The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017] See more...

Aliases for SLC6A1 Gene

Aliases for SLC6A1 Gene

  • Solute Carrier Family 6 Member 1 2 3 4 5
  • GABATR 2 3 4
  • GAT1 2 3 4
  • Solute Carrier Family 6 (Neurotransmitter Transporter, GABA), Member 1 2 3
  • Solute Carrier Family 6 (Neurotransmitter Transporter), Member 1 2 3
  • Sodium- And Chloride-Dependent GABA Transporter 1 3 4
  • GABA Transporter 1 2 3
  • GABATHG 2 3
  • SLC6A1 5
  • GABT1 4
  • GAT-1 4
  • MAE 3

External Ids for SLC6A1 Gene

Previous GeneCards Identifiers for SLC6A1 Gene

  • GC03P010986

Summaries for SLC6A1 Gene

Entrez Gene Summary for SLC6A1 Gene

  • The protein encoded by this gene is a gamma-aminobutyric acid (GABA) transporter that localizes to the plasma membrane. The encoded protein removes GABA from the synaptic cleft, restoring it to presynaptic terminals. [provided by RefSeq, Jan 2017]

GeneCards Summary for SLC6A1 Gene

SLC6A1 (Solute Carrier Family 6 Member 1) is a Protein Coding gene. Diseases associated with SLC6A1 include Myoclonic-Atonic Epilepsy and Myoclonic-Astastic Epilepsy. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Benzodiazepine Pathway, Pharmacodynamics. Gene Ontology (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 SLC6A11.

UniProtKB/Swiss-Prot Summary for SLC6A1 Gene

  • Terminates the action of GABA by its high affinity sodium-dependent reuptake into presynaptic terminals.

Tocris 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 have been identified and localized to neurons and glia.

Gene Wiki entry for SLC6A1 Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC6A1 Gene

Genomics for SLC6A1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLC6A1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J010992 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 272.3 +0.7 715 1.8 ZNF600 ZIC2 SP2 CTCF ZNF2 ZNF530 GLIS1 ZNF398 EGR1 ZFP69B SLC6A1 TAMM41 HSALNG0024130 HRH1
GH03J011011 Promoter/Enhancer 0.6 EPDnew dbSUPER 250.4 +19.4 19436 0.1 ZNF623 SLC6A1 SLC6A1-AS1 HSALNG0024130 HRH1
GH03J010983 Enhancer 0.9 Ensembl dbSUPER 14.6 -9.2 -9185 2 ZNF654 YY1 CTCF RXRA RAD21 RFX5 SMC3 JUND PKNOX1 HNF4A SLC6A1 piR-38580-200 ENSG00000286962 SLC6A11
GH03J011181 Enhancer 1.2 Ensembl ENCODE dbSUPER 10.4 +191.9 191893 7 NCOR1 ZNF600 IKZF1 BRCA1 CEBPB ELK1 MAX ZNF217 EP300 RXRA SLC6A1-AS1 SLC6A1 HSALNG0024145 lnc-VGLL4-6 HRH1 ATG7
GH03J010955 Enhancer 1 Ensembl ENCODE dbSUPER 11.5 -35.2 -35186 4 ZIC2 ZBTB48 SCRT1 GLIS1 NFIA ZNF184 ZBTB8A MNT ZNF692 OSR2 SLC6A1 SLC6A1-AS1 SLC6A11 HSALNG0024127 ENSG00000286962
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC6A1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC6A1

Top Transcription factor binding sites by QIAGEN in the SLC6A1 gene promoter:
  • GATA-1
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • MyoD
  • MZF-1
  • Pax-2
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for SLC6A1 Gene

Latest Assembly
47,062 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
46,500 bases
Plus strand

(GRCh37/hg19 by Ensembl)
46,524 bases
Plus strand

Genomic View for SLC6A1 Gene

Genes around SLC6A1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC6A1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC6A1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC6A1 Gene

