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SLC6A1 solute carrier family 6 member 1 [ Homo sapiens (human) ]

Gene ID: 6529, updated on 3-Apr-2024

Summary

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Official Symbol
SLC6A1provided by HGNC
Official Full Name
solute carrier family 6 member 1provided by HGNC
Primary source
HGNC:HGNC:11042
See related
Ensembl:ENSG00000157103 MIM:137165; AllianceGenome:HGNC:11042
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
MAE; GAT1; GABATR; hGAT-1; GABATHG
Summary
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]
Expression
Biased expression in brain (RPKM 26.6), liver (RPKM 15.1) and 2 other tissues See more
Orthologs
mouse all
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Genomic context

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See SLC6A1 in Genome Data Viewer
Location:
3p25.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (10992748..11039247)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (10987230..11033712)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (11034434..11080933)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes 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 solute carrier family 6 member 11 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 uncharacterized LOC101927467 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:11178289-11179488 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19426 Neighboring gene uncharacterized LOC105376951 Neighboring gene histamine receptor H1

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. SLC6A1-Related Neurodevelopmental Disorder. Adam MP, et al. , 1993. PMID 36780407
  2. Experimental and Bioinformatic Insights into the Effects of Epileptogenic Variants on the Function and Trafficking of the GABA Transporter GAT-1. Piniella D, et al. Int J Mol Sci, 2023 Jan 4. PMID 36674476, Free PMC Article
  3. Structural basis of GABA reuptake inhibition. Motiwala Z, et al. Nature, 2022 Jun. PMID 35676483, Free PMC Article
  4. Integrated Analysis of DNA Repair Genes Identifies SLC6A1 as a New Marker for the Clinical Outcome of Patients with Colorectal Cancer. Wang QQ, et al. Dis Markers, 2022. PMID 35251372, Free PMC Article
  5. Common molecular mechanisms of SLC6A1 variant-mediated neurodevelopmental disorders in astrocytes and neurons. Mermer F, et al. Brain, 2021 Sep 4. PMID 34028503, Free PMC Article

See all (91) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.
    Title: SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis.
  2. Patient-derived SLC6A1 variant S295L results in an epileptic phenotype similar to haploinsufficient mice.
    Title: Patient-derived SLC6A1 variant S295L results in an epileptic phenotype similar to haploinsufficient mice.
  3. Ketone bodies promote stroke recovery via GAT-1-dependent cortical network remodeling.
    Title: Ketone bodies promote stroke recovery via GAT-1-dependent cortical network remodeling.
  4. Assessing the impact of the de novo SLC6A1 mutation in schizophrenia through a comprehensive case study.
    Title: Assessing the impact of the de novo SLC6A1 mutation in schizophrenia through a comprehensive case study.
  5. Experimental and Bioinformatic Insights into the Effects of Epileptogenic Variants on the Function and Trafficking of the GABA Transporter GAT-1.
    Title: Experimental and Bioinformatic Insights into the Effects of Epileptogenic Variants on the Function and Trafficking of the GABA Transporter GAT-1.
  6. Astrocytic GABA transporter 1 deficit in novel SLC6A1 variants mediated epilepsy: Connected from protein destabilization to seizures in mice and humans.
    Title: Astrocytic GABA transporter 1 deficit in novel SLC6A1 variants mediated epilepsy: Connected from protein destabilization to seizures in mice and humans.
  7. New Genetic Variants in CYP2B6 and SLC6A Support the Role of Oxidative Stress in Familial Meniere's Disease.
    Title: New Genetic Variants in CYP2B6 and SLC6A Support the Role of Oxidative Stress in Familial Ménière's Disease.
  8. Structural basis of GABA reuptake inhibition.
    Title: Structural basis of GABA reuptake inhibition.
  9. Neurodevelopmental phenotypes associated with pathogenic variants in SLC6A1.
    Title: Neurodevelopmental phenotypes associated with pathogenic variants in SLC6A1.
  10. Common molecular mechanisms of SLC6A1 variant-mediated neurodevelopmental disorders in astrocytes and neurons.
    Title: Common molecular mechanisms of SLC6A1 variant-mediated neurodevelopmental disorders in astrocytes and neurons.
Submit: New GeneRIF Correction See all GeneRIFs (55)

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

Associated conditions

Description Tests
Myoclonic-atonic epilepsy
MedGen: CN231318 OMIM: 616421 GeneReviews: SLC6A1-Related Neurodevelopmental Disorder
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-09-25)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2019-09-25)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Does parental expressed emotion moderate genetic effects in ADHD? An exploration using a genome wide association scan.
EBI GWAS Catalog
Genome-wide association study identifies three common variants associated with serologic response to vitamin E supplementation in men.
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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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables gamma-aminobutyric acid transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
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 IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables gamma-aminobutyric acid:sodium:chloride symporter activity TAS
Traceable Author Statement
more info
  
enables identical protein binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sodium:chloride symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in amino acid transport IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of associative learning ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in chemical synaptic transmission TAS
Traceable Author Statement
more info
 PubMed 
involved_in chloride transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in gamma-aminobutyric acid import IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in gamma-aminobutyric acid import ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in gamma-aminobutyric acid reuptake TAS
Traceable Author Statement
more info
  
