rs4388249

This is a upstream gene variant variant in the MAN2A1 gene.

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GWAS Catalog Trait Associations (3)

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

blood protein amount

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele T
OR 0.05
p 3.0e-16
N 47,745
Large GWAS
European

melanocyte protein PMEL measurement

Pietzner M et al. “Mapping the proteo-genomic convergence of human diseases.” Science (new York, N.y.) 374(6569):eabj1541 (2021)
Allele T
OR 0.14
p 1.0e-14
N 10,708
Large GWAS
European

schizophrenia

Li Z et al. “Genome-wide association analysis identifies 30 new susceptibility loci for schizophrenia.” Nature Genetics 49(11):1576-1583 (2017)
Allele T
OR 1.07
p 8.0e-9
N 108,341
Large GWAS
multi-ancestry
Ikeda M et al. “Genome-Wide Association Study Detected Novel Susceptibility Genes for Schizophrenia and Shared Trans-Populations/Diseases Genetic Effect.” Schizophrenia Bulletin 45(4):824-834 (2019)
Allele T
OR 1.06
p 2.0e-8
N 122,624
Large GWAS
multi-ancestry
“Biological insights from 108 schizophrenia-associated genetic loci.” Nature 511(7510):421-7 (2014)
Allele T
OR 1.08
p 3.0e-8
N 83,550
Large GWAS
multi-ancestry
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Research that mentions this SNP (1)

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Common variants in QPCT gene confer risk of schizophrenia in the Han Chinese population
MethodsRaja Amjad Waheed Khan et al.(2016)· American Journal of Medical Genetics Part B: Neuropsychiatric Genetics

This paper presents CalPen, a web-based tool for calculating penetrance (disease likelihood given a mutation) in complex genetic disorders. The authors validated CalPen against published penetrance calculations for schizophrenia-associated copy number variants (CNVs) and single nucleotide polymorphisms (SNPs). They analyzed 15 CNVs in 39,059 schizophrenia patients and 55,084 controls (average penetrance 7%, ranging from ~1.4% for 15q11.2 deletions to ~20% for 22q11.21 CNVs) and 145 SNPs in 45,405 patients and 122,761 controls (average penetrance 0.7%, with rs1801028 showing the highest at 1.6%).

Traits studied:Schizophrenia
PubMedDOIMetascience Observatory

About MAN2A1

This gene encodes a glycosyl hydrolase that localizes to the Golgi and catalyzes the final hydrolytic step in the asparagine-linked oligosaccharide (N-glycan) maturation pathway. Mutations in the mouse homolog of this gene have been shown to cause a systemic autoimmune disease similar to human systemic lupus erythematosus. [provided by RefSeq, Dec 2013]

View all MAN2A1 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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