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GRIN3B - ENSG00000116032

glutamate ionotropic receptor NMDA type subunit 3B

Also known as: GluN3B

Location: chr19:1,000,418-1,009,731

Gene Type: protein coding

More information
NCBI Gene
116444
HUGO
HGNC:16768
Ensembl
ENSG00000116032
VEGA
OTTHUMG00000181904
OMIM
606651
UniProtKB
O60391

Genomic Context

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Gene-based Trait Associations

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ADSP WES: Alzheimer's Disease ADSP

Results from gene-level rare and functional variant aggregation tests for association to AD supported by significane of p < 0.5 / #genes.

Individual score test statistics for rare, predicted functional, and loss of function variants colocated with the gene were aggregated to compute gene level p-values.

See NIAGADS Accession NG00065 for more information.

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Accession Population N SNPs p-value Sign. Level rho CMAF CMAC Covariates Variant Filter Caveats
NG00065 Caribbean Hispanic 1 0.025 N/A 0 5.1e-03 4.0 PCs and sequencing center VEP HIGH
NG00065 Caribbean Hispanic 1 0.025 N/A 0 5.1e-03 4.0 PCs and sequencing center LOF
NG00065 Caribbean Hispanic 1 0.026 N/A 0 5.1e-03 4.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF
NG00065 Caribbean Hispanic 1 0.026 N/A 0 5.1e-03 4.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH
NG00065 Caribbean Hispanic 1 0.028 N/A 0 5.1e-03 4.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF
NG00065 Caribbean Hispanic 1 0.028 N/A 0 5.1e-03 4.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH
NG00065 European 10 0.076 N/A 1 9.6e-04 20.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 European 10 0.076 N/A 1 9.6e-04 20.1 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 Meta 10 0.080 N/A 0 1.1e-03 24.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes LOF N/A
NG00065 Meta 10 0.080 N/A 0 1.1e-03 24.1 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP HIGH N/A
NG00065 Caribbean Hispanic 19 0.141 N/A 0 0.126 99.3 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 10 0.144 N/A 1 9.6e-04 20.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 European 10 0.144 N/A 1 9.6e-04 20.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 Caribbean Hispanic 19 0.146 N/A 0 0.126 99.3 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 19 0.148 N/A 0 0.126 99.3 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 10 0.162 N/A 0 1.1e-03 24.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) LOF N/A
NG00065 Meta 10 0.162 N/A 0 1.1e-03 24.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP HIGH N/A
NG00065 European 137 0.403 N/A 1 0.158 3308.9 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 143 0.406 N/A 0 0.163 3527.5 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 Meta 143 0.426 N/A 1 0.163 3527.5 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 143 0.468 N/A 1 0.163 3527.5 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 137 0.474 N/A 1 0.158 3308.9 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 European 137 0.499 N/A 1 0.158 3308.9 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 European 10 0.651 N/A 1 9.6e-04 20.1 PCs and sequencing center VEP HIGH N/A
NG00065 European 10 0.651 N/A 1 9.6e-04 20.0 PCs and sequencing center LOF N/A
NG00065 Meta 10 0.736 N/A 0 1.1e-03 24.0 PCs and sequencing center LOF N/A
NG00065 Meta 10 0.736 N/A 0 1.1e-03 24.1 PCs and sequencing center VEP HIGH N/A

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the GRIN3B gene.

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The GRIN3B gene contains 1,495 variants records (corresponding to 1,348 unique genomic positions).

The following variants, contained within ±100kb of GRIN3B, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of GRIN3B that have genome-wide significance in a NIAGADS Alzheimer's Disease GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

