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SLC6A1 Gene

protein-coding   GIFtS: 67
GCID: GC03P011009

Solute Carrier Family 6 (Neurotransmitter Transporter),...

(Previous names: solute carrier family 6 (neurotransmitter transporter, GABA),...)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Solute Carrier Family 6 (Neurotransmitter Transporter), Member 11 2     GAT-12 3
GABATR2 3 5     GAT12 3
Solute Carrier Family 6 (Neurotransmitter Transporter, GABA), Member 11 2     GABATHG2
GABA Transporter 11 2     Sodium- And Chloride-Dependent GABA Transporter 12
Solute Carrier Family 6 Member 12 3     GABT13

External Ids:    HGNC: 110421   Entrez Gene: 65292   Ensembl: ENSG000001571037   OMIM: 1371655   UniProtKB: P305313   
ORGUL members:         

Export aliases for SLC6A1 gene to outside databases

Previous GC identifer: GC03P010986


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SLC6A1 Gene:
The SLC6A1 gene encodes a gamma-aminobutyric acid (GABA) transporter, which removes GABA from the synaptic cleft
(Hirunsatit et al., 2009 (PubMed 19077666)).(supplied by OMIM, Jul 2009)

GeneCards Summary for SLC6A1 Gene:
SLC6A1 (solute carrier family 6 (neurotransmitter transporter), member 1) is a protein-coding gene. Diseases associated with SLC6A1 include female stress incontinence, and insomnia. GO annotations related to this gene include neurotransmitter:sodium symporter activity and gamma-aminobutyric acid:sodium symporter activity. An important paralog of this gene is SLC6A6.

UniProtKB/Swiss-Prot: SC6A1_HUMAN, P30531
Function: Terminates the action of GABA by its high affinity sodium-dependent reuptake into presynaptic terminals

summary for SLC6A1 Gene:
GABA transporters are sodium- and chloride-dependent members of the solute carrier family 6 (SLC6) that
mediate the rapid removal of GABA and maintain low extracellular levels. Four 12-TM domain transporters
(GAT-1, GAT-2, GAT-3 and BGT-1) have been identified and localized to neurons and glia. While GAT-1, GAT-2,
GAT-3 and BGT-1 bind GABA with varying affinities, they share structural motifs including 12-TM domains,
extracellular glycosylation sites and intracellular consensus sites for phosphorylation. A vesicular
transporter (VGAT) has also been identified. This member of the SCL32 family is both structurally and
functionally distinct, containing 10-TM domains and being found in GABAergic and glycinergic neurons. Some
anticonvulsants have been reported to act upon the GABA transporters. There is evidence to suggest that GABA
transporters are linked to epilepsy, affective disorders and schizophrenia.

Gene Wiki entry for SLC6A1 (GABA transporter 1) Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NT_022517.19  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SLC6A1 gene promoter:
         HOXA9   HOXA9B   Pax-2   MyoD   Meis-1b   GATA-1   MZF-1   PPAR-gamma1   PPAR-gamma2   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSLC6A1 promoter sequence
   Search Chromatin IP Primers for SLC6A1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SLC6A1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p25.3   Ensembl cytogenetic band:  3p25.3   HGNC cytogenetic band: 3p25.3

SLC6A1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SLC6A1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03P011009:  view genomic region     (about GC identifiers)

Start:
11,034,410 bp from pter      End:
11,080,935 bp from pter
Size:
46,526 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SC6A1_HUMAN, P30531 (See protein sequence)
Recommended Name: Sodium- and chloride-dependent GABA transporter 1  
Size: 599 amino acids; 67074 Da
Subunit: Interacts with MPP5 (By similarity)
Miscellaneous: This protein is the target of psychomotor stimulants such as amphetamines or cocaine
Secondary accessions: Q8N4K8

Explore the universe of human proteins at neXtProt for SLC6A1: NX_P30531

Explore proteomics data for SLC6A1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Asn176, Asn181, Asn184
  • Modification sites at PhosphoSitePlus

  • See SLC6A1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_003033.3  
    ENSEMBL proteins: 
     ENSP00000287766   ENSP00000411689   ENSP00000445171  
    Reactome Protein details: P30531

    SLC6A1 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    SLC: Solute carriers

