875636
|Title=Associations between single nucleotide polymorphisms and haplotypes in cytokine and cytokine receptor genes and immunity to measles vaccination.
|OA=1
}}

{{PMID Auto
|PMID=21911588
|Title=IL2RA gene polymorphism rs2104286 A>G seen in multiple sclerosis is associated with intermediate uveitis: possible parallel pathways?
}}

{{PMID Auto
|PMID=22262655
|Title=The IL-7Ralpha pathway is quantitatively and functionally altered in CD8 T cells in multiple sclerosis.
}}

{{GET Evidence
|gene=IL7R
|aa_change=Thr244Ile
|aa_change_short=T244I
|impact=protective
|qualified_impact=Low clinical importance, Likely protective
|inheritance=undefined
|quality_scores=Array
|dbsnp_id=rs6897932
|overall_frequency_n=2261
|overall_frequency_d=10758
|overall_frequency=0.210169
|n_genomes=17
|n_genomes_annotated=0
|n_haplomes=18
|n_articles=5
|n_articles_annotated=5
|qualityscore_in_silico=!
|qualitycomment_in_silico=Y
|qualityscore_in_vitro=1
|qualitycomment_in_vitro=Y
|qualityscore_case_control=5
|qualityscore_familial=0
|qualitycomment_familial=Y
|qualityscore_severity=4
|qualityscore_treatability=3
|gene_in_genetests=Y
|in_gwas=Y
|in_pharmgkb=Y
|genetests_testable=Y
|nblosum100=3
|autoscore=3
|webscore=N
|n_web_uneval=10
|variant_evidence=0
|clinical_importance=1
|summary_short=The reference genome variant for this allele has been associated with a slight increased risk of multiple sclerosis. Thus, this variant can be treated as a "protective" variant -- carriers of this variant are slightly less likely to have MS. Because the disease is rare and the effect of this variant is not very strong, the absolute decreased risk for carriers of this variant is less than .05% (less than 1 in 2000).
}}

{{PMID Auto GWAS
  |PMID=21833088
  |Trait=Multiple sclerosis
  |Title=Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
  |RiskAllele=G
  |Pval=2E-8
  |OR=1.11
  |ORtxt=[1.09-1.13]
  |OA=1
}}

{{PMID Auto
|PMID=24166352
|Title=The Promoter SNP, but not the Alternative Splicing SNP, is Linked to Multiple Sclerosis Among Jordanian Patients
}}

{{PMID Auto
|PMID=24242875
|Title=Interleukin-7 Receptor Single Nucleotide Polymorphism rs6897932 (C/T) and the Susceptibility to Systemic Lupus Erythematosus
}}

{{PMID Auto
|PMID=24337176
|Title=Association analysis of IL7R polymorphisms with inflammatory demyelinating diseases
}}

{{PMID Auto
|PMID=24357513
|Title=The variant interleukin 1f7 rs3811047 G&gt;A was associated with a decreased risk of gastric cardiac adenocarcinoma in a Chinese Han population
}}

{{PMID Auto
|PMID=22492128
|Title=Association of SNPs rs6498169 and rs10984447 with multiple sclerosis in Saudi patients: a model of the usefulness of familial aggregates in identifying genetic linkage in a multifactorial disease.
}}

{{PMID Auto
|PMID=23454692
|Title=Concentration and activity of the soluble form of the interleukin-7 receptor alpha in type 1 diabetes identifies an interplay between hyperglycemia and immune function.
}}

{{PMID Auto
|PMID=23462217
|Title=Polymorphisms in the interleukin-7 receptor alpha gene and mortality in untreated HIV-infected individuals.
}}

{{PMID Auto
|PMID=23692589
|Title=Polymorphism in the interleukin-7 receptor-alpha and outcome after allogeneic hematopoietic cell transplantation with matched unrelated donor.
}}

{{on chip | 23andMe v1}}
{{on chip | 23andMe v2}}
{{on chip | 23andMe v3}}
{{on chip | 23andMe v4}}
{{on chip | Affy GenomeWide 6}}
{{on chip | HumanOmni1Quad}}
{{on chip | Illumina Human 1M}}