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

Gene ID: 6529, updated on 5-Jul-2020

Summary

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
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; 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

Genomic context

See SLC6A1 in Genome Data Viewer
Location:
3p25.3
Exon count:
18
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (10992734..11039249)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (11034420..11080935)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 606 Neighboring gene solute carrier family 6 member 11 Neighboring gene uncharacterized LOC105376950 Neighboring gene SLC6A1 antisense RNA 1 Neighboring gene uncharacterized LOC101927467 Neighboring gene uncharacterized LOC105376951 Neighboring gene histamine receptor H1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Myoclonic-atonic epilepsy
MedGen: C4085238 OMIM: 616421 GeneReviews: Not available
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

NHGRI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
gamma-aminobutyric acid transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
gamma-aminobutyric acid:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
gamma-aminobutyric acid:sodium symporter activity IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sodium:chloride symporter activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
associative learning ISS
Inferred from Sequence or Structural Similarity
more info
 
chemical synaptic transmission TAS
Traceable Author Statement
more info
PubMed 
chloride transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
gamma-aminobutyric acid import IDA
Inferred from Direct Assay
more info
PubMed 
gamma-aminobutyric acid import ISS
Inferred from Sequence or Structural Similarity
more info
 
inorganic anion import across plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
memory ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of synaptic transmission, GABAergic IEA
Inferred from Electronic Annotation
more info
 
neurotransmitter reuptake IEA
Inferred from Electronic Annotation
more info
 
positive regulation of gamma-aminobutyric acid secretion IEA
Inferred from Electronic Annotation
more info
 
response to calcium ion IEA
Inferred from Electronic Annotation
more info
 
response to cocaine IEA
Inferred from Electronic Annotation
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to inorganic substance IDA
Inferred from Direct Assay
more info
PubMed 
response to lead ion IEA
Inferred from Electronic Annotation
more info
 
response to purine-containing compound IEA
Inferred from Electronic Annotation
more info
 
response to sucrose IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
sodium ion import across plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
synapse organization ISS
Inferred from Sequence or Structural Similarity
more info
 
transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
 
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
membrane TAS
Traceable Author Statement
more info
PubMed 
neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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)

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_001348250.1NP_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
    UniProtKB/TrEMBL
    A0A024R2G0
    Related
    ENSP00000494346.1, ENST00000642767.1
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
  2. NM_001348251.1NP_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
    Related
    ENSP00000493813.1, ENST00000644314.1
    Conserved Domains (1) summary
    cl00456
    Location:1479
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. NM_001348252.1NP_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
    B7Z3C5
    Related
    ENSP00000494002.1, ENST00000646072.1
    Conserved Domains (1) summary
    cl00456
    Location:1421
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. NM_001348253.1NP_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
    B7Z3C5
    Related
    ENSP00000495375.1, ENST00000645776.1
    Conserved Domains (1) summary
    cl00456
    Location:1421
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. NM_003042.4NP_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
    UniProtKB/TrEMBL
    A0A024R2G0
    Related
    ENSP00000287766.4, ENST00000287766.10
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    10992734..11039249
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007071.2XP_016862560.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531
    UniProtKB/TrEMBL
    A0A024R2G0
    Related
    ENSP00000496348.1, ENST00000642515.1
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
  2. XM_017007072.2XP_016862561.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    UniProtKB/Swiss-Prot
    P30531
    UniProtKB/TrEMBL
    A0A024R2G0
    Related
    ENSP00000496390.1, ENST00000645974.1
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
  3. XM_011534025.3XP_011532327.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    See identical proteins and their annotated locations for XP_011532327.1

    UniProtKB/Swiss-Prot
    P30531
    UniProtKB/TrEMBL
    A0A024R2G0
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
  4. XM_011534027.3XP_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
    UniProtKB/TrEMBL
    A0A024R2G0
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
  5. XM_005265410.5XP_005265467.1  sodium- and chloride-dependent GABA transporter 1 isoform X1

    See identical proteins and their annotated locations for XP_005265467.1

    UniProtKB/Swiss-Prot
    P30531
    UniProtKB/TrEMBL
    A0A024R2G0
    Related
    ENSP00000494136.1, ENST00000643396.1
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
  6. XM_005265411.5XP_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
    UniProtKB/TrEMBL
    A0A024R2G0
    Conserved Domains (1) summary
    cd11506
    Location:2599
    SLC6sbd_GAT1; Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain
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