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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
  • Na(+)/Cl(-) Betaine/GABA Transporter 3 4
  • Betaine/GABA Transporter-1 2 3
  • BGT-1 3 4
  • Sodium- And Chloride-Dependent Betaine Transporter 3
  • 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 Spinocerebellar Ataxia 11. Among its related pathways are Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds and Neurotransmitter Release Cycle. 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 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.

No data available for Entrez Gene Summary , CIViC summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC6A12 Gene

Genomics for SLC6A12 Gene

Regulatory Elements for SLC6A12 Gene

Enhancers for SLC6A12 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH12G000211 1.7 FANTOM5 Ensembl ENCODE dbSUPER 19.1 +1.5 1470 2.6 ARID4B RAD21 GLIS2 PCBP1 EGR2 CEBPB ZNF398 NR2F2 CEBPA MXD3 SLC6A12 KDM5A CCDC77 LOC101929384
GH12G000537 1.8 FANTOM5 Ensembl ENCODE dbSUPER 14.8 -324.3 -324320 3.1 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 YY1 TCF12 ZNF121 SLC30A9 B4GALNT3 SLC6A12 ERC1 PIR41391 GC12M000504
GH12G000210 1.2 ENCODE dbSUPER 20.3 +3.4 3445 0.9 FOXA2 ATF1 DMAP1 ZSCAN9 RARA YY1 GATA4 EGR2 KLF11 SP5 SLC6A12 LOC101929384
GH12G000219 1.4 Ensembl ENCODE dbSUPER 15.8 -5.6 -5629 0.9 ELF3 RB1 ARID4B ZNF2 ZNF48 RAD21 ZNF121 GLIS2 ELK1 SCRT2 SLC6A12 GC12P000235
GH12G000152 1.2 ENCODE dbSUPER 11.2 +61.8 61794 1.3 RB1 ARID4B ZNF48 RAD21 GLIS2 ZNF366 ZNF143 MIXL1 THAP11 ZNF263 ENSG00000255671 LOC101929384 SLC6A12 SLC6A13 LOC574538 LOC102723544 IQSEC3 ENSG00000256694
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC6A12 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the SLC6A12 gene promoter:

Genomic Location for SLC6A12 Gene

Chromosome:
12
Start:
187,458 bp from pter
End:
214,570 bp from pter
Size:
27,113 bases
Orientation:
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:
    P48065-S6A12_HUMAN
    Recommended name:
    Sodium- and chloride-dependent betaine transporter
    Protein Accession:
    P48065
    Secondary Accessions:
    • A0AV52
    • B2R992
    • D3DUN8

    Protein attributes for SLC6A12 Gene

    Size:
    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 isoforms=183
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC6A12 Gene

Domains & Families for SLC6A12 Gene

Gene Families for SLC6A12 Gene

HGNC:
IUPHAR :

Protein Domains for SLC6A12 Gene

Suggested Antigen Peptide Sequences for SLC6A12 Gene

Graphical View of Domain Structure for InterPro Entry

P48065

UniProtKB/Swiss-Prot:

S6A12_HUMAN :
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A12 subfamily.
Family:
  • 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

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 5flanking region of the 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.

Gene Ontology (GO) - Molecular Function for SLC6A12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005215 transporter activity IBA --
GO:0005328 neurotransmitter:sodium symporter activity IEA --
GO:0005332 gamma-aminobutyric acid:sodium symporter activity IEA --
GO:0005515 protein binding IPI 21525870
GO:0015171 amino acid transmembrane transporter activity TAS --
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

Inhibitory RNA 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

COMPARTMENTS
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
cytosol 2
nucleus 1

Gene Ontology (GO) - Cellular Components for SLC6A12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 7861179
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:0006810 transport TAS 7861179
GO:0006836 neurotransmitter transport IEA --
GO:0006865 amino acid transport TAS --
GO:0015812 gamma-aminobutyric acid 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 34
Aspirin Approved, Vet_approved Pharma Channel blocker 1152
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
(R/S)-EF-1502
Inhibition, Inhibitor
LU32-176B
Inhibition, Inhibitor
NNC052090
Inhibition, Inhibitor
sodium
  • Sodium
  • Sodium ion
7440-23-5
Tiagabine hydrochloride
145821-59-6

(5) Tocris Compounds for SLC6A12 Gene

Compound Action Cas Number
(S)-SNAP 5114 GABA uptake inhibitor 157604-55-2
CI 966 hydrochloride Selective inhibitor of GAT-1 110283-66-4
NNC 05-2090 hydrochloride GABA uptake inhibitor; moderately BGT-1 selective 184845-18-9
NNC 711 Selective inhibitor of GAT-1 145645-62-1
Tiagabine hydrochloride GABA uptake inhibitor; anticonvulsant 145821-59-6
genes like me logo Genes that share compounds with SLC6A12: view

