GRID2 glutamate ionotropic receptor delta type subunit 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: GRID2provided by HGNC
Official Full Name: glutamate ionotropic receptor delta type subunit 2provided by HGNC
Primary source: HGNC:HGNC:4576
See related: Ensembl:ENSG00000152208 MIM:602368; AllianceGenome:HGNC:4576
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: GluD2; SCAR18
Summary: The protein encoded by this gene is a member of the family of ionotropic glutamate receptors which are the predominant excitatory neurotransmitter receptors in the mammalian brain. The encoded protein is a multi-pass membrane protein that is expressed selectively in cerebellar Purkinje cells. A point mutation in the mouse ortholog, associated with the phenotype named 'lurcher', in the heterozygous state leads to ataxia resulting from selective, cell-autonomous apoptosis of cerebellar Purkinje cells during postnatal development. Mice homozygous for this mutation die shortly after birth from massive loss of mid- and hindbrain neurons during late embryogenesis. This protein also plays a role in synapse organization between parallel fibers and Purkinje cells. Alternate splicing results in multiple transcript variants encoding distinct isoforms. Mutations in this gene cause cerebellar ataxia in humans. [provided by RefSeq, Apr 2014]
Expression: Low expression observed in reference dataset See more
Orthologs: mouse all
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Genomic context

Location:: 4q22.1-q22.2

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (92303966..93810456)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (95630513..97125831)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (93225117..94695717)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Clinical features, functional consequences, and rescue pharmacology of missense GRID1 and GRID2 human variants.
Title: Clinical features, functional consequences, and rescue pharmacology of missense GRID1 and GRID2 human variants.
Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect.
Title: Neurodevelopmental Syndrome with Intellectual Disability, Speech Impairment, and Quadrupedia Is Associated with Glutamate Receptor Delta 2 Gene Defect.
Autosomal recessive spinocerebellar ataxia 18 caused by homozygous exon 14 duplication in GRID2 and review of the literature.
Title: Autosomal recessive spinocerebellar ataxia 18 caused by homozygous exon 14 duplication in GRID2 and review of the literature.
Association of Gene Variations in Ionotropic Glutamate Receptor and Attention-Deficit/Hyperactivity Disorder in the Chinese Population: A Two-Stage Case-Control Study.
Title: Association of Gene Variations in Ionotropic Glutamate Receptor and Attention-Deficit/Hyperactivity Disorder in the Chinese Population: A Two-Stage Case-Control Study.
Report on a consanguineous family with autosomal recessive childhood onset of cerebellar ataxia and delayed psychomotor development. Using whole exome sequencing we identified a novel homozygous missense variant [c.2128C > T, p.(Arg710Trp)] in GRID2 that segregates with the disease. The missense variant is located in a conserved region encoding the extracellular serine-binding domain of the GluD2 protein.
Title: Homozygous GRID2 missense mutation predicts a shift in the D-serine binding domain of GluD2 in a case with generalized brain atrophy and unusual clinical features.
GRID2 gene can be a suppressor in TNF-induced neurodegeneration which may help to understand the main factors leading to autism.
Title: Potential of GRID2 receptor gene for preventing TNF-induced neurodegeneration in autism.
Glutamate system genes including have been associated with disease risk in recent analyses from the Psychiatric Genomics Consortium.
Title: Antipsychotic pharmacogenomics in first episode psychosis: a role for glutamate genes.
findings suggest a possible role of GRID2 in the susceptibility to develop mevalonate kinase deficiency. GRID2 gene associated with MKD: The rs1450500 SNP was differently distributed in patients with MKD with respect to those with recurrent fever.
Title: GRID2 a novel gene possibly associated with mevalonate kinase deficiency.
We demonstrated for the first time GRID2 expression and localization in human and murine retina, providing evidence for a novel functional role of GRID2 in the retina.
Title: Early-onset autosomal recessive cerebellar ataxia associated with retinal dystrophy: new human hotfoot phenotype caused by homozygous GRID2 deletion.
GRID2 point mutations: cerebellar ataxia is the core phenotype, but with variable severity ranging from very mild adult-onset to congenital-onset linked to both the heterozygous and homozygous state of the variant, and the position of the mutation.
Title: GRID2 mutations span from congenital to mild adult-onset cerebellar ataxia.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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

Associated conditions

Description	Tests
Autosomal recessive spinocerebellar ataxia 18 MedGen: C4015505 OMIM: 616204 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-50210 (e-PCR)
- UniSTS:77824