    IUPHAR Guide to PHARMACOLOGY protein family classification: GAT1
    GABA transporter subfamily

    2 InterPro protein domains:
     IPR000175 Na/ntran_symport
     IPR002980 Na/ntran_symport_GABA_GAT1

    Graphical View of Domain Structure for InterPro Entry P30531

    ProtoNet protein and cluster: P30531

    1 Blocks protein domain: IPB002980 GAT-1 GABA neurotransmitter transporter signature

    UniProtKB/Swiss-Prot: SC6A1_HUMAN, P30531
    Domain: The PDZ domain-binding motif is involved in the interaction with MPP5
    Similarity: Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A1 subfamily


    SLC6A1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SC6A1_HUMAN, P30531
    Function: Terminates the action of GABA by its high affinity sodium-dependent reuptake into presynaptic terminals

         Genatlas biochemistry entry for SLC6A1:
    solute carrier family 6,member A1,neurotransmitter transporter,GABA,see COLOT1

         Gene Ontology (GO): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005328neurotransmitter:sodium symporter activity IEA--
    GO:0005332gamma-aminobutyric acid:sodium symporter activity IEA--
    GO:0005515protein binding ----
         
    SLC6A1 for ontologies           About GeneDecksing


    Phenotypes:
         5 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Slc6a1):
     behavior/neurological  growth/size/body  nervous system  normal  taste/olfaction 

    SLC6A1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Slc6a1tm1Mlit for SLC6A1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SLC6A1
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SLC6A1

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SLC6A1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SLC6A1

    miRNA
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    Block miRNA regulation of human, mouse, rat SLC6A1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SLC6A1 (see all 73):
    hsa-miR-579 hsa-miR-376b hsa-miR-938 hsa-miR-128 hsa-miR-3613-3p hsa-miR-200b hsa-miR-192* hsa-miR-92b
    SwitchGear 3'UTR luciferase reporter plasmidSLC6A1 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC6A1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SC6A1_HUMAN, P30531: Cell membrane; Multi-pass membrane protein. Membrane; Multi-pass membrane protein.
    Note=Localized at the plasma membrane and in a subset of intracellular vesicles. Localized at the presynaptic
    terminals of interneurons (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    cytosol1
    endoplasmic reticulum1
    golgi apparatus1
    mitochondrion1
    nucleus1
    peroxisome1

    Gene Ontology (GO): Selected cellular component terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0005887integral component of plasma membrane IEA--
    GO:0009986cell surface IEA--
    GO:0016020membrane TAS2387399
    GO:0016021integral component of membrane TAS8530094

    SLC6A1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for SLC6A1 About   (see all 7)  
    See pathways by source

    SuperPathContained pathways About
    1Benzodiazepine Pathway, Pharmacodynamics
    Benzodiazepine Pathway, Pharmacodynamics
    Reuptake of GABA0.00
    2Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
    SLC-mediated transmembrane transport0.47
    Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds0.38
    Transmembrane transport of small molecules0.47
    Na+/Cl- dependent neurotransmitter transporters0.00
    3Transmission across Chemical Synapses
    Transmission across Chemical Synapses0.72
    Neuronal System0.68
    4Neurotransmitter Release Cycle
    Neurotransmitter Release Cycle0.32
    GABA synthesis, release, reuptake and degradation0.00
    5Circadian entrainment
    GABAergic synapse0.53

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for SLC6A1
        Monoamine Transport


    2 Reactome Pathways for SLC6A1
        Na+/Cl- dependent neurotransmitter transporters
    Reuptake of GABA

    1 PharmGKB Pathway for SLC6A1
        Benzodiazepine Pathway, Pharmacodynamics

    1 Kegg Pathway  (Kegg details for SLC6A1):
        GABAergic synapse


    SLC6A1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including SLC6A1: 
              GABA & Glutamate in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for SLC6A1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    1 Interacting protein for SLC6A1 (P305313 ENSP000002877664) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    STX1AQ166233, ENSP000002228124I2D: score=2 STRING: ENSP00000222812
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 20):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006810transport NAS8530094
    GO:0006836neurotransmitter transport ----
    GO:0007268synaptic transmission TAS--
    GO:0007269neurotransmitter secretion TAS--
    GO:0007612learning IEA--

