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GABRB3 gamma-aminobutyric acid type A receptor subunit beta3 [ Homo sapiens (human) ]

Gene ID: 2562, updated on 11-Apr-2024

Summary

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Official Symbol
GABRB3provided by HGNC
Official Full Name
gamma-aminobutyric acid type A receptor subunit beta3provided by HGNC
Primary source
HGNC:HGNC:4083
See related
Ensembl:ENSG00000166206 MIM:137192; AllianceGenome:HGNC:4083
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
ECA5; DEE43; EIEE43
Summary
This gene encodes a member of the ligand-gated ionic channel family. The encoded protein is one the subunits of a multi-subunit chloride channel that serves as the receptor for gamma-aminobutyric acid, a major inhibitory neurotransmitter of the mammalian nervous system. This gene is located on the long arm of chromosome 15 in a cluster with two other genes encoding related subunits of the family. This gene may be associated with the pathogenesis of several disorders including Angelman syndrome, Prader-Willi syndrome, nonsyndromic orofacial clefts, epilepsy and autism. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2013]
Expression
Biased expression in brain (RPKM 22.9), gall bladder (RPKM 6.3) and 7 other tissues See more
Orthologs
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Genomic context

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See GABRB3 in Genome Data Viewer
Location:
15q12
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (26543552..26773763, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (24283987..24515087, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (26788699..27018910, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903568 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:26570561-26571281 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:26606040-26606210 Neighboring gene uncharacterized LOC105370740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26655893-26656682 Neighboring gene long intergenic non-protein coding RNA 2248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26707088-26707588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:26776555-26777054 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:26791415-26792614 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:26860170-26861369 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:26893977-26894477 Neighboring gene uncharacterized LOC124903578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:26933878-26934623 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:26963662-26964469 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:26964470-26965276 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:26965277-26966083 Neighboring gene uncharacterized LOC112268151 Neighboring gene NANOG hESC enhancer GRCh37_chr15:27010978-27011567 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:27011568-27012156 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:27012157-27012746 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:27034764-27035963 Neighboring gene ribosomal protein L9 pseudogene 26 Neighboring gene gamma-aminobutyric acid type A receptor subunit alpha5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:27174238-27174786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:27189763-27190342

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. Gain-of-function and loss-of-function GABRB3 variants lead to distinct clinical phenotypes in patients with developmental and epileptic encephalopathies. Absalom NL, et al. Nat Commun, 2022 Apr 5. PMID 35383156, Free PMC Article
  2. Structural mapping of GABRB3 variants reveals genotype-phenotype correlations. Johannesen KM, et al. Genet Med, 2022 Mar. PMID 34906499
  3. GABRB3-related epilepsy: novel variants, clinical features and therapeutic implications. Yang Y, et al. J Neurol, 2022 May. PMID 34698933
  4. Synaptic clustering differences due to different GABRB3 mutations cause variable epilepsy syndromes. Shi YW, et al. Brain, 2019 Oct 1. PMID 31435640, Free PMC Article
  5. Functional analysis of haplotypes and promoter activity at the 5' region of the human GABRB3 gene and associations with schizophrenia. Liu Y, et al. Mol Genet Genomic Med, 2019 May. PMID 30908890, Free PMC Article

See all (131) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Integrated analysis identifies GABRB3 as a biomarker in prostate cancer.
    Title: Integrated analysis identifies GABRB3 as a biomarker in prostate cancer.
  2. Correlations of receptor desensitization of gain-of-function GABRB3 variants with clinical severity.
    Title: Correlations of receptor desensitization of gain-of-function GABRB3 variants with clinical severity.
  3. Association of GABRG3, GABRB3, HTR2A gene variants with autism spectrum disorder.
    Title: Association of GABRG3, GABRB3, HTR2A gene variants with autism spectrum disorder.
  4. Gabrb3 is required for the functional integration of pyramidal neuron subtypes in the somatosensory cortex.
    Title: Gabrb3 is required for the functional integration of pyramidal neuron subtypes in the somatosensory cortex.
  5. GABA Receptor SNPs and Elevated Plasma GABA Levels Affect the Severity of the Indian ASD Probands.
    Title: GABA Receptor SNPs and Elevated Plasma GABA Levels Affect the Severity of the Indian ASD Probands.
  6. GABRB3-related epilepsy: novel variants, clinical features and therapeutic implications.
    Title: GABRB3-related epilepsy: novel variants, clinical features and therapeutic implications.
  7. Gain-of-function and loss-of-function GABRB3 variants lead to distinct clinical phenotypes in patients with developmental and epileptic encephalopathies.
    Title: Gain-of-function and loss-of-function GABRB3 variants lead to distinct clinical phenotypes in patients with developmental and epileptic encephalopathies.
  8. Structural mapping of GABRB3 variants reveals genotype-phenotype correlations.
    Title: Structural mapping of GABRB3 variants reveals genotype-phenotype correlations.
  9. Gene expression meta-analysis reveals the down-regulation of three GABA receptor subunits in the superior temporal gyrus of patients with schizophrenia.
    Title: Gene expression meta-analysis reveals the down-regulation of three GABA receptor subunits in the superior temporal gyrus of patients with schizophrenia.
  10. Photoaffinity labeling identifies an intersubunit steroid-binding site in heteromeric GABA type A (GABAA) receptors.
    Title: Photoaffinity labeling identifies an intersubunit steroid-binding site in heteromeric GABA type A (GABA(A)) receptors.
Submit: New GeneRIF Correction See all GeneRIFs (72)

