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

    Gene ID: 6538, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See SLC6A11 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (10816228..10940714)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (10810506..10935188)
    RS_2024_09 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 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. 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
    2. Gaba transporter SLC6A11 gene polymorphism associated with tardive dyskinesia. Son WY, et al. Nord J Psychiatry, 2014 Feb. PMID 23795861
    3. 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
    4. 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
    5. Cloning of the human homologue of the GABA transporter GAT-3 and identification of a novel inhibitor with selectivity for this site. Borden LA, et al. Recept Channels, 1994. PMID 7874447

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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