    SLC6A1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Compounds for SLC6A1 available from Tocris Bioscience    About this table
    CompoundAction CAS #
    NNC 05-2090 hydrochlorideGABA uptake inhibitor; moderately BGT-1 selective[184845-43-0]
    Tiagabine hydrochlorideGABA uptake inhibitor; anticonvulsant[145821-59-6]
    SKF 89976A hydrochloridePotent GABA uptake inhibitor. Penetrates blood brain barrier[85375-15-1]
    (S)-SNAP 5114GABA uptake inhibitor[157604-55-2]
    NNC 711Selective inhibitor of GAT-1[145645-62-1]

    1 HMDB Compound for SLC6A1    About this table
    CompoundSynonyms CAS #PubMed Ids
    SodiumSodium (see all 2)7440-23-5--

    3 DrugBank Compounds for SLC6A1    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    TiagabineTiagabina [INN-Spanish] (see all 2)115103-54-3targetinhibitor16377242 16420077 18007567 20512624 11752352 17069932
    ClobazamAedon (see all 23)22316-47-8transporterOther22242724
    Guvacine-- 498-96-4targetinhibitor20512624

    8 IUPHAR Ligands for SLC6A1 (GAT1)    About this table
    LigandTypeActionAffinityPubmed IDs
    tiagabine
    InhibitorInhibition5.6 - 7--
    NNC-711
    InhibitorInhibition5.9 - 6.9--
    SKF89976A
    InhibitorInhibition6.9--
    CI-966
    InhibitorInhibition6.6--
    (R/S) EF-1500
    InhibitorInhibition4.9 - 5.7--
    LU32-176B
    InhibitorInhibition5.4--
    [3H]tiagabine
    NoneNone5.4--
    (R/S)-EF-1502
    InhibitorInhibition5.4--

    Selected Novoseek inferred chemical compound relationships for SLC6A1 gene (see all 15)    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    gaba 87.8 177 9623887 (3), 12526990 (3), 9116226 (3), 10197772 (3) (see all 78)
    tiagabine 84.2 13 15451399 (2), 9674039 (1), 19393020 (1), 8939442 (1) (see all 9)
    sk&f-89976a 79.8 1 10373701 (1)
    nipecotic acid 72.5 1 11520322 (1)
    glutamate 42.4 10 11744314 (2), 12526990 (1), 19294962 (1), 15269970 (1) (see all 6)
    sodium 33.9 2 7479969 (1), 19201752 (1)
    betaine 30.9 1 9045687 (1)
    chloride 23.9 1 7479969 (1)
    dopamine 22.7 3 17210573 (1), 11750035 (1), 12351264 (1)
    haloperidol 20.5 1 15467974 (1)



    SLC6A1 for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SLC6A1 gene: 
    NM_003042.3  

    Unigene Cluster for SLC6A1:

    Solute carrier family 6 (neurotransmitter transporter, GABA), member 1
    Hs.443874  [show with all ESTs]
    Unigene Representative Sequence: NM_003042
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000287766(uc010hdq.3) ENST00000425938 ENST00000462473 ENST00000460480
    ENST00000495636 ENST00000536032
    miRNA
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    hsa-miR-579 hsa-miR-376b hsa-miR-938 hsa-miR-128 hsa-miR-3613-3p hsa-miR-200b hsa-miR-192* hsa-miR-92b
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      QuantiTect SYBR Green Assays in human, mouse, rat SLC6A1
      QuantiFast Probe-based Assays in human, mouse, rat SLC6A1

    Additional mRNA sequence: 

    AK090958.1 AK295702.1 BC033904.1 BC057291.1 X54673.1 

    5 DOTS entries:

    DT.91710327  DT.102822043  DT.100752409  DT.95266752  DT.99998044 

    Selected AceView cDNA sequences (see all 82):

    R96402 H19539 BG059905 F03388 F02829 BX952118 H38688 BX099972 
    AV654804 AL138189 AI570251 BM809058 CA414784 X54673 AL133858 BC057291 
    BC033904 BG567511 AW339119 AV659277 H19464 AW957131 W56493 H20294 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SLC6A1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTCCCACTTC
    SLC6A1 Expression
    About this image