Proteins for SLC6A1 Gene

  • Protein details for SLC6A1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium- and chloride-dependent GABA transporter 1
    Protein Accession:
    Secondary Accessions:
    • Q8N4K8

    Protein attributes for SLC6A1 Gene

    599 amino acids
    Molecular mass:
    67074 Da
    Quaternary structure:
    • Interacts with MPP5.
    • This protein is the target of psychomotor stimulants such as amphetamines or cocaine.

neXtProt entry for SLC6A1 Gene

Post-translational modifications for SLC6A1 Gene

  • Glycosylation at Asn176, Asn181, and Asn184
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC6A1 Gene

Domains & Families for SLC6A1 Gene

Gene Families for SLC6A1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • FDA approved drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC6A1 Gene

  • GAT-1 GABA neurotransmitter transporter signature

Suggested Antigen Peptide Sequences for SLC6A1 Gene

GenScript: Design optimal peptide antigens:
  • Transporter (B7Z3C5_HUMAN)
  • Solute carrier family 6 member 1 (SC6A1_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • The PDZ domain-binding motif is involved in the interaction with MPP5.
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A1 subfamily.
  • The PDZ domain-binding motif is involved in the interaction with MPP5.
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A1 subfamily.
genes like me logo Genes that share domains with SLC6A1: view

Function for SLC6A1 Gene

Molecular function for SLC6A1 Gene

UniProtKB/Swiss-Prot Function:
Terminates the action of GABA by its high affinity sodium-dependent reuptake into presynaptic terminals.
GENATLAS Biochemistry:
solute carrier family 6,member A1,neurotransmitter transporter,GABA,see COLOT1

Phenotypes From GWAS Catalog for SLC6A1 Gene

Gene Ontology (GO) - Molecular Function for SLC6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005332 gamma-aminobutyric acid:sodium symporter activity IEA,IDA 10973981
GO:0005515 protein binding IPI 29997244
GO:0015185 gamma-aminobutyric acid transmembrane transporter activity IEA,ISS --
GO:0015293 symporter activity IEA --
GO:0015378 sodium:chloride symporter activity IDA 10973981
genes like me logo Genes that share ontologies with SLC6A1: view
genes like me logo Genes that share phenotypes with SLC6A1: view

Human Phenotype Ontology for SLC6A1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC6A1 Gene

MGI Knock Outs for SLC6A1:

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC6A1

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC6A1 Gene

Localization for SLC6A1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC6A1 Gene

Cell membrane. Multi-pass membrane protein. Membrane. Multi-pass membrane protein. Cell junction, synapse, presynapse. Note=Localized at the plasma membrane and in a subset of intracellular vesicles. Localized at the presynaptic terminals of interneurons (By similarity). {ECO:0000250}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC6A1 gene
Compartment Confidence
plasma membrane 5
mitochondrion 3
extracellular 2
cytoskeleton 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA,TAS --
GO:0005887 integral component of plasma membrane IEA --
GO:0009986 cell surface IEA,IBA 21873635
GO:0016020 membrane IEA,TAS 2387399
GO:0016021 integral component of membrane IEA,TAS 8530094
genes like me logo Genes that share ontologies with SLC6A1: view

Pathways & Interactions for SLC6A1 Gene

genes like me logo Genes that share pathways with SLC6A1: view

Pathways by source for SLC6A1 Gene

Gene Ontology (GO) - Biological Process for SLC6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006836 neurotransmitter transport IEA --
GO:0007268 chemical synaptic transmission TAS 8530094
GO:0007612 learning IEA --
GO:0007613 memory IEA,ISS --
GO:0008306 associative learning IEA,ISS --
genes like me logo Genes that share ontologies with SLC6A1: view

