rs3087456

This is a regulatory region variant variant in the CIITA gene.

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GWAS Catalog Trait Associations (1)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

leukocyte quantity

Orrù V et al. “Complex genetic signatures in immune cells underlie autoimmunity and inform therapy.” Nature Genetics 52(10):1036-1045 (2020)
Allele A
OR 0.44
p 4.0e-55
N 3,580
Large GWAS
European
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ClinVar annotation

Benign★☆☆☆
1 submitter4 publications

MHC class II deficiency

View on ClinVar →
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Research that mentions this SNP (2)

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HLA-DRB1*1501 and Spinal Cord Magnetic Resonance Imaging Lesions in Multiple Sclerosis
AssociationN=95Sombekke MH et al.(2009)· Archives of Neurology

A retrospective association study of 95 Brazilian multiple sclerosis (MS) patients examined HLA alleles and five SNPs (rs4774, rs3087456, rs6897932, rs731236, rs1033182) for associations with MRI lesion load. The HLA-DQA1*04:01 allele was significantly associated with higher lesion load on T2/FLAIR MRI sequences (p=0.02), with 71% of carriers showing above-median lesion load compared to 41% of non-carriers. No significant associations were found between the five SNPs and any MRI features studied.

Traits studied:Black holes (T1 lesions)Enhanced lesionsMRI lesion loadMultiple Sclerosis
PubMedDOIMetascience Observatory
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Investigation of the MHC2TA gene, associated with rheumatoid arthritis in a Swedish population, in a UK rheumatoid arthritis cohort
AssociationN=2,312Stephen Eyre et al.(2006)· Arthritis &amp; Rheumatism

This Swedish case-control study tested the association of the CIITA -168A>G promoter SNP (rs3087456) with myasthenia gravis (MG) in 446 patients and 1866 controls. The study found no significant association with MG overall (p=0.092) or in any clinical subgroup. The authors reviewed 17 replication studies of this SNP across multiple autoimmune disorders, concluding that the initial positive findings for rs3087456 in rheumatoid arthritis, multiple sclerosis, and myocardial infarction may need to be reconsidered due to widespread replication failure.

Traits studied:Autoimmune Addison's diseaseCeliac diseaseCommon variable immunodeficiencyGranulomatosis with polyangiitisIgA deficiencyInflammatory bowel diseaseMultiple sclerosisMyasthenia gravisMyocardial infarctionRheumatoid arthritisSystemic lupus erythematosus
PubMedDOIMetascience Observatory

About CIITA

This gene encodes a protein with an acidic transcriptional activation domain, 4 LRRs (leucine-rich repeats) and a GTP binding domain. The protein is located in the nucleus and acts as a positive regulator of class II major histocompatibility complex gene transcription, and is referred to as the "master control factor" for the expression of these genes. The protein also binds GTP and uses GTP binding to facilitate its own transport into the nucleus. Once in the nucleus it does not bind DNA but rather uses an intrinsic acetyltransferase (AT) activity to act in a coactivator-like fashion. Mutations in this gene have been associated with bare lymphocyte syndrome type II (also known as hereditary MHC class II deficiency or HLA class II-deficient combined immunodeficiency), increased susceptibility to rheumatoid arthritis, multiple sclerosis, and possibly myocardial infarction. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2013]

View all CIITA variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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