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GRIN3A glutamate ionotropic receptor NMDA type subunit 3A [ Homo sapiens (human) ]

Gene ID: 116443, updated on 18-Nov-2024

Summary

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Official Symbol
GRIN3Aprovided by HGNC
Official Full Name
glutamate ionotropic receptor NMDA type subunit 3Aprovided by HGNC
Primary source
HGNC:HGNC:16767
See related
Ensembl:ENSG00000198785 MIM:606650; AllianceGenome:HGNC:16767
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
NR3A; GluN3A; NMDAR-L; NMDAR3A
Summary
This gene encodes a subunit of the N-methyl-D-aspartate (NMDA) receptors, which belong to the superfamily of glutamate-regulated ion channels, and function in physiological and pathological processes in the central nervous system. This subunit shows greater than 90% identity to the corresponding subunit in rat. Studies in the knockout mouse deficient in this subunit suggest that this gene may be involved in the development of synaptic elements by modulating NMDA receptor activity. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 4.0), prostate (RPKM 0.5) and 3 other tissues See more
Orthologs
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Genomic context

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See GRIN3A in Genome Data Viewer
Location:
9q31.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (101569352..101738647, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (113744124..113912649, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (104331634..104500929, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene TMEM246 antisense RNA 1 Neighboring gene post-GPI attachment to proteins GalNAc transferase 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:104275376-104275886 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:104275887-104276395 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:104276396-104276905 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:104286647-104287146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28726 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:104316489-104316706 Neighboring gene ring finger protein 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28727 Neighboring gene uncharacterized LOC105376186 Neighboring gene protein phosphatase 3 regulatory subunit B, beta Neighboring gene Sharpr-MPRA regulatory region 1857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:104500238-104500762 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:104500763-104501286 Neighboring gene MT-ND3 pseudogene 4 Neighboring gene uncharacterized LOC105376187

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Genetics of glucocorticoid-associated osteonecrosis in children with acute lymphoblastic leukemia. Karol SE, et al. Blood, 2015 Oct 8. PMID 26265699, Free PMC Article
  2. A population-specific uncommon variant in GRIN3A associated with schizophrenia. Takata A, et al. Biol Psychiatry, 2013 Mar 15. PMID 23237318
  3. The NMDA receptor subunit GluN3A protects against 3-nitroproprionic-induced striatal lesions via inhibition of calpain activation. Martínez-Turrillas R, et al. Neurobiol Dis, 2012 Dec. PMID 22801082
  4. Association between GRIN3A gene polymorphism in Kawasaki disease and coronary artery aneurysms in Taiwanese children. Lin YJ, et al. PLoS One, 2013. PMID 24278430, Free PMC Article
  5. Significant association of glutamate receptor, ionotropic N-methyl-D-aspartate 3A (GRIN3A), with nicotine dependence in European- and African-American smokers. Ma JZ, et al. Hum Genet, 2010 Mar. PMID 20084518, Free PMC Article

See all (96) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Excitatory GluN1/GluN3A glycine receptors (eGlyRs) in brain signaling.
    Title: Excitatory GluN1/GluN3A glycine receptors (eGlyRs) in brain signaling.
  2. Correlations between GRIN2B and GRIN3A gene polymorphisms and postpartum depressive symptoms in Chinese parturients undergoing cesarean section: A prospective cohort study.
    Title: Correlations between GRIN2B and GRIN3A gene polymorphisms and postpartum depressive symptoms in Chinese parturients undergoing cesarean section: A prospective cohort study.
  3. Pathogenesis of sporadic Alzheimer's disease by deficiency of NMDA receptor subunit GluN3A.
    Title: Pathogenesis of sporadic Alzheimer's disease by deficiency of NMDA receptor subunit GluN3A.
  4. Demonstration of critical role of GRIN3A in nicotine dependence through both genetic association and molecular functional studies.
    Title: Demonstration of critical role of GRIN3A in nicotine dependence through both genetic association and molecular functional studies.
  5. Structural features in the glycine-binding sites of the GluN1 and GluN3A subunits regulate the surface delivery of NMDA receptors.
    Title: Structural features in the glycine-binding sites of the GluN1 and GluN3A subunits regulate the surface delivery of NMDA receptors.
  6. GRIN3A locus was associated with thyroid antibodies levels in females.
    Title: Genome-wide meta-analysis identifies novel gender specific loci associated with thyroid antibodies level in Croatians.
  7. Results suggest that GRIN3A rs17189632 and GRIN3B rs2240158 may contribute to the susceptibility of heroin addiction.
    Title: Association between genetic variations of NMDA receptor NR3 subfamily genes and heroin addiction in male Han Chinese.
  8. discuss current evidence for emerging roles for GluN3NMDARs in the physiology and pathology of the CNS.
    Title: Emerging roles of GluN3-containing NMDA receptors in the CNS.
  9. Increased expression levels of MAPT and GRIN3A may lead to the abnormal pathologic condition of nerve tissue in macrodactyly and, to a certain extent, may have potential applications in nerve regeneration.
    Title: GRIN3A and MAPT stimulate nerve overgrowth in macrodactyly.
  10. The rare variants in GRIN3A were significantly associated with smoking status.
    Title: The contribution of rare and common variants in 30 genes to risk nicotine dependence.
Submit: New GeneRIF Correction See all GeneRIFs (39)

