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SLC6A12 solute carrier family 6 member 12 [ Homo sapiens (human) ]

Gene ID: 6539, updated on 7-Jun-2020

Summary

Official Symbol
SLC6A12provided by HGNC
Official Full Name
solute carrier family 6 member 12provided by HGNC
Primary source
HGNC:HGNC:11045
See related
Ensembl:ENSG00000111181 MIM:603080
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
BGT1; GAT2; BGT-1
Expression
Biased expression in liver (RPKM 12.1), kidney (RPKM 10.0) and 5 other tissues See more
Orthologs

Genomic context

See SLC6A12 in Genome Data Viewer
Location:
12p13.33
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (190081..214157, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (299243..323740, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain ArfGEF 3 Neighboring gene uncharacterized LOC574538 Neighboring gene uncharacterized LOC105369592 Neighboring gene SLC6A12 antisense RNA 1 Neighboring gene solute carrier family 6 member 13 Neighboring gene uncharacterized LOC102723544 Neighboring gene lysine demethylase 5A

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

NHGRI GWAS Catalog

Description
An atlas of genetic influences on human blood metabolites.
NHGRI GWA Catalog
Genetic variants associated with glycine metabolism and their role in insulin sensitivity and type 2 diabetes.
NHGRI GWA Catalog
New loci associated with kidney function and chronic kidney disease.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ38727

Gene Ontology Provided by GOA

Function Evidence Code Pubs
amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
 
gamma-aminobutyric acid:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neurotransmitter binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
amino acid transport TAS
Traceable Author Statement
more info
 
gamma-aminobutyric acid transport IEA
Inferred from Electronic Annotation
more info
 
transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
integral component of membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of plasma membrane IEA
Inferred from Electronic Annotation
more info
 
neuron projection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium- and chloride-dependent betaine transporter
Names
Na(+)/Cl(-) betaine/GABA transporter
betaine/GABA transporter-1
gamma-aminobutyric acid transporter
solute carrier family 6 (neurotransmitter transporter), member 12
solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12

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.

mRNA and Protein(s)

  1. NM_001122847.3NP_001116319.1  sodium- and chloride-dependent betaine transporter

    See identical proteins and their annotated locations for NP_001116319.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC007406, BC036838, DA093632
    Consensus CDS
    CCDS8501.1
    UniProtKB/Swiss-Prot
    P48065
    Related
    ENSP00000352702.4, ENST00000359674.8
    Conserved Domains (1) summary
    cd11511
    Location:35575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
  2. NM_001122848.3NP_001116320.1  sodium- and chloride-dependent betaine transporter

    See identical proteins and their annotated locations for NP_001116320.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC007406, AI241640, BC036838, DA390883, DA406088, L42300
    Consensus CDS
    CCDS8501.1
    UniProtKB/Swiss-Prot
    P48065
    Conserved Domains (1) summary
    cd11511
    Location:35575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
  3. NM_001206931.2NP_001193860.1  sodium- and chloride-dependent betaine transporter

    See identical proteins and their annotated locations for NP_001193860.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC007406, AK313690
    Consensus CDS
    CCDS8501.1
    UniProtKB/Swiss-Prot
    P48065
    Related
    ENSP00000444268.1, ENST00000536824.5
    Conserved Domains (1) summary
    cd11511
    Location:35575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
  4. NM_003044.5NP_003035.3  sodium- and chloride-dependent betaine transporter

    See identical proteins and their annotated locations for NP_003035.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) and variants 2, 3 and 4 encode the same protein.
    Source sequence(s)
    AC007406, U27699
    Consensus CDS
    CCDS8501.1
    UniProtKB/Swiss-Prot
    P48065
    Related
    ENSP00000399136.2, ENST00000424061.6
    Conserved Domains (1) summary
    cd11511
    Location:35575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; 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_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    190081..214157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005253748.4XP_005253805.1  sodium- and chloride-dependent betaine transporter isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:35570
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_011521010.1XP_011519312.1  sodium- and chloride-dependent betaine transporter isoform X1

    See identical proteins and their annotated locations for XP_011519312.1

    UniProtKB/Swiss-Prot
    P48065
    Conserved Domains (1) summary
    cd11511
    Location:35575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain
  3. XM_005253747.4XP_005253804.1  sodium- and chloride-dependent betaine transporter isoform X2

    Conserved Domains (1) summary
    cl00456
    Location:35567
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. XM_006719005.3XP_006719068.1  sodium- and chloride-dependent betaine transporter isoform X4

    Conserved Domains (1) summary
    cl00456
    Location:35567
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
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