involved_in inorganic anion import across plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of memory ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of synaptic transmission, GABAergic IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of gamma-aminobutyric acid secretion IEA
Inferred from Electronic Annotation
more info
  
involved_in response to calcium ion IEA
Inferred from Electronic Annotation
more info
  
involved_in response to cocaine IEA
Inferred from Electronic Annotation
more info
  
involved_in response to estradiol IEA
Inferred from Electronic Annotation
more info
  
involved_in response to inorganic substance IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to lead ion IEA
Inferred from Electronic Annotation
more info
  
involved_in response to purine-containing compound IEA
Inferred from Electronic Annotation
more info
  
involved_in response to sucrose IEA
Inferred from Electronic Annotation
more info
  
involved_in response to toxic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in sodium ion import across plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of synapse organization ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in axon ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
located_in neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
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 1
Names
GABA transporter 1
solute carrier family 6 (neurotransmitter transporter), member 1
solute carrier family 6 (neurotransmitter transporter, GABA), member 1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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.

Genomic

  1. NG_053003.1 RefSeqGene

    Range
    5020..51519
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001348250.2 → NP_001335179.1  sodium- and chloride-dependent GABA transporter 1 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform.
    Source sequence(s)
    AC024910
    Consensus CDS
    CCDS2603.1
    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
    UniProtKB/TrEMBL
    A0A2R8YDD5
    Related
    ENSP00000494346.1, ENST00000642767.1
    Conserved Domains (1) summary
    cd11506
    Location:2 → 599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

  2. NM_001348251.2 → NP_001335180.1  sodium- and chloride-dependent GABA transporter 1 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses two alternate splice junctions compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform (a).
    Source sequence(s)
    AC024910
    Consensus CDS
    CCDS87043.1
    UniProtKB/TrEMBL
    A0A2R8Y4I3, A0A2R8Y867
    Related
    ENSP00000493813.1, ENST00000644314.1
    Conserved Domains (1) summary
    cl00456
    Location:1 → 479
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  3. NM_001348252.2 → NP_001335181.1  sodium- and chloride-dependent GABA transporter 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice junction and lacks an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (c).
    Source sequence(s)
    AC024910
    Consensus CDS
    CCDS87044.1
    UniProtKB/TrEMBL
    A0A2R8Y867, B7Z3C5
    Related
    ENSP00000494002.1, ENST00000646072.1
    Conserved Domains (1) summary
    cl00456
    Location:1 → 421
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  4. NM_001348253.2 → NP_001335182.1  sodium- and chloride-dependent GABA transporter 1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses two alternate splice junctions and lacks an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (c).
    Source sequence(s)
    AC024910
    Consensus CDS
    CCDS87044.1
    UniProtKB/TrEMBL
    A0A2R8Y867, B7Z3C5
    Related
    ENSP00000495375.1, ENST00000645776.1
    Conserved Domains (1) summary
    cl00456
    Location:1 → 421
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  5. NM_003042.4 → NP_003033.3  sodium- and chloride-dependent GABA transporter 1 isoform a

    See identical proteins and their annotated locations for NP_003033.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform (a).
    Source sequence(s)
    AC024910, BC033904, BC057291, DA162953
    Consensus CDS
    CCDS2603.1
    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
    UniProtKB/TrEMBL
    A0A2R8YDD5
    Related
    ENSP00000287766.4, ENST00000287766.10
    Conserved Domains (1) summary
    cd11506
    Location:2 → 599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; 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
    10992748..11039247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011534027.4 → XP_011532329.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    See identical proteins and their annotated locations for XP_011532329.1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
    UniProtKB/TrEMBL
    A0A2R8YDD5
    Conserved Domains (1) summary
    cd11506
    Location:2 → 599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

  2. XM_005265411.6 → XP_005265468.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    See identical proteins and their annotated locations for XP_005265468.1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
    UniProtKB/TrEMBL
    A0A2R8YDD5
    Related
    ENSP00000494136.1, ENST00000643396.1
    Conserved Domains (1) summary
    cd11506
    Location:2 → 599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

  3. XM_017007071.3 → XP_016862560.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
    UniProtKB/TrEMBL
    A0A2R8YDD5
    Related
    ENSP00000496348.1, ENST00000642515.1
    Conserved Domains (1) summary
    cd11506
    Location:2 → 599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

  4. XM_017007072.3 → XP_016862561.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
    UniProtKB/TrEMBL
    A0A2R8YDD5
    Conserved Domains (1) summary
    cd11506
    Location:2 → 599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    10987230..11033712
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347613.1 → XP_054203588.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8

  2. XM_054347617.1 → XP_054203592.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8

  3. XM_054347612.1 → XP_054203587.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8

  4. XM_054347616.1 → XP_054203591.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8

  5. XM_054347615.1 → XP_054203590.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8

  6. XM_054347614.1 → XP_054203589.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531, Q8N4K8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P30531.2 GenPept UniProtKB/Swiss-Prot:P30531

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