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SLC6A11 solute carrier family 6 member 11 [ Homo sapiens (human) ]

Gene ID: 6538, updated on 11-Apr-2024

Summary

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Official Symbol
SLC6A11provided by HGNC
Official Full Name
solute carrier family 6 member 11provided by HGNC
Primary source
HGNC:HGNC:11044
See related
Ensembl:ENSG00000132164 MIM:607952; AllianceGenome:HGNC:11044
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
GAT3; GAT4; GAT-3
Summary
The protein encoded by this gene is a sodium-dependent transporter that uptakes gamma-aminobutyric acid (GABA), an inhibitory neurotransmitter, which ends the GABA neurotransmission. Defects in this gene may result in epilepsy, behavioral problems, or intellectual problems. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]
Expression
Biased expression in brain (RPKM 2.2), esophagus (RPKM 0.8) and 3 other tissues See more
Orthologs
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Genomic context

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Location:
3p25.3
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (10816228..10940714)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (10810506..10935188)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10857913..10982400)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATPase plasma membrane Ca2+ transporting 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10670941-10671440 Neighboring gene ATP2B2 intronic transcript 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10749701-10750202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10750203-10750702 Neighboring gene MPRA-validated peak4540 silencer Neighboring gene Sharpr-MPRA regulatory region 1605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10813659-10814160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10814161-10814660 Neighboring gene long intergenic non-protein coding RNA 606 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:10876658-10876792 Neighboring gene MPRA-validated peak4541 silencer Neighboring gene uncharacterized LOC105376950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10976470-10977424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10977664-10978170 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10978171-10978676 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:11009752-11010252 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:11010253-11010753 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:11024802-11025580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:11034754-11035278 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_64297 Neighboring gene SLC6A1 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 1670 Neighboring gene solute carrier family 6 member 1 Neighboring gene uncharacterized LOC101927467

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. Downregulation of GABA Transporter 3 (GAT3) is Associated with Deficient Oxidative GABA Metabolism in Human Induced Pluripotent Stem Cell-Derived Astrocytes in Alzheimer's Disease. Salcedo C, et al. Neurochem Res, 2021 Oct. PMID 33710537
  2. GATA4 mutations are uncommon in patients with 46,XY disorders of sex development without heart anomaly. Igarashi M, et al. Asian J Androl, 2018 Nov-Dec. PMID 29735817, Free PMC Article
  3. Gaba transporter SLC6A11 gene polymorphism associated with tardive dyskinesia. Son WY, et al. Nord J Psychiatry, 2014 Feb. PMID 23795861
  4. Development and validation of an LC-ESI-MS/MS quantification method for a potential γ-aminobutyric acid transporter 3 (GAT3) marker and its application in preliminary MS binding assays. Polley M, et al. Biomed Chromatogr, 2013 May. PMID 23225341
  5. Association of a synonymous GAT3 polymorphism with antiepileptic drug pharmacoresistance. Kim DU, et al. J Hum Genet, 2011 Sep. PMID 21776001

