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

Summary

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: mouse all
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Genomic context

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_000009.12 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
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?

Excitatory GluN1/GluN3A glycine receptors (eGlyRs) in brain signaling.
Title: Excitatory GluN1/GluN3A glycine receptors (eGlyRs) in brain signaling.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed
Genome-wide association analyses suggest NELL1 influences adverse metabolic response to HCTZ in African Americans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. 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 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

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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

SHGC-86259 (e-PCR)
- UniSTS:104489

GRIN3A_972 (e-PCR)
- UniSTS:277298

SHGC-148080 (e-PCR)
- UniSTS:176183

WI-14669 (e-PCR)
- UniSTS:65346

RH91980 (e-PCR)
- UniSTS:88400

SHGC-79388 (e-PCR)
- UniSTS:103281

SHGC-107521 (e-PCR)
- UniSTS:170417

G10443 (e-PCR)
- UniSTS:15285

D9S1054E (e-PCR)
- UniSTS:151271

SHGC-79539 (e-PCR)
- UniSTS:103664

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)

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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

101569352..101738647 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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