rs1046089

This is a variant in the PRRC2A gene that changes a arginine to an histidine.

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GWAS Catalog Trait Associations (1)

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

age at menopause

Stolk L et al. “Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.” Nature Genetics 44(3):260-8 (2012)
Allele A
OR 0.21
p 2.0e-16
N 38,968
Large GWAS
European
Perry JR et al. “A genome-wide association study of early menopause and the combined impact of identified variants.” Human Molecular Genetics 22(7):1465-72 (2013)
Allele A
OR 0.19
p 4.0e-11
N 17,091
Large GWAS
European
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ClinVar annotation

Benign
1 submitter

PRRC2A-related disorder

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

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A Comprehensive Family-Based Replication Study of Schizophrenia Genes
AssociationN=28,251Karolina A. Aberg et al.(2013)· JAMA Psychiatry

This comprehensive family-based replication study tested 8,107 SNPs in 6,298 individuals (3,286 schizophrenia cases) from 1,811 nuclear families, following a meta-analysis of 18 schizophrenia GWAS studies. The study replicated major findings in TCF4 (P=2.53×10⁻¹⁰) and NOTCH4 (P=3.16×10⁻⁷), and identified novel susceptibility loci including POM121L2 (P=3.51×10⁻⁷), AS3MT (P=9.01×10⁻⁷), CNNM2 (P=6.07×10⁻⁷), and NT5C2 (P=4.09×10⁻⁷). Pathway analyses revealed significant enrichment in neuronal function (axonal guidance, neuronal systems, L1 cell adhesion) and immune system pathways (antigen processing, T-cell adhesion molecules).

Traits studied:Schizophrenia
PubMedDOIMetascience Observatory
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A genetic association study in the Gambia using tagging polymorphisms in the major histocompatibility complex class III region implicates a HLA-B associated transcript 2 polymorphism in severe malaria susceptibility
AssociationN=2,162Mahamadou Diakite et al.(2009)· Human Genetics

A case-control association study of 2162 Gambian individuals identified a BAT2 polymorphism (rs1046089) significantly associated with severe malaria (G vs A OR=0.73, P<10⁻⁶ for allelic test; recessive model GG vs GA/AA OR=0.48, P<10⁻⁶). Haplotype analysis confirmed BAT2-associated variants conferred ~40% reduced risk. Secondary findings included AIF1 (rs2259571, OR=0.57, P=0.004) and TNF-238 (rs361525, OR=1.33, P=0.04) associations, though only BAT2 remained significant after Bonferroni correction.

Traits studied:Cerebral malariaSevere malariaSevere malarial anaemia
PubMedDOIMetascience Observatory

About PRRC2A

A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for TNF alpha and TNF beta. These genes are all within the human major histocompatibility complex class III region. This gene has microsatellite repeats which are associated with the age-at-onset of insulin-dependent diabetes mellitus (IDDM) and possibly thought to be involved with the inflammatory process of pancreatic beta-cell destruction during the development of IDDM. This gene is also a candidate gene for the development of rheumatoid arthritis. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2010]

View all PRRC2A variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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