Aliases for SLC6A12 Gene

Aliases for SLC6A12 Gene

  • Solute Carrier Family 6 Member 12 2 3 4 5
  • Solute Carrier Family 6 (Neurotransmitter Transporter, Betaine/GABA), Member 12 2 3
  • Solute Carrier Family 6 (Neurotransmitter Transporter), Member 12 2 3
  • Sodium- And Chloride-Dependent Betaine Transporter 3 4
  • Na(+)/Cl(-) Betaine/GABA Transporter 3 4
  • Betaine/GABA Transporter-1 2 3
  • BGT-1 3 4
  • Gamma-Aminobutyric Acid Transporter 3
  • BGT1 3
  • GAT2 3

External Ids for SLC6A12 Gene

Previous GeneCards Identifiers for SLC6A12 Gene

  • GC12M000153
  • GC12M000299

Summaries for SLC6A12 Gene

GeneCards Summary for SLC6A12 Gene

SLC6A12 (Solute Carrier Family 6 Member 12) is a Protein Coding gene. Diseases associated with SLC6A12 include Traumatic Glaucoma and Posterolateral Myocardial Infarction. Among its related pathways are Synaptic vesicle cycle and Neurotransmitter Release Cycle. Gene Ontology (GO) annotations related to this gene include neurotransmitter:sodium symporter activity and gamma-aminobutyric acid:sodium symporter activity. An important paralog of this gene is SLC6A13.

UniProtKB/Swiss-Prot Summary for SLC6A12 Gene

  • Transports betaine and GABA. May have a role in regulation of GABAergic transmission in the brain through the reuptake of GABA into presynaptic terminals, as well as in osmotic regulation.

Tocris Summary for SLC6A12 Gene

  • GABA transporters are sodium- and chloride-dependent members of the solute carrier family 6 (SLC6) that mediate the rapid removal of GABA and maintain low extracellular levels. Four 12-TM domain transporters have been identified and localized to neurons and glia.

Additional gene information for SLC6A12 Gene

No data available for Entrez Gene Summary , CIViC Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC6A12 Gene

Genomics for SLC6A12 Gene

GeneHancer (GH) Regulatory Elements for SLC6A12 Gene

Promoters and enhancers for SLC6A12 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J000211 Promoter/Enhancer 1.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 519 +1.6 1569 1.6 NCOR1 KDM6A ZBTB26 RBM25 SIN3A NR2F2 SRSF1 POLR2A SAP130 NR3C1 SLC6A12 lnc-SLC6A12-1 KDM5A CCDC77 LOC101929384
GH12J000212 Promoter/Enhancer 1.4 EPDnew ENCODE dbSUPER 500.7 +4.1 4050 0.1 EP300 FOXK2 NCOR1 KDM6A TCF7 FOXA1 ZBTB25 TGIF2 SKI TEAD1 SLC6A12 lnc-SLC6A12-1 LOC101929384
GH12J000215 Promoter/Enhancer 1.2 EPDnew Ensembl dbSUPER 505.1 +0.4 369 0.4 POLR2G TEAD4 PCBP1 ZFHX2 RXRA ZNF398 HNF4A EGR2 PRDM1 SLC6A12 lnc-SLC6A12-1 LOC101929384
GH12J000214 Promoter 0.5 EPDnew 500.7 +0.0 8 0.1 PCBP1 ZNF398 SLC6A12 lnc-SLC6A12-1 LOC101929384
GH12J000210 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 20.2 +3.2 3226 1.3 NCOR1 TCF7 FOXA1 RFX1 ZBTB25 TGIF2 SKI ZBTB26 TBX3 ZKSCAN8 SLC6A12 lnc-SLC6A12-1 LOC101929384
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC6A12 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC6A12

Top Transcription factor binding sites by QIAGEN in the SLC6A12 gene promoter:
  • AREB6
  • GATA-2
  • Tal-1
  • YY1

