rs2523393

This is a regulatory region variant variant in the HLA-F gene.

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GWAS Catalog Trait Associations (1)

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

multiple sclerosis

De Jager PL et al. “Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.” Nature Genetics 41(7):776-782 (2009)
Allele A
OR 1.28
p 1.0e-17
N 9,844
Meta-analysis
European
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Research that mentions this SNP (1)

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Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin
AssociationN=6,738Adrienne Tin et al.(2013)· Human Genetics

Genome-wide association study of plasma beta-2 microglobulin (B2M) levels in 6,738 European Americans identified two genome-wide significant loci: the HLA region on chromosome 6 (rs9264638, p=1.8×10⁻²³) and SH2B3 on chromosome 12 (rs3184504, p=3.1×10⁻⁸). Six index SNPs in the HLA region accounted for 3.2% of log(B2M) variance and their associations were largely explained by imputed classical HLA alleles (HLA-A, HLA-B, HLA-C). The HLA locus was not associated with estimated glomerular filtration rate, while the SH2B3 locus had previously been implicated as an eGFR locus, confirming B2M as a kidney function biomarker.

Traits studied:Chronic kidney diseaseGlomerular filtration rate (eGFRcr)Kidney functionPlasma beta-2 microglobulin levels
PubMedDOIMetascience Observatory

About HLA-F

This gene belongs to the HLA class I heavy chain paralogues. It encodes a non-classical heavy chain that forms a heterodimer with a beta-2 microglobulin light chain, with the heavy chain anchored in the membrane. Unlike most other HLA heavy chains, this molecule is localized in the endoplasmic reticulum and Golgi apparatus, with a small amount present at the cell surface in some cell types. It contains a divergent peptide-binding groove, and is thought to bind a restricted subset of peptides for immune presentation. This gene exhibits few polymorphisms. Multiple transcript variants encoding different isoforms have been found for this gene. These variants lack a coding exon found in transcripts from other HLA paralogues due to an altered splice acceptor site, resulting in a shorter cytoplasmic domain. [provided by RefSeq, Jul 2008]

View all HLA-F variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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