No data available for SIGNOR curated interactions for SLC6A1 Gene

Drugs & Compounds for SLC6A1 Gene

(23) Drugs for SLC6A1 Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Tiagabine Approved, Investigational Pharma Inhibitor, Inhibition, Target 21
Clobazam Approved, Illicit Pharma Transporter, other 26
Cocaine Approved, Illicit Pharma inhibitor 616
Guvacine Experimental Pharma Target, inhibitor 0
(R/S) EF-1500 Pharma Inhibitor, Inhibition 0

(9) Additional Compounds for SLC6A1 Gene - From: IUPHAR, Novoseek, HMDB, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Na(+)
  • Na+
  • SODIUM ion
  • Sodium(1+)
Inhibitor, Inhibition
Inhibitor, Inhibition
(+-)-Nipecotic acid

(5) Tocris Compounds for SLC6A1 Gene

Compound Action Cas Number
(+-)-Nipecotic acid GABA uptake inhibitor 60252-41-7
(S)-SNAP 5114 GABA uptake inhibitor 157604-55-2
CI 966 hydrochloride Selective inhibitor of GAT-1 110283-66-4
Guvacine hydrochloride Specific GABA uptake inhibitor 6027-91-4
SKF 89976A hydrochloride Potent GABA uptake inhibitor. Penetrates blood brain barrier 85375-15-1
genes like me logo Genes that share compounds with SLC6A1: view

Transcripts for SLC6A1 Gene

mRNA/cDNA for SLC6A1 Gene

6 NCBI additional mRNA sequence :
41 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC6A1

Alternative Splicing Database (ASD) splice patterns (SP) for SLC6A1 Gene

No ASD Table

Relevant External Links for SLC6A1 Gene

GeneLoc Exon Structure for

Expression for SLC6A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC6A1 Gene

mRNA differential expression in normal tissues according to GTEx for SLC6A1 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x5.2), Brain - Putamen (basal ganglia) (x4.8), Brain - Amygdala (x4.8), Brain - Caudate (basal ganglia) (x4.7), Brain - Frontal Cortex (BA9) (x4.3), and Brain - Nucleus accumbens (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for SLC6A1 Gene

This gene is overexpressed in Frontal cortex (43.6) and Retina (16.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC6A1 Gene

Protein tissue co-expression partners for SLC6A1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC6A1

SOURCE GeneReport for Unigene cluster for SLC6A1 Gene:


Evidence on tissue expression from TISSUES for SLC6A1 Gene

  • Nervous system(4.9)
  • Liver(2.8)
  • Eye(2.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC6A1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with SLC6A1: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt for SLC6A1 Gene

Orthologs for SLC6A1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC6A1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC6A1 29 30
  • 98.38 (n)
(Monodelphis domestica)
Mammalia SLC6A1 30
  • 95 (a)
(Canis familiaris)
Mammalia SLC6A1 29 30
  • 93.43 (n)
(Bos Taurus)
Mammalia SLC6A1 29 30
  • 91.99 (n)
(Mus musculus)
Mammalia Slc6a1 29 16 30
  • 90.21 (n)
(Rattus norvegicus)
Mammalia Slc6a1 29
  • 90.09 (n)
(Ornithorhynchus anatinus)
Mammalia SLC6A1 30
  • 75 (a)
(Gallus gallus)
Aves SLC6A1 29 30
  • 78.82 (n)
(Anolis carolinensis)
Reptilia SLC6A1 30
  • 91 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100127682 29
  • 77.85 (n)
(Danio rerio)
Actinopterygii slc6a1b 29 30
  • 77.2 (n)
slc6a1a 30
  • 73 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta CG1732 29 30 31
  • 58.41 (n)
SerT 31
  • 46 (a)
CG5549 31
  • 41 (a)
ine 31
  • 40 (a)
CG10804 31
  • 38 (a)
BG:DS03431.1 31
  • 35 (a)
CG3252 31
  • 34 (a)
CG4476 31
  • 34 (a)
CG7075 31
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009768 29
  • 30.6 (n)
(Caenorhabditis elegans)
Secernentea snf-11 29 30 31
  • 56.28 (n)
snf-3 31
  • 41 (a)
snf-4 31
  • 31 (a)
snf-9 31
  • 31 (a)
snf-6 31
  • 30 (a)
snf-12 31
  • 30 (a)
snf-5 31
  • 28 (a)
snf-1 31
  • 23 (a)
snf-8 31
  • 23 (a)
Species where no ortholog for SLC6A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SLC6A1 Gene