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
Developmental and epileptic encephalopathy, 43
MedGen: C4310712 OMIM: 617113 GeneReviews: Not available
Compare labs
Epilepsy, childhood absence, susceptibility to, 5
MedGen: C2677087 OMIM: 612269 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2012-04-25)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2012-04-25)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB.
EBI GWAS Catalog
Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
EBI GWAS Catalog
Joint influence of small-effect genetic variants on human longevity.
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)

Genotypes

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

  • MGC9051

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GABA-A receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables GABA-A receptor activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables GABA-gated chloride ion channel activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables GABA-gated chloride ion channel activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables GABA-gated chloride ion channel activity ISS
Inferred from Sequence or Structural Similarity
more info
  
contributes_to chloride channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables neurotransmitter receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in cellular response to histamine IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chloride transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chloride transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in chloride transmembrane transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chloride transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chloride transmembrane transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in gamma-aminobutyric acid signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in gamma-aminobutyric acid signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in gamma-aminobutyric acid signaling pathway NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in inhibitory synapse assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of membrane potential IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in roof of mouth development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in synaptic transmission, GABAergic NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of GABA-A receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of GABA-A receptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of GABA-A receptor complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of GABA-A receptor complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of GABA-A receptor complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of chloride channel complex IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of transmembrane transporter complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
gamma-aminobutyric acid receptor subunit beta-3
Names
GABA-alpha receptor beta-2 subunit
GABAA receptor beta-3 subunit
gamma-aminobutyric acid (GABA) A receptor, beta 3
gamma-aminobutyric acid A receptor beta 3
gamma-aminobutyric acid type A receptor beta3 subunit
gamma-aminobutyric acid type A receptor subunit beta 3

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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

  1. NG_012836.1 RefSeqGene

    Range
    5715..235229
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000814.6 → NP_000805.1  gamma-aminobutyric acid receptor subunit beta-3 isoform 1 precursor

    See identical proteins and their annotated locations for NP_000805.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1, which is of the same length as isoform 2, but has a distinct N-terminus.
    Source sequence(s)
    AC009878, AC104569, M82919
    Consensus CDS
    CCDS10019.1
    UniProtKB/Swiss-Prot
    B7Z2W1, B7Z825, F5H3D2, H7BYV8, P28472, Q14352, Q96FM5
    UniProtKB/TrEMBL
    A0A1B0GVW3
    Related
    ENSP00000308725.5, ENST00000311550.10
    Conserved Domains (1) summary
    TIGR00860
    Location:10 → 471
    LIC; Cation transporter family protein

  2. NM_001191320.2 → NP_001178249.1  gamma-aminobutyric acid receptor subunit beta-3 isoform 3

    See identical proteins and their annotated locations for NP_001178249.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks three exons in the 5' coding region and initiates translation at an in-frame downstream start codon, compared to variant 1. Variants 3 and 5 encode the same isoform (3), which is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC009878, AK302822, M82919
    Consensus CDS
    CCDS53920.1
    UniProtKB/TrEMBL
    A0A1B0GVW3
    Related
    ENSP00000489768.1, ENST00000636466.1
    Conserved Domains (2) summary
    pfam02931
    Location:1 → 158
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:165 → 383
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

  3. NM_001191321.3 → NP_001178250.1  gamma-aminobutyric acid receptor subunit beta-3 isoform 4

    See identical proteins and their annotated locations for NP_001178250.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks three exons in the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. It encodes isoform 4, which is shorter and has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AK056018, AK295167, AK302822, AL120032, BC010641, BE220174, CB162957, CD013894, DA138788
    Consensus CDS
    CCDS53921.1
    UniProtKB/TrEMBL
    A0A1B0GVW3
    Related
    ENSP00000383049.3, ENST00000400188.7
    Conserved Domains (2) summary
    pfam02931
    Location:6 → 172
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:179 → 397
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

  4. NM_001278631.2 → NP_001265560.1  gamma-aminobutyric acid receptor subunit beta-3 isoform 3

    See identical proteins and their annotated locations for NP_001265560.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate internal exon and initiates translation at a downstream start codon, compared to variant 1. Variants 3 and 5 encode the same isoform (3), which is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK056018, AL120032, BC010641, BE220174, CB162957, CD013894, DA138788, DB479831
    Consensus CDS
    CCDS53920.1
    UniProtKB/TrEMBL
    A0A1B0GVW3
    Conserved Domains (2) summary
    pfam02931
    Location:1 → 158
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:165 → 383
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

  5. NM_021912.5 → NP_068712.1  gamma-aminobutyric acid receptor subunit beta-3 isoform 2 precursor

    See identical proteins and their annotated locations for NP_068712.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' terminal exon compared to variant 1. It encodes isoform 2, which is of the same length, but has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC009878, AK315311, BC010641, CD652458
    Consensus CDS
    CCDS10018.1
    UniProtKB/TrEMBL
    B2RCW8, X5DQY4
    Related
    ENSP00000299267.4, ENST00000299267.9
    Conserved Domains (1) summary
    TIGR00860
    Location:23 → 471
    LIC; Cation transporter family protein

RNA

  1. NR_103801.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate 5' and 3' exon structure compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC011196, BC038837
    Related
    ENST00000556166.2

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

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    26543552..26773763 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521428.4 → XP_011519730.1  gamma-aminobutyric acid receptor subunit beta-3 isoform X1

    UniProtKB/TrEMBL
    A0A1B0GVW3
    Related
    ENST00000635832.1
    Conserved Domains (2) summary
    pfam02931
    Location:22 → 184
    Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain
    pfam02932
    Location:191 → 409
    Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    24283987..24515087 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377668.1 → XP_054233643.1  gamma-aminobutyric acid receptor subunit beta-3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P28472.1 GenPept UniProtKB/Swiss-Prot:P28472

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