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

Gene ID: 6539, updated on 3-Apr-2024

Summary

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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; AllianceGenome:HGNC:11045
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
Summary
Enables monocarboxylic acid transmembrane transporter activity. Involved in monocarboxylic acid transport. Predicted to be located in plasma membrane. Predicted to be integral component of membrane. Predicted to be active in neuron projection. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in liver (RPKM 12.1), kidney (RPKM 10.0) and 5 other tissues See more
Orthologs
all
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Genomic context

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Location:
12p13.33
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (183848..214157, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (179876..211078, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (299247..323323, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene IQ motif and Sec7 domain ArfGEF 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:254331-254832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:254833-255332 Neighboring gene uncharacterized LOC574538 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:262202-263116 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:277504-277977 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:282005-282530 Neighboring gene IQSEC3 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:282531-283057 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:283058-283583 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 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 solute carrier family 6 member 13 Neighboring gene uncharacterized LOC102723544 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:415875-417074 Neighboring gene lysine demethylase 5A

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. Structural and molecular aspects of betaine-GABA transporter 1 (BGT1) and its relation to brain function. Kickinger S, et al. Neuropharmacology, 2019 Dec 15. PMID 31108110
  2. Combined effect between two functional polymorphisms of SLC6A12 gene is associated with temporal lobe epilepsy. Li J, et al. J Genet, 2015 Dec. PMID 26690518
  3. Mutation of a single threonine in the cytoplasmic NH2 terminus disrupts trafficking of renal betaine-GABA transporter 1 during hypertonic stress. Schweikhard ES, et al. Am J Physiol Renal Physiol, 2014 Jul 1. PMID 24829506
  4. Association between the SLC6A12 gene and negative symptoms of schizophrenia in a Korean population. Park HJ, et al. Psychiatry Res, 2011 Oct 30. PMID 21367462
  5. Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population. Pasaje CF, et al. Ann Hum Genet, 2010 Jul. PMID 20597903

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Protein kinases as regulators of osmolyte accumulation under stress conditions: An overview.
    Title: Protein kinases as regulators of osmolyte accumulation under stress conditions: An overview.
  2. This review gathers the current structural and functional knowledge on BGT1 with emphasis on brain relevance, discusses all available compounds, and tries to shed light on the molecular determinants driving BGT1 selectivity--{REVIEW}
    Title: Structural and molecular aspects of betaine-GABA transporter 1 (BGT1) and its relation to brain function.
  3. The SLC6A12 expression levels in peripheral blood mononuclear cells were significantly higher in TLE patients.
    Title: Combined effect between two functional polymorphisms of SLC6A12 gene is associated with temporal lobe epilepsy.
  4. T40 may be important for the trafficking and insertion of BGT1 in the plasma membrane
    Title: Mutation of a single threonine in the cytoplasmic NH2 terminus disrupts trafficking of renal betaine-GABA transporter 1 during hypertonic stress.
  5. JAK2 is a novel regulator of the GABA transporter BGT1.
    Title: Up-regulation of the betaine/GABA transporter BGT1 by JAK2.
  6. This study found that rs216250 of SLC6A12 was correlated with the Scale for the Assessment of Negative Symptoms (SANS) scores.
    Title: Association between the SLC6A12 gene and negative symptoms of schizophrenia in a Korean population.
  7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population.
  8. Results showed that two polymorphisms and a haplotype in SLC6A12, were significantly associated with AIA after multiple testing corrections.
    Title: Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population.
  9. 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.
  10. The primary structure of BGT-1 predicts two putative phosphorylation sites for the Ca2+/diacylglycerol-dependent protein kinase (PKC), which regulates BGT-1 function by phosphorylation events in a transport system expressed in cultured astrocytoma cells.
    Title: Gamma-aminobutyric acid transporter (BGT-1) expressed in human astrocytoma U373 MG cells: pharmacological and molecular characterization and phorbol ester-induced inhibition.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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 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

