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

    Gene ID: 2562, updated on 9-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (26543552..26773763, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (24283987..24515087, complement)
    RS_2024_09 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. Lack of evidence of an allelic association of a functional GABRB3 exon 1a promoter polymorphism with idiopathic generalized epilepsy. Hempelmann A, et al. Epilepsy Res, 2007 Apr. PMID 17215107
    2. Mutations in GABRB3: From febrile seizures to epileptic encephalopathies. Møller RS, et al. Neurology, 2017 Jan 31. PMID 28053010, Free PMC Article
    3. Genetic analysis of GABRB3 at 15q12 as a candidate gene of schizophrenia. Huang CC, et al. Psychiatr Genet, 2014 Aug. PMID 24865167
    4. Polymorphisms in GABRB3 and oral clefting in the Brazilian population. Filézio MR, et al. DNA Cell Biol, 2013 Mar. PMID 23438326
    5. [Polymorphisms of rs4906902 and rs8179184 loci in the promoter of the GABRB3 gene and their relevance with schizophrenia]. Sun XF, et al. Fa Yi Xue Za Zhi, 2012 Jun. PMID 22812221

    See all (140) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. An association study in the Taiwan Biobank elicits the GABAA receptor genes GABRB3, GABRA5, and GABRG3 as candidate loci for sleep duration in the Taiwanese population.
      Title: An association study in the Taiwan Biobank elicits the GABAA receptor genes GABRB3, GABRA5, and GABRG3 as candidate loci for sleep duration in the Taiwanese population.
    2. Role of beta3 subunit of the GABA type A receptor in triple negative breast cancer proliferation, migration, and cell cycle progression.
      Title: Role of β3 subunit of the GABA type A receptor in triple negative breast cancer proliferation, migration, and cell cycle progression.
    3. Integrated analysis identifies GABRB3 as a biomarker in prostate cancer.
      Title: Integrated analysis identifies GABRB3 as a biomarker in prostate cancer.
    4. 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.
    5. Association of GABRG3, GABRB3, HTR2A gene variants with autism spectrum disorder.
      Title: Association of GABRG3, GABRB3, HTR2A gene variants with autism spectrum disorder.
    6. 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.
    7. 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.
    8. GABRB3-related epilepsy: novel variants, clinical features and therapeutic implications.
      Title: GABRB3-related epilepsy: novel variants, clinical features and therapeutic implications.
    9. 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.
    10. Structural mapping of GABRB3 variants reveals genotype-phenotype correlations.
      Title: Structural mapping of GABRB3 variants reveals genotype-phenotype correlations.
    Submit: New GeneRIF Correction See all GeneRIFs (74)

    Phenotypes

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    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)

    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables GABA-A receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables GABA-A receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 
    Process Evidence Code Pubs
    involved_in cellular response to histamine IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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 roof of mouth development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptic transmission, GABAergic IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 dendritic spine IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    is_active_in postsynaptic membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in postsynaptic specialization membrane ISS
    Inferred from Sequence or Structural Similarity
    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
    GABAAR subunit beta-3
    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_2024_08

    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

      UniProtKB/TrEMBL
      A0A1B0GVW3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P28472.1 GenPept UniProtKB/Swiss-Prot:P28472

    Gene LinkOut

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