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Downregulation of GABA Transporter 3 (GAT3) is Associated with Deficient Oxidative GABA Metabolism in Human Induced Pluripotent Stem Cell-Derived Astrocytes in Alzheimer's Disease.
    Title: Downregulation of GABA Transporter 3 (GAT3) is Associated with Deficient Oxidative GABA Metabolism in Human Induced Pluripotent Stem Cell-Derived Astrocytes in Alzheimer's Disease.
  2. GAT-1 (rs2697153) and GAT-3 (rs2272400) polymorphisms are associated with febrile seizures and temporal lobe epilepsy.
    Title: GAT-1 (rs2697153) and GAT-3 (rs2272400) polymorphisms are associated with febrile seizures and temporal lobe epilepsy.
  3. we performed GATA4 mutation screening for 119 patients with 46, XY DSD without heart anomalies
    Title: GATA4 mutations are uncommon in patients with 46,XY disorders of sex development without heart anomaly.
  4. GAT-3 expression was selectively decreased in the central amygdala of alcohol-dependent people compared to those who died of unrelated causes.
    Title: A molecular mechanism for choosing alcohol over an alternative reward.
  5. GABA-transporter 3 was reduced by about 62% in severe hippocampal sclerosis samples
    Title: Hippocampal GABA transporter distribution in patients with temporal lobe epilepsy and hippocampal sclerosis.
  6. 3p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and stereotypic behavior.
    Title: 3p25.3 microdeletion of GABA transporters SLC6A1 and SLC6A11 results in intellectual disability, epilepsy and stereotypic behavior.
  7. results suggest that GABA receptor signaling pathway was associated with the increased susceptibility to TD in Korean schizophrenic patients
    Title: Gaba transporter SLC6A11 gene polymorphism associated with tardive dyskinesia.
  8. Binding assays employing membrane preparations obtained from a stably GAT3 expressing HEK293 cell line and DDPM-1007 as nonlabeled GAT3 marker were performed. In these experiments specific binding of DDPM-1007 at GAT3 could be unambiguously detected.
    Title: Development and validation of an LC-ESI-MS/MS quantification method for a potential γ-aminobutyric acid transporter 3 (GAT3) marker and its application in preliminary MS binding assays.
  9. The results suggest that GAT3 c.1572T may be one of the contributing factors with a modest effect on antiepileptic drug (AEDs) pharmacoresistance in the epileptic brain.
    Title: Association of a synonymous GAT3 polymorphism with antiepileptic drug pharmacoresistance.
  10. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction See all GeneRIFs (12)

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
Genome-wide association analysis implicates the involvement of eight loci with response to tocilizumab for the treatment of rheumatoid arthritis.
EBI GWAS Catalog
Genome-wide Interrogation of Longitudinal FEV1 in Children with Asthma.
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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General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables amino acid binding IEA
Inferred from Electronic Annotation
more info
  
enables gamma-aminobutyric acid:sodium:chloride symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables gamma-aminobutyric acid:sodium:chloride symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables gamma-aminobutyric acid:sodium:chloride symporter activity TAS
Traceable Author Statement
more info
  
enables monocarboxylic acid transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables taurine:sodium symporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in amino acid transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gamma-aminobutyric acid reuptake TAS
Traceable Author Statement
more info
  
involved_in monocarboxylic acid transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to xenobiotic stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in taurine transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in cell projection IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
  
located_in presynaptic membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
sodium- and chloride-dependent GABA transporter 3
Names
GABA transporter 3
solute carrier family 6 (neurotransmitter transporter), member 11
solute carrier family 6 (neurotransmitter transporter, GABA), member 11

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_001317406.3 → NP_001304335.1  sodium- and chloride-dependent GABA transporter 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the C-terminus compared to isoform 1.
    Source sequence(s)
    AC018495, BC036083
    Consensus CDS
    CCDS82734.1
    UniProtKB/Swiss-Prot
    P48066
    Related
    ENSP00000404120.1, ENST00000454147.1
    Conserved Domains (1) summary
    cl00456
    Location:49 → 208
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  2. NM_014229.3 → NP_055044.1  sodium- and chloride-dependent GABA transporter 3 isoform 1

    See identical proteins and their annotated locations for NP_055044.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC027128, AK312719, S75989
    Consensus CDS
    CCDS2602.1
    UniProtKB/Swiss-Prot
    B2R6U6, P48066, Q8IYC9
    Related
    ENSP00000254488.2, ENST00000254488.7
    Conserved Domains (1) summary
    cd11508
    Location:49 → 590
    SLC6sbd_GAT3; Na(+)- and Cl(-)-dependent GABA transporter 3; solute-binding domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    10816228..10940714
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534033.3 → XP_011532335.1  sodium- and chloride-dependent GABA transporter 3 isoform X2

    Conserved Domains (1) summary
    cl00456
    Location:49 → 374
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  2. XM_047448764.1 → XP_047304720.1  sodium- and chloride-dependent GABA transporter 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    10810506..10935188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347622.1 → XP_054203597.1  sodium- and chloride-dependent GABA transporter 3 isoform X2

  2. XM_054347621.1 → XP_054203596.1  sodium- and chloride-dependent GABA transporter 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48066.1 GenPept UniProtKB/Swiss-Prot:P48066

Gene LinkOut

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