Genomic Locations for SLC6A12 Gene

Genomic Locations for SLC6A12 Gene
27,113 bases
Minus strand
24,494 bases
Minus strand

Genomic View for SLC6A12 Gene

Genes around SLC6A12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC6A12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC6A12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC6A12 Gene

Proteins for SLC6A12 Gene

  • Protein details for SLC6A12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Sodium- and chloride-dependent betaine transporter
    Protein Accession:
    Secondary Accessions:
    • A0AV52
    • B2R992
    • D3DUN8

    Protein attributes for SLC6A12 Gene

    614 amino acids
    Molecular mass:
    69368 Da
    Quaternary structure:
    • Interacts with LIN7C.

neXtProt entry for SLC6A12 Gene

Post-translational modifications for SLC6A12 Gene

  • Glycosylation at Asn171 and Asn183
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC6A12 Gene

Domains & Families for SLC6A12 Gene

Gene Families for SLC6A12 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC6A12 Gene

  • Betaine transporter signature

Suggested Antigen Peptide Sequences for SLC6A12 Gene

GenScript: Design optimal peptide antigens:
  • Transporter (F5H2T6_HUMAN)
  • Solute carrier family 6 member 12 (S6A12_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A12 subfamily.
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A12 subfamily.
genes like me logo Genes that share domains with SLC6A12: view

Function for SLC6A12 Gene

Molecular function for SLC6A12 Gene

UniProtKB/Swiss-Prot Function:
Transports betaine and GABA. May have a role in regulation of GABAergic transmission in the brain through the reuptake of GABA into presynaptic terminals, as well as in osmotic regulation.
GENATLAS Biochemistry:
solute carrier family 6,member A12,neurotransmitter transporter,betaine/GABA,expressed in brain,kidney,activated by tonicity responsive enhancers (TONE1-TONE2),located in the 5'flanking region of the gene

Phenotypes From GWAS Catalog for SLC6A12 Gene

Gene Ontology (GO) - Molecular Function for SLC6A12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005328 neurotransmitter:sodium symporter activity IEA --
GO:0005332 gamma-aminobutyric acid:sodium symporter activity IBA 21873635
GO:0005515 protein binding IPI 21525870
GO:0015171 amino acid transmembrane transporter activity TAS --
GO:0015293 symporter activity IEA --
genes like me logo Genes that share ontologies with SLC6A12: view
genes like me logo Genes that share phenotypes with SLC6A12: view

Animal Models for SLC6A12 Gene

MGI Knock Outs for SLC6A12:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC6A12

CRISPR Products

miRNA for SLC6A12 Gene

miRTarBase miRNAs that target SLC6A12

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC6A12 Gene

Localization for SLC6A12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC6A12 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC6A12 gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
cytosol 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC6A12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS,IBA --
GO:0005887 integral component of plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 7861179
GO:0043005 neuron projection IBA 21873635
genes like me logo Genes that share ontologies with SLC6A12: view

Pathways & Interactions for SLC6A12 Gene

genes like me logo Genes that share pathways with SLC6A12: view

Gene Ontology (GO) - Biological Process for SLC6A12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003333 amino acid transmembrane transport IEA --
GO:0006836 neurotransmitter transport IEA --
GO:0006865 amino acid transport TAS --
GO:0015812 gamma-aminobutyric acid transport IEA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SLC6A12: view

No data available for SIGNOR curated interactions for SLC6A12 Gene

Drugs & Compounds for SLC6A12 Gene

(12) Drugs for SLC6A12 Gene - From: DrugBank, PharmGKB, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Betaine Approved Nutra 42
Aspirin Approved, Vet_approved Pharma Channel blocker 1440
Guvacine Experimental Pharma Target, inhibitor 0
(R/S) EF-1500 Pharma Inhibition, Inhibitor 0
(R)-EF-1520 Pharma 0