SHGC-51584 (e-PCR)
- UniSTS:65029

SHGC4-1553 (e-PCR)
- UniSTS:57606

RH119932 (e-PCR)
- UniSTS:133133

RH119596 (e-PCR)
- UniSTS:133911

SHGC-50409 (e-PCR)
- UniSTS:48154

D4S2364 (e-PCR)
- UniSTS:2341

SHGC-107742 (e-PCR)
- UniSTS:173862

SHGC-111791 (e-PCR)
- UniSTS:168751

SHGC-79101 (e-PCR)
- UniSTS:95806

D4S965 (e-PCR)
- UniSTS:25153

SHGC-146786 (e-PCR)
- UniSTS:175429

D4S650 (e-PCR)
- UniSTS:148294

D4S2692 (e-PCR)
- UniSTS:152391

D4S2693 (e-PCR)
- UniSTS:152392

G16769 (e-PCR)
- UniSTS:65869

D4S799 (e-PCR)
- UniSTS:148301

RH92539 (e-PCR)
- UniSTS:84813

WI-13806 (e-PCR)
- UniSTS:70996

SHGC-105322 (e-PCR)
- UniSTS:169304

SHGC-67661 (e-PCR)
- UniSTS:28763

SHGC-110334 (e-PCR)
- UniSTS:167781

SHGC-132008 (e-PCR)
- UniSTS:170601

SHGC-24441 (e-PCR)
- UniSTS:63593

SHGC-51119 (e-PCR)
- UniSTS:19324

D4S2351 (e-PCR)
- UniSTS:149888

D4S1135 (e-PCR)
- UniSTS:69250

Grid2 (e-PCR), detects polymorphism
- UniSTS:143255

Grid2 (e-PCR), detects polymorphism
- UniSTS:143256

SHGC-154327 (e-PCR)
- UniSTS:178079

D4S3224 (e-PCR)
- UniSTS:21410

D4S3264 (e-PCR)
- UniSTS:56237

G34300 (e-PCR)
- UniSTS:64176

G09726 (e-PCR)
- UniSTS:82354

D4S2404 (e-PCR), detects polymorphism
- UniSTS:17849

SHGC-78763 (e-PCR)
- UniSTS:95673

SHGC-85257 (e-PCR)
- UniSTS:104382

G54560 (e-PCR)
- UniSTS:117698

STS-Z70764 (e-PCR)
- UniSTS:69317

SHGC-78799 (e-PCR)
- UniSTS:95685

D4S477 (e-PCR)
- UniSTS:59336

G59222 (e-PCR)
- UniSTS:136395

D4S2667 (e-PCR)
- UniSTS:36566

D4S312 (e-PCR)
- UniSTS:54755

D4S542 (e-PCR)
- UniSTS:41214

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables PDZ domain binding	ISS Inferred from Sequence or Structural Similarity more info
enables glutamate receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables scaffold protein binding	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 cerebellar granule cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in excitatory postsynaptic potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in excitatory synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glutamate receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules	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 monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of long-term synaptic depression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synapse assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in prepulse inhibition	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuron apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of neuron projection development	IEA Inferred from Electronic Annotation more info
involved_in regulation of postsynaptic density assembly	IEA Inferred from Electronic Annotation more info
involved_in regulation of presynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glutamatergic	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic transmission, glutamatergic	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
part_of ionotropic glutamate receptor complex	ISS Inferred from Sequence or Structural Similarity more info
located_in parallel fiber to Purkinje cell synapse	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in postsynaptic density membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: glutamate receptor ionotropic, delta-2

Names: gluR delta-2 subunit; glutamate receptor delta-2 subunit; glutamate receptor, ionotropic, delta 2

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.

Genomic

NG_034113.2 RefSeqGene

Range

5002..1475602

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001286838.1 → NP_001273767.1 glutamate receptor ionotropic, delta-2 isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AB209318, AC104077, AW295056, BC099653, BC099654

Consensus CDS

CCDS68758.1

UniProtKB/TrEMBL

A0A087X043

Related

ENSP00000421257.1, ENST00000510992.5

Conserved Domains (3) summary

cd13731
Location:345 → 711

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily

pfam00060
Location:473 → 747

Lig_chan; Ligand-gated ion channel

cl10011
Location:28 → 332

Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
NM_001510.4 → NP_001501.2 glutamate receptor ionotropic, delta-2 isoform 1 precursor

See identical proteins and their annotated locations for NP_001501.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB209318, AC104077, AC112695, AW295056, BC099653

