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Aliases for SLC6A1 Gene

Aliases for SLC6A1 Gene

  • Solute Carrier Family 6 Member 1 2 3 4 5
  • Solute Carrier Family 6 (Neurotransmitter Transporter, GABA), Member 1 2 3
  • Solute Carrier Family 6 (Neurotransmitter Transporter), Member 1 2 3
  • GABA Transporter 1 2 3
  • GABATR 3 4
  • GAT1 3 4
  • Sodium- And Chloride-Dependent GABA Transporter 1 3
  • GABATHG 3
  • 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 Neurotransmitter Release Cycle. 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 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 , fRNAdb sequence ontologies and piRNA Summary for SLC6A1 Gene

Genomics for SLC6A1 Gene

Regulatory Elements for SLC6A1 Gene

Enhancers for SLC6A1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G010992 1.1 ENCODE dbSUPER 22.3 -0.5 -518 0.4 CTCF KLF1 ZNF777 KLF17 RBBP5 ZIC2 ZNF2 ZFHX2 GLIS2 ZNF366 SLC6A1 TAMM41 LOC105376950
GH03G010993 1 ENCODE dbSUPER 19.1 -0.2 -235 0.2 CTCF KLF1 ZNF777 KLF17 RBBP5 ZFHX2 GLIS2 ZNF366 PATZ1 ZNF600 SLC6A1 LOC105376950
GH03G011182 1.5 Ensembl ENCODE dbSUPER 10.4 +192.2 192210 5.2 ATF1 PKNOX1 SIN3A BRCA1 TCF12 ZNF766 GATA2 ELK1 ZNF143 FOS SLC6A1-AS1 SLC6A1 LOC102723663 LOC105376951
GH03G011198 1.4 Ensembl ENCODE dbSUPER 10.3 +208.3 208250 4.0 ZSCAN4 ZFP64 ZBTB40 ZNF335 GATA2 SCRT2 ZNF143 SMARCC2 FOS THAP11 TAMM41 VGLL4 TATDN2 SLC6A1-AS1 SLC6A1 ATG7 LOC102723663 LOC105376951
GH03G011194 1.4 Ensembl ENCODE dbSUPER 10.3 +204.0 204002 3.6 PKNOX1 SIN3A FEZF1 RAD21 GATA2 ZNF366 ZSCAN5C FOS ZNF263 ZNF654 SLC6A1-AS1 SLC6A1 ATG7 LOC102723663 LOC105376951
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC6A1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SLC6A1 Gene

Chromosome:
3
Start:
10,992,724 bp from pter
End:
11,039,249 bp from pter
Size:
46,526 bases
Orientation:
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:
    P30531-SC6A1_HUMAN
    Recommended name:
    Sodium- and chloride-dependent GABA transporter 1
    Protein Accession:
    P30531
    Secondary Accessions:
    • Q8N4K8

    Protein attributes for SLC6A1 Gene

    Size:
    599 amino acids
    Molecular mass:
    67074 Da
    Quaternary structure:
    • Interacts with MPP5.
    Miscellaneous:
    • 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 isoforms=184
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC6A1 Gene

Domains & Families for SLC6A1 Gene

Gene Families for SLC6A1 Gene

HGNC:
IUPHAR :

Suggested Antigen Peptide Sequences for SLC6A1 Gene

Graphical View of Domain Structure for InterPro Entry

P30531

UniProtKB/Swiss-Prot:

SC6A1_HUMAN :
  • 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.
Domain:
  • The PDZ domain-binding motif is involved in the interaction with MPP5.
Family:
  • 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

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

Gene Ontology (GO) - Molecular Function for SLC6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005328 neurotransmitter:sodium symporter activity IEA --
GO:0005332 gamma-aminobutyric acid:sodium symporter activity TAS --
GO:0015293 symporter activity IEA --
GO:0046872 metal ion binding IEA --
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:

Animal Model Products

Inhibitory RNA Products

Clone Products

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. 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

COMPARTMENTS
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
extracellular 2
mitochondrion 2
cytoskeleton 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SLC6A1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0009986 cell surface IEA --
GO:0016020 membrane TAS 2387399
GO:0016021 integral component of membrane TAS,IEA 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:0006810 transport NAS 8530094
GO:0006836 neurotransmitter transport IEA --
GO:0007268 chemical synaptic transmission TAS 8530094
GO:0007612 learning IEA --
GO:0009636 response to toxic substance IEA --
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 Pharma Inhibition, Inhibitor, inhibitor, Target 20
Clobazam Approved, Illicit Pharma Transporter, Other 20
Cocaine Approved, Illicit Pharma inhibitor 511
Guvacine Experimental Pharma Target, inhibitor 0
(R/S) EF-1500 Pharma Inhibition, Inhibitor 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
7440-23-5
(R/S)-EF-1502
Inhibition, Inhibitor
LU32-176B
Inhibition, Inhibitor
Tiagabine hydrochloride
145821-59-6

(5) Tocris Compounds for SLC6A1 Gene

Compound Action Cas Number
(S)-SNAP 5114 GABA uptake inhibitor 157604-55-2
CI 966 hydrochloride Selective inhibitor of GAT-1 110283-66-4
NNC 05-2090 hydrochloride GABA uptake inhibitor; moderately BGT-1 selective 184845-18-9
NNC 711 Selective inhibitor of GAT-1 145645-62-1
Tiagabine hydrochloride GABA uptake inhibitor; anticonvulsant 145821-59-6
genes like me logo Genes that share compounds with SLC6A1: view