Clone Names

  • FLJ38727

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables amino acid transmembrane transporter activity TAS
Traceable Author Statement
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 monocarboxylic acid transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in amino acid transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in amino acid transport TAS
Traceable Author Statement
more info
  
involved_in gamma-aminobutyric acid reuptake TAS
Traceable Author Statement
more info
  
involved_in gamma-aminobutyric acid transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycine betaine transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in monocarboxylic acid transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
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 membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
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 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)

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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_001122847.3 → NP_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
    A0AV52, B2R992, D3DUN8, P48065
    UniProtKB/TrEMBL
    B3KWG3
    Related
    ENSP00000352702.4, ENST00000359674.8
    Conserved Domains (1) summary
    cd11511
    Location:35 → 575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain

  2. NM_001122848.3 → NP_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
    A0AV52, B2R992, D3DUN8, P48065
    UniProtKB/TrEMBL
    B3KWG3
    Related
    ENSP00000508194.1, ENST00000684302.1
    Conserved Domains (1) summary
    cd11511
    Location:35 → 575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain

  3. NM_001206931.2 → NP_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
    A0AV52, B2R992, D3DUN8, P48065
    UniProtKB/TrEMBL
    B3KWG3
    Related
    ENSP00000444268.1, ENST00000536824.5
    Conserved Domains (1) summary
    cd11511
    Location:35 → 575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain

  4. NM_003044.5 → NP_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
    A0AV52, B2R992, D3DUN8, P48065
    UniProtKB/TrEMBL
    B3KWG3
    Related
    ENSP00000399136.2, ENST00000424061.6
    Conserved Domains (1) summary
    cd11511
    Location:35 → 575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; 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
    183848..214157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429417.1 → XP_047285373.1  sodium- and chloride-dependent betaine transporter isoform X5

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

    UniProtKB/TrEMBL
    B3KWG3
    Conserved Domains (1) summary
    cl00456
    Location:35 → 570
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  3. XM_047429416.1 → XP_047285372.1  sodium- and chloride-dependent betaine transporter isoform X3

  4. XM_011521010.2 → XP_011519312.1  sodium- and chloride-dependent betaine transporter isoform X1

    See identical proteins and their annotated locations for XP_011519312.1

    UniProtKB/Swiss-Prot
    A0AV52, B2R992, D3DUN8, P48065
    UniProtKB/TrEMBL
    B3KWG3
    Conserved Domains (1) summary
    cd11511
    Location:35 → 575
    SLC6sbd_BGT1; Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain

  5. XM_047429419.1 → XP_047285375.1  sodium- and chloride-dependent betaine transporter isoform X6

  6. XM_047429418.1 → XP_047285374.1  sodium- and chloride-dependent betaine transporter isoform X6

  7. XM_005253747.5 → XP_005253804.1  sodium- and chloride-dependent betaine transporter isoform X2

    UniProtKB/TrEMBL
    B3KWG3
    Conserved Domains (1) summary
    cl00456
    Location:35 → 567
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

  8. XM_006719005.4 → XP_006719068.1  sodium- and chloride-dependent betaine transporter isoform X4

    UniProtKB/TrEMBL
    B3KWG3
    Conserved Domains (1) summary
    cl00456
    Location:35 → 567
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    179876..211078 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373001.1 → XP_054228976.1  sodium- and chloride-dependent betaine transporter isoform X5

  2. XM_054372996.1 → XP_054228971.1  sodium- and chloride-dependent betaine transporter isoform X1

  3. XM_054373003.1 → XP_054228978.1  sodium- and chloride-dependent betaine transporter isoform X6

  4. XM_054373002.1 → XP_054228977.1  sodium- and chloride-dependent betaine transporter isoform X6

  5. XM_054372998.1 → XP_054228973.1  sodium- and chloride-dependent betaine transporter isoform X3

  6. XM_054372999.1 → XP_054228974.1  sodium- and chloride-dependent betaine transporter isoform X3

  7. XM_054372997.1 → XP_054228972.1  sodium- and chloride-dependent betaine transporter isoform X2

  8. XM_054373000.1 → XP_054228975.1  sodium- and chloride-dependent betaine transporter isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P48065.2 GenPept UniProtKB/Swiss-Prot:P48065

Gene LinkOut

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