Transcripts for SLC6A12 Gene

Unigene Clusters for SLC6A12 Gene

Solute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12:
Representative Sequences:

CRISPR Products

Inhibitory RNA 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: - - -
SP5:
SP6: -
SP7: - - - -
SP8: - - -
SP9: - - -
SP10: - - - -
SP11:

ExUns: 20 ^ 21 ^ 22
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SLC6A12 Gene

GeneLoc Exon Structure for
SLC6A12
ECgene alternative splicing isoforms for
SLC6A12

Expression for SLC6A12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for SLC6A12 Gene



Protein tissue co-expression partners for SLC6A12 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC6A12 Gene:

SLC6A12

SOURCE GeneReport for Unigene cluster for SLC6A12 Gene:

Hs.437174

mRNA Expression by UniProt/SwissProt for SLC6A12 Gene:

P48065-S6A12_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia SLC6A12 34 35
  • 99.13 (n)
dog
(Canis familiaris)
Mammalia SLC6A12 34 35
  • 89.2 (n)
mouse
(Mus musculus)
Mammalia Slc6a12 34 16 35
  • 85.99 (n)
rat
(Rattus norvegicus)
Mammalia Slc6a12 34
  • 85.02 (n)
cow
(Bos Taurus)
Mammalia SLC6A12 35
  • 84 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLC6A12 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC6A13 34
  • 72.3 (n)
SLC6A12 35
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC6A12 35
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492029 34
  • 71.07 (n)
zebrafish
(Danio rerio)
Actinopterygii slc6a13 35
  • 62 (a)
OneToMany
slc6a13l 35
  • 59 (a)
OneToMany
slc6a11a 35
  • 58 (a)
OneToMany
SLC6A12 (3 of 8) 35
  • 55 (a)
OneToMany
SLC6A12 (5 of 8) 35
  • 55 (a)
OneToMany
SLC6A12 (4 of 8) 35
  • 54 (a)
OneToMany
SLC6A12 (7 of 8) 35
  • 54 (a)
OneToMany
SLC6A12 (8 of 8) 35
  • 54 (a)
OneToMany
Dr.25768 34
fruit fly
(Drosophila melanogaster)
Insecta CG1732 36
  • 53 (a)
ine 36
  • 42 (a)
CG5549 36
  • 41 (a)
CG10804 36
  • 36 (a)
CG8850 36
  • 36 (a)
BG:DS03431.1 36
  • 35 (a)
CG4476 36
  • 35 (a)
CG7075 36
  • 35 (a)
worm
(Caenorhabditis elegans)
Secernentea snf-11 36
  • 48 (a)
snf-3 36
  • 42 (a)
snf-4 36
  • 33 (a)
snf-12 36
  • 31 (a)
snf-2 36
  • 31 (a)
snf-6 36
  • 30 (a)
snf-1 36
  • 24 (a)
snf-8 36
  • 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

ENSEMBL:
Gene Tree for SLC6A12 (if available)
TreeFam:
Gene Tree for SLC6A12 (if available)

Paralogs for SLC6A12 Gene

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

Variants for SLC6A12 Gene

Sequence variations from dbSNP and Humsavar for SLC6A12 Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs1000060618 -- 207,691(+) ACTAG(C/T)CTGTG intron-variant
rs1000120998 -- 213,003(+) AAGAG(A/G)CTAGA intron-variant
rs1000211201 -- 205,415(+) CTTCA(C/T)GTCAG intron-variant, downstream-variant-500B
rs1000415090 -- 207,953(+) CCCCA(C/T)GGCCA intron-variant
rs1000435189 -- 197,140(+) ATCCA(C/T)CCATC intron-variant

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)

Relevant External Links for SLC6A12 Gene

Human Gene Mutation Database (HGMD)
SLC6A12
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC6A12

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

Disorders for SLC6A12 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SLC6A12 Gene - From: DISEASES and GeneCards

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

Relevant External Links for SLC6A12

Genetic Association Database (GAD)
SLC6A12
Human Genome Epidemiology (HuGE) Navigator
SLC6A12
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC6A12
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 Lett. 1995) 2 3 4 22 64
  2. Cloning and expression of a betaine/GABA transporter from human brain. (PMID: 7861179) Borden L.A. … Weinshank R.L. (J. Neurochem. 1995) 3 4 22 64
  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 Clin Pract 2010) 3 46 64
  4. Association of SLC6A12 variants with aspirin-intolerant asthma in a Korean population. (PMID: 20597903) Pasaje C.F. … Shin H.D. (Ann. Hum. Genet. 2010) 3 46 64
  5. Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment. (PMID: 19086053) GratacA^s M. … Carracedo A. (Am. J. Med. Genet. B Neuropsychiatr. Genet. 2009) 3 46 64

Products for SLC6A12 Gene

Sources for SLC6A12 Gene

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