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

EBI GWAS Catalog

Description
Genetics of coronary artery calcification among African Americans, a meta-analysis.
EBI GWAS Catalog
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

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 gp120-mediated human cell death involves the NMDA receptor complex; antagonists of the NMDA receptor reverse the gp120-mediated effects 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 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 causes an activation of phospholipase A2, resulting in the increased release of arachidonic acid, which may sensitize the NMDA receptor 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

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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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

Homology

Clone Names

  • FLJ45414

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to NMDA glutamate receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables NMDA glutamate receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
contributes_to NMDA glutamate receptor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables calcium channel activity IEA
Inferred from Electronic Annotation
more info
  
enables glutamate receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables glycine binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein phosphatase 2A binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables serine binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables transmitter-gated monoatomic ion channel 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 calcium ion transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in dendrite development 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 modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in monoatomic cation transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of dendritic spine development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in prepulse inhibition IEA
Inferred from Electronic Annotation
more info
  
involved_in presynaptic modulation of chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of postsynaptic membrane potential IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of synaptic plasticity ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in response to ethanol IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rhythmic process 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 IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
part_of monoatomic ion channel complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in neuron projection IDA
Inferred from Direct Assay
more info
 PubMed 
located_in neuronal cell body IDA
Inferred from Direct Assay
more info
 PubMed 
part_of neurotransmitter receptor complex IDA
Inferred from Direct Assay
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
  
is_active_in postsynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
located_in synapse IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
glutamate receptor ionotropic, NMDA 3A
Names
N-methyl-D-aspartate receptor subtype 3A
glutamate [NMDA] receptor subunit 3A
glutamate receptor, ionotropic, N-methyl-D-aspartate 3A

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)

  1. NM_133445.3 → NP_597702.2  glutamate receptor ionotropic, NMDA 3A precursor

    See identical proteins and their annotated locations for NP_597702.2

    Status: REVIEWED

    Source sequence(s)
    AF416558, AL356516, AL591377, BC167432
    Consensus CDS
    CCDS6758.1
    UniProtKB/Swiss-Prot
    B3DLF9, Q5VTR3, Q8TCU5, Q8TF29, Q8WXI6
    UniProtKB/TrEMBL
    A2RUE7
    Related
    ENSP00000355155.3, ENST00000361820.6
    Conserved Domains (4) summary
    cd06377
    Location:30 → 497
    PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family
    cd13720
    Location:512 → 908
    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:676 → 942
    Lig_chan; Ligand-gated ion channel
    pfam01094
    Location:127 → 469
    ANF_receptor; Receptor family ligand binding region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    101569352..101738647 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518211.3 → XP_011516513.1  glutamate receptor ionotropic, NMDA 3A isoform X1

    UniProtKB/TrEMBL
    A2RUE7
    Conserved Domains (4) summary
    cd06377
    Location:30 → 497
    PBP1_iGluR_NMDA_NR3; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family
    cd13720
    Location:512 → 908
    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:676 → 922
    Lig_chan; Ligand-gated ion channel
    pfam01094
    Location:127 → 469
    ANF_receptor; Receptor family ligand binding region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    113744124..113912649 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054361948.1 → XP_054217923.1  glutamate receptor ionotropic, NMDA 3A isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TCU5.2 GenPept UniProtKB/Swiss-Prot:Q8TCU5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
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