    SLC6A1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 9) fully expand
     
     Brain (Nervous System)    fully expand to see all 10 entries
             Adult Endothelial Cells Blood Brain Barrier
             Midbrain tegmentum
             Oligodendrocyte-like cells
     
     Neural Tube (Nervous System)    fully expand to see all 3 entries
             Metencephalon
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             GABAergic Amacrine Cells Inner Nuclear Layer
             Lens
     
     Oligodendrocytes (Nervous System)    fully expand to see all 2 entries
             Oligodendrocyte-like cells
     
     Neurons
             GABAergic Amacrine Cells Inner Nuclear Layer
    SLC6A1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SLC6A1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.443874
        Pathway & Disease-focused RT2 Profiler PCR Array including SLC6A1: 
              GABA & Glutamate in human mouse rat

    Primer
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    QuantiFast Probe-based Assays in human, mouse, rat SLC6A1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SLC6A1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SLC6A1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Slc6a11 , 5 solute carrier family 6 (neurotransmitter transporter, more1, 5 90.21(n)1
    98(a)1
      6 (53.05 cM)5
    2323331  NM_178703.41  NP_848818.11 
     1142826355 
    chicken
    (Gallus gallus)
    Aves SLC6A11 solute carrier family 6 (neurotransmitter transporter, more 78.82(n)
    93.31(a)
      415960  XM_414303.3  XP_414303.1 
    lizard
    (Anolis carolinensis)
    Reptilia SLC6A16
    solute carrier family 6 (neurotransmitter transpor...
    91(a)
    1 ↔ 1
    2(157489157-157611931)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1001276821 uncharacterized LOC100127682 77.85(n)
    90.32(a)
      100127682  NM_001113022.1  NP_001106493.1 
    zebrafish
    (Danio rerio)
    Actinopterygii 570760642   -- 78.24(n)    57076064 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG17321 , 3 GABA:sodium symporter3
    CG17321
    59(a)
    (best of 9)3
    58.41(n)1
    59.12(a)1
      102C23
    438051  NM_143673.31  NP_651930.21 
    worm
    (Caenorhabditis elegans)
    Secernentea snf-111 , 3 Na(+)/Cl(-)-dependent GABA transporter3
    snf-111
    50(a)
    (best of 9)3
    56.28(n)1
    54.35(a)1
      V(11307950-11311658)3
    1917701  NM_073472.51  NP_505873.21 


    ENSEMBL Gene Tree for SLC6A1 (if available)
    TreeFam Gene Tree for SLC6A1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SLC6A1 gene
    SLC6A62  SLC6A112  SLC6A122  SLC6A82  SLC6A52  SLC6A142  SLC6A32  SLC6A42  
    SLC6A132  SLC6A22  SLC6A72  SLC6A92  
    18 SIMAP similar genes for SLC6A1 using alignment to 3 protein entries:     SC6A1_HUMAN (see all proteins):
    SLC6A13    SLC6A6    SLC6A11    SLC6A12    SLC6A8    SLC6A4
    SLC6A7    SLC6A3    SLC6A5    SLC6A2    SLC6A9    SLC6A14
    SLC6A15    SLC6A18    SLC6A19    SLC6A20    DKFZp761I0921    SLC6A17

    SLC6A1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SLC6A1 (see all 826)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1122228131,2
    C--11032492(+) AGTTTG/CTGTTT 1 -- us2k11Minor allele frequency- C:0.50CSA 2
    rs14001541,2
    C,F,A--11032556(-) gggacA/Gtgtga 1 -- us2k112Minor allele frequency- G:0.25NA WA CSA EA 374
    rs1468001371,2
    --11032694(+) ATTGAC/GGTTCT 1 -- us2k10--------
    rs17108731,2
    C,F,H--11032829(-) gaactG/Caggtc 1 -- us2k129Minor allele frequency- C:0.48NS EA NA WA CSA 2777
    rs1395971421,2
    --11032950(+) GGTTTA/GTGCGG 1 -- us2k10--------
    rs1443309861,2
    C--11032954(+) TGTGCA/GGTTAT 1 -- us2k10--------
    rs17288181,2
    C,F,A,H--11032992(-) gtgatG/Cccagt 1 -- us2k119Minor allele frequency- C:0.45EA NA NS WA CSA 837
    rs1857092271,2
    --11033101(+) CCAACA/GGAAGT 1 -- us2k10--------
    rs790018191,2
    C,F--11033133(+) GATCAG/ATGGTG 1 -- us2k11Minor allele frequency- A:0.02EA 120
    rs1509747341,2
    --11033195(+) GTGTGA/GGGAAA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SLC6A1 (11034410 - 11080935 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for SLC6A1:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv809e201CNV Deletion23290073
    nsv436362CNV Deletion17901297
    nsv436869CNV Insertion17901297
    nsv518622CNV Loss19592680
    nsv508209CNV Loss20534489
    nsv876534CNV Loss21882294
    esv4117CNV Complex18987735