Consensus CDS

CCDS3637.1

UniProtKB/Swiss-Prot

E9PH24, O43424, Q4KKU8, Q4KKU9, Q4KKV0, Q59FZ1

UniProtKB/TrEMBL

A0A087X043

Related

ENSP00000282020.4, ENST00000282020.9

Conserved Domains (2) summary

cd13731
Location:440 → 806

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily

cd06391
Location:28 → 429

PBP1_iGluR_delta_2; N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

92303966..93810456

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047450133.1 → XP_047306089.1 glutamate receptor ionotropic, delta-2 isoform X7
XM_024454024.2 → XP_024309792.1 glutamate receptor ionotropic, delta-2 isoform X2

UniProtKB/TrEMBL

A0A087X043

Conserved Domains (2) summary

cd06391
Location:28 → 443

PBP1_iGluR_delta_2; N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family

cd13731
Location:456 → 822

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily
XM_017008122.3 → XP_016863611.1 glutamate receptor ionotropic, delta-2 isoform X9
XM_017008120.3 → XP_016863609.1 glutamate receptor ionotropic, delta-2 isoform X5

UniProtKB/TrEMBL

A0A087X043
XM_047450132.1 → XP_047306088.1 glutamate receptor ionotropic, delta-2 isoform X6
XM_011531893.3 → XP_011530195.2 glutamate receptor ionotropic, delta-2 isoform X1

UniProtKB/TrEMBL

A0A087X043
XM_017008118.2 → XP_016863607.1 glutamate receptor ionotropic, delta-2 isoform X3

UniProtKB/TrEMBL

A0A087X043
XM_017008121.2 → XP_016863610.1 glutamate receptor ionotropic, delta-2 isoform X8
XM_017008127.2 → XP_016863616.1 glutamate receptor ionotropic, delta-2 isoform X14
XM_017008119.2 → XP_016863608.1 glutamate receptor ionotropic, delta-2 isoform X4

UniProtKB/TrEMBL

A0A087X043

Related

ENSP00000483084.1, ENST00000611049.4
XM_047450134.1 → XP_047306090.1 glutamate receptor ionotropic, delta-2 isoform X11
XM_047450135.1 → XP_047306091.1 glutamate receptor ionotropic, delta-2 isoform X11
XM_047450136.1 → XP_047306092.1 glutamate receptor ionotropic, delta-2 isoform X11
XM_011531894.3 → XP_011530196.1 glutamate receptor ionotropic, delta-2 isoform X10

UniProtKB/TrEMBL

A0A087X043

Conserved Domains (3) summary

cd13731
Location:212 → 578

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily

pfam00060
Location:340 → 614

Lig_chan; Ligand-gated ion channel

cl10011
Location:2 → 199

Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
XM_024454025.2 → XP_024309793.1 glutamate receptor ionotropic, delta-2 isoform X12

Conserved Domains (2) summary

cd13731
Location:121 → 487

PBP2_iGluR_delta_2; The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily

cl10011
Location:1 → 108

Periplasmic_Binding_Protein_Type_1; Type 1 periplasmic binding fold superfamily
XM_047450137.1 → XP_047306093.1 glutamate receptor ionotropic, delta-2 isoform X13

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

95630513..97125831

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054349824.1 → XP_054205799.1 glutamate receptor ionotropic, delta-2 isoform X7
XM_054349819.1 → XP_054205794.1 glutamate receptor ionotropic, delta-2 isoform X2
XM_054349826.1 → XP_054205801.1 glutamate receptor ionotropic, delta-2 isoform X9
XM_054349822.1 → XP_054205797.1 glutamate receptor ionotropic, delta-2 isoform X5
XM_054349823.1 → XP_054205798.1 glutamate receptor ionotropic, delta-2 isoform X6
XM_054349818.1 → XP_054205793.1 glutamate receptor ionotropic, delta-2 isoform X1
XM_054349820.1 → XP_054205795.1 glutamate receptor ionotropic, delta-2 isoform X3
XM_054349825.1 → XP_054205800.1 glutamate receptor ionotropic, delta-2 isoform X8
XM_054349833.1 → XP_054205808.1 glutamate receptor ionotropic, delta-2 isoform X14
XM_054349821.1 → XP_054205796.1 glutamate receptor ionotropic, delta-2 isoform X4
XM_054349828.1 → XP_054205803.1 glutamate receptor ionotropic, delta-2 isoform X11
XM_054349829.1 → XP_054205804.1 glutamate receptor ionotropic, delta-2 isoform X11
XM_054349830.1 → XP_054205805.1 glutamate receptor ionotropic, delta-2 isoform X11
XM_054349827.1 → XP_054205802.1 glutamate receptor ionotropic, delta-2 isoform X10
XM_054349831.1 → XP_054205806.1 glutamate receptor ionotropic, delta-2 isoform X12
XM_054349832.1 → XP_054205807.1 glutamate receptor ionotropic, delta-2 isoform X13