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Relative Position Variant ADSP? Allele p-Value Track Accession
in gene N/A 6.0e-25 ADSP Single-Variant Risk Association: European (Model 1) NG00065
in gene N/A 6.0e-25 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
in gene N/A 6.0e-25 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 8.2e-20 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 8.2e-20 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 8.2e-20 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream N/A 4.4e-17 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 4.4e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 4.4e-17 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream N/A 8.6e-17 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 8.6e-17 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 8.6e-17 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream A 1.1e-15 IGAP 2013: Stages 1 and 2 NG00036
downstream G 1.4e-15 IGAP 2013: Stages 1 and 2 NG00036
downstream N/A 1.2e-14 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
downstream N/A 1.2e-14 ADSP Single-Variant Risk Association: European (Model 2) NG00065
downstream N/A 1.2e-14 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream G 4.2e-13 IGAP 2013: Stages 1 and 2 NG00036
downstream G 5.2e-13 IGAP 2013: Stages 1 and 2 NG00036
in gene N/A 6.0e-13 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 2) NG00065
in gene N/A 6.0e-13 ADSP Single-Variant Risk Association: European (Model 2) NG00065
in gene N/A 6.0e-13 ADSP Single-Variant Risk Association: meta analysis (Model 2) NG00065
downstream G 1.9e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream A 5.5e-12 IGAP 2013: Stages 1 and 2 NG00036
downstream T 4.9e-11 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.5e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream T 7.8e-10 IGAP 2013: Stages 1 and 2 NG00036
downstream C 1.3e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream G 1.5e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.7e-9 IGAP 2013: Stage 1 NG00036
downstream C 1.7e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.9e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.2e-9 ADGC African Americans 2013: APOE Adj NG00039
downstream A 2.3e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream T 2.9e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream G 4.3e-9 IGAP 2013: Stage 1 NG00036
downstream A 4.7e-9 IGAP 2013: Stages 1 and 2 NG00036
downstream A 4.7e-9 IGAP 2013: Stage 1 NG00036
downstream C 9.2e-9 IGAP 2013: Stages 1 and 2 NG00036
upstream N/A 1.1e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
upstream N/A 1.1e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream N/A 1.1e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream G 1.2e-8 IGAP 2013: Stage 1 NG00036
downstream G 1.3e-8 IGAP 2013: Stage 1 NG00036
downstream G 1.3e-8 IGAP 2013: Stage 1 NG00036
downstream G 1.5e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream T 1.7e-8 IGAP 2013: Stage 1 NG00036
downstream A 1.8e-8 IGAP 2013: Stage 1 NG00036
downstream G 2.0e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream N/A 2.0e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
downstream N/A 2.0e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
downstream N/A 2.0e-8 ADSP Single-Variant Risk Association: meta analysis (Model 1) NG00065
downstream A 3.1e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream T 3.1e-8 ADGC African Americans 2013: APOE Adj NG00039

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of GRIN3B that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of GRIN3B, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of GRIN3B that have genome-wide significance in a NIAGADS GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)

Variants contained within ±100kb of GRIN3B that are associated with a trait in the NHGRI GWAS Catalog.

Functional Genomics

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Explore all functional genomics annotations within the region of the GRIN3B gene (chr19:1000418-1009731)

Transcription Factor Binding Site Overlap in Gene Promoter Region (ENCODE ChIP-SEQ)

ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks) within the promoter region of this gene. See methods for more information.

Functional Annotation

Gene Ontology

Functional annotations were obtained from UniProt-GOA gene association files.

Click on a term accession number to view term details at the Gene Ontology Consortium.

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Ontology GO Accession Term Evidence Code
BP GO:0070588 calcium ion transmembrane transport IEA
BP GO:0098655 cation transmembrane transport IEA
BP GO:0060079 excitatory postsynaptic potential IEA
BP GO:0035235 ionotropic glutamate receptor signaling pathway ISS
BP GO:0034220 ion transmembrane transport IEA
BP GO:0006811 ion transport IEA
BP GO:0051205 protein insertion into membrane ISS,IEA
BP GO:0051924 regulation of calcium ion transport ISS,IEA
BP GO:0006810 transport IEA
CC GO:0030054 cell junction IEA
CC GO:0016021 integral component of membrane IEA
CC GO:0016020 membrane IEA
CC GO:0043025 neuronal cell body IEA,ISS
CC GO:0017146 NMDA selective glutamate receptor complex ISS,IBA,NAS,IEA
CC GO:0005886 plasma membrane IEA
CC GO:0045211 postsynaptic membrane IEA
CC GO:0045202 synapse IEA
MF GO:0005262 calcium channel activity ISS,IEA
MF GO:0005261 cation channel activity ISS
MF GO:0005234 extracellular-glutamate-gated ion channel activity IEA
MF GO:0016594 glycine binding ISS
MF GO:0005216 ion channel activity IEA
MF GO:0004970 ionotropic glutamate receptor activity IEA
MF GO:0042165 neurotransmitter binding ISS
MF GO:0030594 neurotransmitter receptor activity ISS
MF GO:0004972 NMDA glutamate receptor activity IBA
MF GO:0004872 receptor activity IEA

KEGG Pathways

Click on a pathway accession number to view term details at KEGG.

Click on the number in the Find Similar column to get a list of genes annotated by the associated pathway.

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Pathway KEGG Accession Graph
Alcoholism hsa05034
Amphetamine addiction hsa05031
cAMP signaling pathway hsa04024
Cocaine addiction hsa05030
Glutamatergic synapse hsa04724
Neuroactive ligand-receptor interaction hsa04080
Nicotine addiction hsa05033