    Human Gene Mutation Database (HGMD): SLC6A1
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SLC6A1
    DNA2.0 Custom Variant and Variant Library Synthesis for SLC6A1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 137165    OMIM disorders: --

    16 diseases for SLC6A1:    
    About MalaCards
    female stress incontinence    insomnia    temporal lobe epilepsy    ganglioglioma
    schizophrenia    anxiety disorder    attention deficit hyperactivity disorder    autism spectrum disorder
    labyrinthitis    neuronitis    glaucoma    neuropathy
    cerebritis    alzheimer's disease    malaria    endotheliitis

    3 diseases from the University of Copenhagen DISEASES database for SLC6A1:
    Glaucoma     Schizophrenia     Female stress incontinence

    SLC6A1 for disorders           About GeneDecksing

    4 Novoseek inferred disease relationships for SLC6A1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    epilepsy 42.2 2 12699773 (1), 17267178 (1)
    schizophrenia 37.8 6 11803235 (2), 12526990 (1), 10553733 (1), 18923069 (1) (see all 5)
    sclerosis 31.6 1 11744314 (1)
    psychiatric disorder 4.64 1 12167498 (1)

    Genetic Association Database (GAD): SLC6A1
    Human Genome Epidemiology (HuGE) Navigator: SLC6A1 (7 documents)

    Export disorders for SLC6A1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SLC6A1 gene, integrated from 10 sources (see all 147):
    (articles sorted by number of sources associating them with SLC6A1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The GABA transporter 1 (SLC6A1): a novel candidate gene for anxiety disorders. (PubMed id 18607529)1, 4, 9 Thoeringer C.K....Erhardt A. (J Neural Transm 2009)
    2. Genome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men. (PubMed id 22437554)1, 4 Major J.M....Albanes D. (J. Nutr. 2012)
    3. A common variant in DRD3 receptor is associated with autism spectrum disorder. (PubMed id 19058789)1, 4 de Krom M....van Ree J.M. (Biol. Psychiatry 2009)
    4. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PubMed id 19086053)1, 4 GratacA^s M....Carracedo A. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009)
    5. HPA axis reactivity: a mechanism underlying the associations among 5-HTTLPR, stress, and depression. (PubMed id 18005940)1, 4 Gotlib I.H....Hallmayer J. (Biol. Psychiatry 2008)
    6. Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan. (PubMed id 18846501)1, 4 Sonuga-Barke E.J....Faraone S.V. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008)
    7. Genome-wide association scan of quantitative traits for attention deficit hyperactivity disorder identifies novel associations and confirms candidate gene associations. (PubMed id 18821565)1, 4 Lasky-Su J....Faraone S.V. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2008)
    8. DAT1 3'-UTR 9R allele: preferential transmission in Indian children with attention deficit hyperactivity disorder. (PubMed id 17440935)1, 4 Das M. and Mukhopadhyay K. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2007)
    9. Assignment of the human GABA transporter gene (GABATHG) locus to chromosome 3p24-p25. (PubMed id 8530094)1, 3 Huang F....Guo L.H. (Genomics 1995)
    10. Cloning of the human brain GABA transporter. (PubMed id 2387399)1, 2 Nelson H.... Nelson N. (FEBS Lett. 1990)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 6529 HGNC: 11042 AceView: SLC6A1 Ensembl:ENSG00000157103 euGenes: HUgn6529
    ECgene: SLC6A1 Kegg: 6529 H-InvDB: SLC6A1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for SLC6A1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for SLC6A1 gene:
    Search GeneIP for patents involving SLC6A1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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