Transcripts for SLC6A1 Gene

Unigene Clusters for SLC6A1 Gene

Solute carrier family 6 (neurotransmitter transporter, GABA), member 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

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

No ASD Table

Relevant External Links for SLC6A1 Gene

GeneLoc Exon Structure for
SLC6A1
ECgene alternative splicing isoforms for
SLC6A1

Expression for SLC6A1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for SLC6A1 Gene



Protein tissue co-expression partners for SLC6A1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLC6A1 Gene:

SLC6A1

SOURCE GeneReport for Unigene cluster for SLC6A1 Gene:

Hs.443874

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
Systems:
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with SLC6A1: view

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia SLC6A1 34 35
  • 98.38 (n)
oppossum
(Monodelphis domestica)
Mammalia SLC6A1 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SLC6A1 34 35
  • 93.43 (n)
cow
(Bos Taurus)
Mammalia SLC6A1 34 35
  • 91.99 (n)
mouse
(Mus musculus)
Mammalia Slc6a1 34 16 35
  • 90.21 (n)
rat
(Rattus norvegicus)
Mammalia Slc6a1 34
  • 90.09 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLC6A1 35
  • 75 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC6A1 34 35
  • 78.82 (n)
lizard
(Anolis carolinensis)
Reptilia SLC6A1 35
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100127682 34
  • 77.85 (n)
zebrafish
(Danio rerio)
Actinopterygii slc6a1b 34 35
  • 77.2 (n)
slc6a1a 35
  • 73 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta CG1732 36 34 35
  • 58.41 (n)
SerT 36
  • 46 (a)
CG5549 36
  • 41 (a)
ine 36
  • 40 (a)
CG10804 36
  • 38 (a)
BG:DS03431.1 36
  • 35 (a)
CG3252 36
  • 34 (a)
CG4476 36
  • 34 (a)
CG7075 36
  • 34 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009768 34
  • 30.6 (n)
worm
(Caenorhabditis elegans)
Secernentea snf-11 36 34 35
  • 56.28 (n)
snf-3 36
  • 41 (a)
snf-4 36
  • 31 (a)
snf-9 36
  • 31 (a)
snf-12 36
  • 30 (a)
snf-6 36
  • 30 (a)
snf-5 36
  • 28 (a)
snf-1 36
  • 23 (a)
snf-8 36
  • 23 (a)
Species where no ortholog for SLC6A1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

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

Paralogs for SLC6A1 Gene

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

Variants for SLC6A1 Gene

Sequence variations from dbSNP and Humsavar for SLC6A1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs794726859 other, Myoclonic-atonic epilepsy (MAE) [MIM:616421] 11,017,342(+) CGACC(A/G)GGACA intron-variant, reference, missense
rs794726860 Pathogenic, Myoclonic-atonic epilepsy (MAE) [MIM:616421] 11,025,786(+) GGATG(C/T)GGCAA reference, missense
VAR_073854 Myoclonic-atonic epilepsy (MAE) [MIM:616421]
VAR_073855 Myoclonic-atonic epilepsy (MAE) [MIM:616421]
rs749240316 Pathogenic 11,026,281(+) TGTTC(A/C/G)CAGGA reference, missense

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)

Relevant External Links for SLC6A1 Gene

Human Gene Mutation Database (HGMD)
SLC6A1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC6A1

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

Disorders for SLC6A1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for SLC6A1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
myoclonic-atonic epilepsy
  • mae
myoclonic-astastic epilepsy
  • myoclonic astatic epilepsy
lingual goiter
female stress incontinence
  • female urinary stress incontinence
rubeosis iridis
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SC6A1_HUMAN
  • 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 mutations affecting the gene represented in this entry.

Relevant External Links for SLC6A1

Genetic Association Database (GAD)
SLC6A1
Human Genome Epidemiology (HuGE) Navigator
SLC6A1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC6A1
genes like me logo Genes that share disorders with SLC6A1: view

No data available for Genatlas for SLC6A1 Gene

Publications for SLC6A1 Gene

  1. The GABA transporter 1 (SLC6A1): a novel candidate gene for anxiety disorders. (PMID: 18607529) Thoeringer C.K. … Erhardt A. (J Neural Transm 2009) 3 22 46 64
  2. Mutations in the GABA Transporter SLC6A1 Cause Epilepsy with Myoclonic-Atonic Seizures. (PMID: 25865495) Carvill G.L. … Mefford H.C. (Am. J. Hum. Genet. 2015) 3 4 64
  3. Genome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men. (PMID: 22437554) Major J.M. … Albanes D. (J. Nutr. 2012) 3 46 64
  4. A common variant in DRD3 receptor is associated with autism spectrum disorder. (PMID: 19058789) de Krom M. … van Ree J.M. (Biol. Psychiatry 2009) 3 46 64
  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) GratacA^s M. … Carracedo A. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009) 3 46 64

Products for SLC6A1 Gene

Sources for SLC6A1 Gene

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