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SLC6A13 solute carrier family 6 member 13 [ Homo sapiens (human) ]

Gene ID: 6540, updated on 11-Apr-2024

Summary

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Official Symbol
SLC6A13provided by HGNC
Official Full Name
solute carrier family 6 member 13provided by HGNC
Primary source
HGNC:HGNC:11046
See related
Ensembl:ENSG00000010379 MIM:615097; AllianceGenome:HGNC:11046
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GAT2; GAT3; GAT-2
Summary
Enables amino acid transmembrane transporter activity and monocarboxylic acid transmembrane transporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in kidney (RPKM 28.5) and liver (RPKM 1.5) See more
Orthologs
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Genomic context

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See SLC6A13 in Genome Data Viewer
Location:
12p13.33
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (220622..262836, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (217551..259667, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (329788..372002, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain ArfGEF 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:277504-277977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:282005-282530 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:282531-283057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:283058-283583 Neighboring gene IQSEC3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:287986-288528 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:291153-291654 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:294419-294609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4100 Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene solute carrier family 6 member 12 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:320888-321660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:322433-323204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:329915-330870 Neighboring gene uncharacterized LOC102723544 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:415875-417074 Neighboring gene lysine demethylase 5A Neighboring gene Sharpr-MPRA regulatory region 4015 Neighboring gene uncharacterized LOC105369594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5778 Neighboring gene coiled-coil domain containing 77

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. High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach. Schlessinger A, et al. J Biol Chem, 2012 Nov 2. PMID 22932902, Free PMC Article
  2. Cloning and characterization of a functional human gamma-aminobutyric acid (GABA) transporter, human GAT-2. Christiansen B, et al. J Biol Chem, 2007 Jul 6. PMID 17502375
  3. Sequence and chromosomal assignment of a human novel cDNA: similarity to gamma-aminobutyric acid transporter. Gong Y, et al. Can J Physiol Pharmacol, 2001 Dec. PMID 11824941
  4. Evidence for a Revised Ion/Substrate Coupling Stoichiometry of GABA Transporters. Willford SL, et al. J Membr Biol, 2015 Aug. PMID 25824654
  5. Substrate-Na+ complex formation: coupling mechanism for gamma-aminobutyrate symporters. Palló A, et al. Biochem Biophys Res Commun, 2009 Jul 24. PMID 19450549

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Evidence for a Revised Ion/Substrate Coupling Stoichiometry of GABA Transporters.
    Title: Evidence for a Revised Ion/Substrate Coupling Stoichiometry of GABA Transporters.
  2. Neurotransmitter transporters including SLC6A6 and SLC6A13 mediate the uptake of 5-aminolevulinic acid (ALA) and can play roles in the enhancement of ALA-induced accumulation of protoporphyrin in cancerous cells.
    Title: Neurotransmitter transporter family including SLC6A6 and SLC6A13 contributes to the 5-aminolevulinic acid (ALA)-induced accumulation of protoporphyrin IX and photodamage, through uptake of ALA by cancerous cells.
  3. Results suggest that gamma-aminobutyric acid transporter 2 GAT-2 is a high selectivity/low affinity transporter.
    Title: High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  5. Meta-analysis and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: New loci associated with kidney function and chronic kidney disease.
  6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  7. homology models of hGAT-2 and hGAT-3 were built and searched for (i) substrate conformation, (ii) prediction of substrate (inhibitor) interaction, and (iii) distinguishable allosteric Zn2+ inhibition by combining docking and MD calculations.
    Title: Substrate-Na+ complex formation: coupling mechanism for gamma-aminobutyrate symporters.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: L-type voltage-dependent calcium channel alpha subunit 1C is a novel candidate gene associated with secondary hyperparathyroidism: an application of haplotype-based analysis for multiple linked single nucleotide polymorphisms.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genetic determinants influencing human serum metabolome among African Americans.
EBI GWAS Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
EBI GWAS Catalog
New loci associated with kidney function and chronic kidney disease.
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 amino acid transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables amino acid:sodium symporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables creatine transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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 TAS
Traceable Author Statement
more info
  
enables monocarboxylic acid transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables taurine transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables taurine:sodium symporter activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in amino acid import across plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in amino acid transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in creatine transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
  
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 monocarboxylic acid transport IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of nitrogen compound transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nitrogen compound transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in taurine transmembrane transport 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 basolateral plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in cell projection IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in extracellular exosome HDA PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
sodium- and chloride-dependent GABA transporter 2
Names
GABA transport protein
GABA transporter 2
solute carrier family 6 (neurotransmitter transporter), member 13
solute carrier family 6 (neurotransmitter transporter, GABA), member 13

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001190997.3 → NP_001177926.1  sodium- and chloride-dependent GABA transporter 2 isoform 2

    See identical proteins and their annotated locations for NP_001177926.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two consecutive exons in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK296127, DB540466
    Consensus CDS
    CCDS53729.1
    UniProtKB/Swiss-Prot
    Q9NSD5
    Related
    ENSP00000407104.2, ENST00000445055.6
    Conserved Domains (1) summary
    cl00456
    Location:32 → 483
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  2. NM_001243392.2 → NP_001230321.1  sodium- and chloride-dependent GABA transporter 2 isoform 3

    See identical proteins and their annotated locations for NP_001230321.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks a splice site and a large portion of the coding region, compared to variant 1. The encoded isoform (3) is significantly shorter and has a disctinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI802118, BC020867
    Consensus CDS
    CCDS58198.1
    UniProtKB/Swiss-Prot
    Q9NSD5
    Related
    ENSP00000389316.1, ENST00000436453.1
    Conserved Domains (1) summary
    cl00456
    Location:32 → 68
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  3. NM_016615.5 → NP_057699.2  sodium- and chloride-dependent GABA transporter 2 isoform 1

    See identical proteins and their annotated locations for NP_057699.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK313511, BM662288, DA374290, DB540466
    Consensus CDS
    CCDS8502.1
    UniProtKB/Swiss-Prot
    B4DJL1, Q8TCC2, Q8WW56, Q9NSD5
    UniProtKB/TrEMBL
    B4DJS3
    Related
    ENSP00000339260.4, ENST00000343164.9
    Conserved Domains (1) summary
    cd11507
    Location:32 → 575
    SLC6sbd_GAT2; Na(+)- and Cl(-)-dependent GABA transporter 2; 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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    220622..262836 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429420.1 → XP_047285376.1  sodium- and chloride-dependent GABA transporter 2 isoform X2

  2. XM_017019845.2 → XP_016875334.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:1 → 332
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  3. XM_006719008.4 → XP_006719071.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:1 → 332
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  4. XM_017019842.2 → XP_016875331.1  sodium- and chloride-dependent GABA transporter 2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    217551..259667 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373005.1 → XP_054228980.1  sodium- and chloride-dependent GABA transporter 2 isoform X2

  2. XM_054373004.1 → XP_054228979.1  sodium- and chloride-dependent GABA transporter 2 isoform X1

  3. XM_054373007.1 → XP_054228982.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

  4. XM_054373006.1 → XP_054228981.1  sodium- and chloride-dependent GABA transporter 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NSD5.3 GenPept UniProtKB/Swiss-Prot:Q9NSD5

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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