(9) Additional Compounds for SLC6A12 Gene - From: IUPHAR, Novoseek, HMDB, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Inhibition, Inhibitor
Inhibition, Inhibitor
Inhibition, Inhibitor
  • Na(+)
  • Na+
  • SODIUM ion
(+-)-Nipecotic acid

(5) Tocris Compounds for SLC6A12 Gene

Compound Action Cas Number
(+-)-Nipecotic acid GABA uptake inhibitor 60252-41-7
(S)-SNAP 5114 GABA uptake inhibitor 157604-55-2
CI 966 hydrochloride Selective inhibitor of GAT-1 110283-66-4
Guvacine hydrochloride Specific GABA uptake inhibitor 6027-91-4
SKF 89976A hydrochloride Potent GABA uptake inhibitor. Penetrates blood brain barrier 85375-15-1
genes like me logo Genes that share compounds with SLC6A12: view

Transcripts for SLC6A12 Gene

mRNA/cDNA for SLC6A12 Gene

16 NCBI additional mRNA sequence :
16 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC6A12 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^
SP1: - - - - - - - -
SP2: - - - - -
SP3: - - -
SP4: - - -
SP6: -
SP7: - - - -
SP8: - - -
SP9: - - -
SP10: - - - -

ExUns: 20 ^ 21 ^ 22

Relevant External Links for SLC6A12 Gene

GeneLoc Exon Structure for

Expression for SLC6A12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC6A12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC6A12 Gene

This gene is overexpressed in Kidney - Cortex (x11.4), Liver (x5.4), and Brain - Putamen (basal ganglia) (x4.7).

Protein differential expression in normal tissues from HIPED for SLC6A12 Gene

This gene is overexpressed in Liver (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC6A12 Gene

Protein tissue co-expression partners for SLC6A12 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC6A12

SOURCE GeneReport for Unigene cluster for SLC6A12 Gene:


mRNA Expression by UniProt/SwissProt for SLC6A12 Gene:

Tissue specificity: Liver, heart, skeletal muscle, placenta, and a widespread distribution in the brain.

Evidence on tissue expression from TISSUES for SLC6A12 Gene

  • Nervous system(4.7)
  • Kidney(4.5)
  • Liver(2.3)
  • Blood(2)
genes like me logo Genes that share expression patterns with SLC6A12: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC6A12 Gene

Orthologs for SLC6A12 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC6A12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC6A12 31 30
  • 99.13 (n)
(Canis familiaris)
Mammalia SLC6A12 31 30
  • 89.2 (n)
(Mus musculus)
Mammalia Slc6a12 17 31 30
  • 85.99 (n)
(Rattus norvegicus)
Mammalia Slc6a12 30
  • 85.02 (n)
(Bos Taurus)
Mammalia SLC6A12 31
  • 84 (a)
(Monodelphis domestica)
Mammalia SLC6A12 31
  • 79 (a)
(Gallus gallus)
Aves SLC6A13 30
  • 72.3 (n)
SLC6A12 31
  • 72 (a)
(Anolis carolinensis)
Reptilia SLC6A12 31
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492029 30
  • 71.07 (n)
(Danio rerio)
Actinopterygii slc6a13 31
  • 62 (a)
slc6a13l 31
  • 59 (a)
slc6a11a 31
  • 58 (a)
SLC6A12 (3 of 8) 31
  • 55 (a)
SLC6A12 (5 of 8) 31
  • 55 (a)
SLC6A12 (8 of 8) 31
  • 54 (a)
SLC6A12 (7 of 8) 31
  • 54 (a)
SLC6A12 (4 of 8) 31
  • 54 (a)
Dr.25768 30
fruit fly
(Drosophila melanogaster)
Insecta CG1732 32
  • 53 (a)
ine 32
  • 42 (a)
CG5549 32
  • 41 (a)
CG8850 32
  • 36 (a)
CG10804 32
  • 36 (a)
CG7075 32
  • 35 (a)
CG4476 32
  • 35 (a)
BG:DS03431.1 32
  • 35 (a)
(Caenorhabditis elegans)
Secernentea snf-11 32
  • 48 (a)
snf-3 32
  • 42 (a)
snf-4 32
  • 33 (a)
snf-2 32
  • 31 (a)
snf-12 32
  • 31 (a)
snf-6 32
  • 30 (a)
snf-8 32
  • 24 (a)
snf-1 32
  • 24 (a)
Species where no ortholog for SLC6A12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC6A12 Gene

