GRIN3B glutamate ionotropic receptor NMDA type subunit 3B [Homo sapiens (human)] - Gene

Summary

Official Symbol: GRIN3Bprovided by HGNC
Official Full Name: glutamate ionotropic receptor NMDA type subunit 3Bprovided by HGNC
Primary source: HGNC:HGNC:16768
See related: Ensembl:ENSG00000116032 MIM:606651; AllianceGenome:HGNC:16768
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NR3B; GluN3B
Summary: The protein encoded by this gene is a subunit of an N-methyl-D-aspartate (NMDA) receptor. The encoded protein is found primarily in motor neurons, where it forms a heterotetramer with GRIN1 to create an excitatory glycine receptor. Variations in this gene have been proposed to be linked to schizophrenia. [provided by RefSeq, Nov 2015]
Expression: Ubiquitous expression in spleen (RPKM 1.5), fat (RPKM 1.0) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19p13.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (1000419..1009732)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (963087..972401)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (1000418..1009731)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GRIN3B missense mutation is an inherited risk factor for schizophrenia.
Title: GRIN3B missense mutation as an inherited risk factor for schizophrenia: whole-exome sequencing in a family with a familiar history of psychotic disorders.
Authors investigated the significance of a common human genetic variation of the NMDAR NR3B subunit
Title: A naturally occurring null variant of the NMDA type glutamate receptor NR3B subunit is a risk factor of schizophrenia.
Rs2240158 of GRIN3B was significantly associated with mismatch negativity in healthy subjects.
Title: A recently-discovered NMDA receptor gene, GRIN3B, is associated with duration mismatch negativity.
our findings suggest that the over-expression of NR3B subunit of NMDA receptor is a long lasting result of chronic opioid abuse.
Title: Expression of NR3B but not NR2D subunit of NMDA receptor in human blood lymphocytes can serve as a suitable peripheral marker for opioid addiction studies.
These observations suggest that the genetic variation of the NR3B subunit of the NMDA receptor is not a risk factor for Alzheimer's dis pathogenesis
Title: Genetic variation in N-methyl-D-aspartate receptor subunit NR3A but not NR3B influences susceptibility to Alzheimer's disease.
Observational study of gene-disease association. (HuGE Navigator)
Title: Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients.
Clinical trial of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Pharmacogenetics of antipsychotic response in the CATIE trial: a candidate gene analysis.
We tested whether genetic dysfunction of GRIN3B is implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS).
Title: Motoneuron-specific NR3B gene: no association with ALS and evidence for a common null allele.
NR3B mRNA expression in the human hippocampal formation (CA1-CA4 and dentate gyrus) and adjacent neocortex may have implications for understanding the role of NMDA receptors for physiological and pathological processes in these forebrain regions.
Title: Cloning and expression of the human NMDA receptor subunit NR3B in the adult human hippocampus.
cross-talk between NR3B and NR4A receptors is a mechanism modulating the transcriptional activities of these orphan nuclear receptors
Title: Cross-talk between the NR3B and NR4A families of orphan nuclear receptors.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-02-02) ClinGen Genome Curation Page Haploinsufficency Dosage sensitivity unlikely (Last evaluated 2021-02-02) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E &#x000cf;&#x000b5;4,and the risk of late-onset Alzheimer disease in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120-induced dephosphorylation of KV2.1 is dependent on NMDA receptor-mediated activation of protein phosphatase 2B or calcineurin	PubMed
	env	HIV-1 gp120 activates forward trafficking and surface clustering of NMDA receptors in membrane microdomains by a PKA-dependent phosphorylation of the NR1 C-terminal Ser897, followed by a PKC-dependent phosphorylation of Ser896	PubMed
	env	HIV-1 gp120 activates NMDA receptor directly and phosphorylates JNK through a gp120-mediated apoptotic pathway in human neuroblastoma cells	PubMed
	env	HIV-1 clade B gp120 significantly downregulates NMDA receptor gene and protein expression and levels of glutamine compared to clade C gp120	PubMed
	env	HIV-1 gp120 binds to cells expressing epsilon1/zeta1 or epsilon2/zeta1 combined NMDA receptor subunits, but not to cells expressing a single epsilon1, epsilon2, or zeta1 NMDA receptor subunit	PubMed
	env	HIV-1 gp120 causes an activation of phospholipase A2, resulting in the increased release of arachidonic acid, which may sensitize the NMDA receptor	PubMed
	env	HIV-1 gp120-mediated human cell death involves the NMDA receptor complex; antagonists of the NMDA receptor reverse the gp120-mediated effects	PubMed
Tat	tat	HIV-1 Tat upregulates the expression of NMDARs for the apoptosis of retinal pigmen epithelium (RPE) cells. Silencing of NMDARs by siRNA abolishes Tat-induced RPE apoptosis	PubMed
	tat	HIV-1 Tat interacts with NMDA receptors in primary neuronal-glial cultures and in hippocampal slice cultures	PubMed
	tat	HIV-1 Tat and methamphetamine inhibit the normal conjunction of signaling between D1 and NMDA receptors, resulting in neural dysfunction and death	PubMed
	tat	HIV-1 Tat induces apoptosis of neurons and neurotoxicity through the activation of both NMDA and non-NMDA receptors	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D19S886 (e-PCR), detects polymorphism
- UniSTS:73125

SGC32341 (e-PCR)
- UniSTS:61144

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
contributes_to NMDA glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
contributes_to calcium channel activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine binding	ISS Inferred from Sequence or Structural Similarity more info
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IDA Inferred from Direct Assay more info	PubMed
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed
enables ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	NAS Non-traceable Author Statement more info	PubMed
enables monoatomic cation channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables neurotransmitter receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in calcium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in ionotropic glutamate receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ionotropic glutamate receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in modulation of chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein insertion into membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of calcium ion transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in regulation of postsynaptic membrane potential	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glutamatergic	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of NMDA selective glutamate receptor complex	ISS Inferred from Sequence or Structural Similarity more info	PubMed
part_of NMDA selective glutamate receptor complex	NAS Non-traceable Author Statement more info	PubMed
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in postsynaptic density membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: glutamate receptor ionotropic, NMDA 3B

Names: N-methyl-D-aspartate receptor subtype 3B; NMDA receptor subunit 3B; NMDA type glutamate receptor subunit NR3B; NMDAR3B; glutamate [NMDA] receptor subunit 3B; glutamate receptor, ionotropic, N-methyl-D-aspartate 3B

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_138690.3 → NP_619635.1 glutamate receptor ionotropic, NMDA 3B precursor

See identical proteins and their annotated locations for NP_619635.1

Status: REVIEWED

Source sequence(s)

AY507106, BK004079, BM977634

Consensus CDS

CCDS32861.1

UniProtKB/Swiss-Prot

O60391, Q5EAK7, Q7RTW9

UniProtKB/TrEMBL

Q5F0I5

Related

ENSP00000234389.3, ENST00000234389.3

Conserved Domains (3) summary

cd06377
Location:19 → 405

PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family

cd13720
Location:415 → 808

PBP2_iGluR_NMDA_Nr3; The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily

pfam00060
Location:576 → 842

Lig_chan; Ligand-gated ion channel