Gene Tree for SLC6A1 (if available)
Gene Tree for SLC6A1 (if available)
Evolutionary constrained regions (ECRs) for SLC6A1: view image
Alliance of Genome Resources:
Additional Orthologs for SLC6A1

Paralogs for SLC6A1 Gene

(18) SIMAP similar genes for SLC6A1 Gene using alignment to 3 proteins:

  • B7Z3C5_HUMAN
  • C9J5P8_HUMAN
genes like me logo Genes that share paralogs with SLC6A1: view

Variants for SLC6A1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC6A1 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
1001393 Uncertain Significance: Myoclonic-atonic epilepsy 11,017,248(+) A/T
NM_003042.4(SLC6A1):c.37A>T (p.Ile13Phe)
1002041 Uncertain Significance: Myoclonic-atonic epilepsy 11,028,736(+) C/T
NM_003042.4(SLC6A1):c.1080C>T (p.Gly360=)
1003093 Uncertain Significance: Myoclonic-atonic epilepsy 11,022,473(+) G/A
1003510 Uncertain Significance: Myoclonic-atonic epilepsy 11,026,347(+) G/A
NM_003042.4(SLC6A1):c.1066G>A (p.Val356Met)
1009642 Uncertain Significance: Myoclonic-atonic epilepsy 11,017,454(+) G/T

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SLC6A1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SLC6A1 Gene

Variant ID Type Subtype PubMed ID
dgv762e201 CNV deletion 23290073
esv3561468 CNV deletion 23714750
esv4117 OTHER complex 18987735
nsv1008628 CNV gain 25217958
nsv1073204 CNV deletion 25765185
nsv1121603 CNV deletion 24896259
nsv1126642 CNV deletion 24896259
nsv436362 CNV deletion 17901297
nsv436869 CNV insertion 17901297
nsv508209 CNV deletion 20534489
nsv518622 CNV loss 19592680

Variation tolerance for SLC6A1 Gene

Residual Variation Intolerance Score: 9.06% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.66; 31.78% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC6A1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC6A1 Gene

Disorders for SLC6A1 Gene

MalaCards: The human disease database

(28) MalaCards diseases for SLC6A1 Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards


  • Myoclonic-atonic epilepsy (MAE) [MIM:616421]: A form of epilepsy characterized by myoclonic-atonic and absence seizures, appearing in early childhood. Patients have delayed development before the onset of seizures and show varying degrees of intellectual disability following seizure onset. {ECO:0000269 PubMed:25865495}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for SLC6A1

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SLC6A1: view

No data available for Genatlas for SLC6A1 Gene

Publications for SLC6A1 Gene

  1. Mutations in the GABA Transporter SLC6A1 Cause Epilepsy with Myoclonic-Atonic Seizures. (PMID: 25865495) Carvill GL … Mefford HC (American journal of human genetics 2015) 3 4 72
  2. The GABA transporter 1 (SLC6A1): a novel candidate gene for anxiety disorders. (PMID: 18607529) Thoeringer CK … Erhardt A (Journal of neural transmission (Vienna, Austria : 1996) 2009) 3 22 40
  3. Defining the phenotypic spectrum of SLC6A1 mutations. (PMID: 29315614) Johannesen KM … Møller RS (Epilepsia 2018) 3 72
  4. Genome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men. (PMID: 22437554) Major JM … Albanes D (The Journal of nutrition 2012) 3 40
  5. 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. (PMID: 19086053) Gratacòs M … Psychiatric Genetics Network Group (American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics 2009) 3 40

Products for SLC6A1 Gene

Sources for SLC6A1 Gene