Gene Tree for SLC6A12 (if available)
Gene Tree for SLC6A12 (if available)
Evolutionary constrained regions (ECRs) for SLC6A12: view image

Paralogs for SLC6A12 Gene

(20) SIMAP similar genes for SLC6A12 Gene using alignment to 3 proteins:

  • S6A12_HUMAN
  • F5H2T6_HUMAN
  • F5H4L6_HUMAN
genes like me logo Genes that share paralogs with SLC6A12: view

Variants for SLC6A12 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC6A12 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
719500 Benign: not provided 198,911(-) C/A SYNONYMOUS_VARIANT
769379 Benign: not provided 192,583(-) C/T SYNONYMOUS_VARIANT
769380 Benign: not provided 198,001(-) C/T SYNONYMOUS_VARIANT
781056 Benign: not provided 204,619(-) T/C SYNONYMOUS_VARIANT
787548 Benign: not provided 196,115(-) G/C INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for SLC6A12 Gene

Structural Variations from Database of Genomic Variants (DGV) for SLC6A12 Gene

Variant ID Type Subtype PubMed ID
dgv1330n100 CNV gain 25217958
dgv1331n100 CNV gain 25217958
dgv87n21 CNV loss 19592680
esv1221367 CNV insertion 17803354
esv1501218 CNV insertion 17803354
esv2319687 CNV deletion 18987734
esv2627142 CNV insertion 19546169
esv3628221 CNV gain 21293372
esv3628226 CNV gain 21293372
nsv1035539 CNV gain 25217958
nsv1050781 CNV loss 25217958
nsv428269 CNV gain+loss 18775914
nsv468947 CNV gain 19166990
nsv470252 CNV gain 18288195
nsv523142 CNV gain 19592680
nsv556853 CNV gain 21841781
nsv556854 CNV loss 21841781
nsv556855 CNV loss 21841781
nsv556856 CNV loss 21841781
nsv556857 CNV gain 21841781
nsv556861 CNV loss 21841781
nsv569 CNV deletion 18451855
nsv832302 CNV gain 17160897

Variation tolerance for SLC6A12 Gene

Residual Variation Intolerance Score: 83.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.49; 43.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC6A12 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC6A12 Gene

Disorders for SLC6A12 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SLC6A12 Gene - From: DISEASES

Disorder Aliases PubMed IDs
traumatic glaucoma
  • glaucoma associated with ocular trauma
posterolateral myocardial infarction
spinocerebellar ataxia 11
  • sca11
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC6A12

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC6A12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC6A12 Gene

Publications for SLC6A12 Gene

  1. Molecular cloning and functional characterization of a GABA/betaine transporter from human kidney. (PMID: 7589472) Rasola A … Bagnasco S (FEBS letters 1995) 2 3 4 23 54
  2. Cloning and expression of a betaine/GABA transporter from human brain. (PMID: 7861179) Borden LA … Weinshank RL (Journal of neurochemistry 1995) 3 4 23 54
  3. 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. (PMID: 20424473) Yokoyama K … Hosoya T (Nephron. Clinical practice 2010) 3 41 54
  4. Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population. (PMID: 20597903) Pasaje CF … Shin HD (Annals of human genetics 2010) 3 41 54
  5. Transcriptomic and genetic studies identify IL-33 as a candidate gene for Alzheimer's disease. (PMID: 19204726) Chapuis J … Lambert JC (Molecular psychiatry 2009) 3 41 54

Products for SLC6A12 Gene

  • Biorbyt antibodies for SLC6A12

Sources for SLC6A12 Gene