rs2596542

This is a downstream gene variant variant in the MICA gene.

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GWAS Catalog Trait Associations (1)

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

hepatocellular carcinoma

Kumar V et al. “Genome-wide association study identifies a susceptibility locus for HCV-induced hepatocellular carcinoma.” Nature Genetics 43(5):455-8 (2011)
Allele A
OR 1.39
p 4.0e-13
N 3,611
Large GWAS
East Asian
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Research that mentions this SNP (2)

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PNPLA3 and TM6SF2 variants as risk factors of hepatocellular carcinoma across various etiologies and severity of underlying liver diseases
AssociationN=6,039Jie Yang et al.(2019)· International Journal of Cancer

This association study of 6039 European subjects (1020 HCC cases, 5019 controls including prospective cohorts) identified PNPLA3 rs738409 (OR=3.91, p=1.14E-09) and TM6SF2 rs58542926 (OR=1.79, p=0.001) as significant risk variants for hepatocellular carcinoma in alcoholic liver disease patients, with a dose-dependent additive effect. PNPLA3 rs738409 was also associated with HCC developed on non-fibrotic liver (OR=2.19, p=0.007), suggesting a direct carcinogenic role independent of cirrhosis.

Traits studied:Alcoholic liver diseaseCirrhosisHepatitis BHepatitis CHepatocellular carcinomaNon-alcoholic fatty liver disease
PubMedDOIMetascience Observatory
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DEPDC5 variants increase fibrosis progression in Europeans with chronic hepatitis C virus infection
AssociationN=1,139Maria Antonella Burza et al.(2016)· Hepatology

DEPDC5 rs1012068 is associated with liver fibrosis progression in Europeans with chronic HCV infection, with a 40% increased risk of cirrhosis (OR 1.40, 95% CI 1.08-1.81, P=0.011) and 50% increased risk of moderate/severe fibrosis (OR 1.52, 95% CI 1.09-2.12, P=0.015). Nonsynonymous DEPDC5 variants increased fibrosis risk by 54% (OR 1.54, P=0.040). MICA rs2596542 showed no association with HCC or cirrhosis in this European cohort. In vitro studies demonstrated DEPDC5 downregulation increases β-catenin expression and MMP2 production in hepatic stellate cells.

Traits studied:Chronic hepatitis CHepatocellular carcinomaLiver cirrhosisLiver fibrosis progression
PubMedDOIMetascience Observatory

About MICA

This gene encodes the highly polymorphic major histocompatability complex class I chain-related protein A. The protein product is expressed on the cell surface, although unlike canonical class I molecules it does not seem to associate with beta-2-microglobulin. It is a ligand for the NKG2-D type II integral membrane protein receptor. The protein functions as a stress-induced antigen that is broadly recognized by intestinal epithelial gamma delta T cells. Variations in this gene have been associated with susceptibility to psoriasis 1 and psoriatic arthritis, and the shedding of MICA-related antibodies and ligands is involved in the progression from monoclonal gammopathy of undetermined significance to multiple myeloma. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2014]

View all MICA variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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