Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SLC6A12 (solute carrier family 6 member 12)

Identity

Alias (NCBI)BGT-1
BGT1
GAT2
HGNC (Hugo) SLC6A12
HGNC Alias symbBGT-1
HGNC Alias namebetaine/GABA transporter-1
HGNC Previous namesolute carrier family 6 (neurotransmitter transporter, betaine/GABA), member 12
 solute carrier family 6 (neurotransmitter transporter), member 12
LocusID (NCBI) 6539
Atlas_Id 73469
Location 12p13.33  [Link to chromosome band 12p13]
Location_base_pair Starts at 190077 and ends at 213447 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

External links

Nomenclature
HGNC (Hugo)SLC6A12   11045
Cards
Entrez_Gene (NCBI)SLC6A12  6539  solute carrier family 6 member 12
AliasesBGT-1; BGT1; GAT2
GeneCards (Weizmann)SLC6A12
Ensembl hg19 (Hinxton)ENSG00000111181 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000111181 [Gene_View]  ENSG00000111181 [Sequence]  chr12:190077-213447 [Contig_View]  SLC6A12 [Vega]
ICGC DataPortalENSG00000111181
TCGA cBioPortalSLC6A12
AceView (NCBI)SLC6A12
Genatlas (Paris)SLC6A12
WikiGenes6539
SOURCE (Princeton)SLC6A12
Genetics Home Reference (NIH)SLC6A12
Genomic and cartography
GoldenPath hg38 (UCSC)SLC6A12  -     chr12:190077-213447 -  12p13.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SLC6A12  -     12p13.33   [Description]    (hg19-Feb_2009)
GoldenPathSLC6A12 - 12p13.33 [CytoView hg19]  SLC6A12 - 12p13.33 [CytoView hg38]
ImmunoBaseENSG00000111181
genome Data Viewer NCBISLC6A12 [Mapview hg19]  
OMIM603080   
Gene and transcription
Genbank (Entrez)AI241640 AK096046 AK125026 AK131564 AK307167
RefSeq transcript (Entrez)NM_001122847 NM_001122848 NM_001206931 NM_003044
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SLC6A12
Alternative Splicing GalleryENSG00000111181
Gene ExpressionSLC6A12 [ NCBI-GEO ]   SLC6A12 [ EBI - ARRAY_EXPRESS ]   SLC6A12 [ SEEK ]   SLC6A12 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC6A12 [ Firebrowse - Broad ]
GenevisibleExpression of SLC6A12 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6539
GTEX Portal (Tissue expression)SLC6A12
Human Protein AtlasENSG00000111181-SLC6A12 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP48065   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP48065  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP48065
Splice isoforms : SwissVarP48065
PhosPhoSitePlusP48065
Domaine pattern : Prosite (Expaxy)NA_NEUROTRAN_SYMP_1 (PS00610)    NA_NEUROTRAN_SYMP_2 (PS00754)    NA_NEUROTRAN_SYMP_3 (PS50267)   
Domains : Interpro (EBI)Na/ntran_symport    Na/ntran_symport_betaine    SNS_sf   
Domain families : Pfam (Sanger)SNF (PF00209)   
Domain families : Pfam (NCBI)pfam00209   
Conserved Domain (NCBI)SLC6A12
DMDM Disease mutations6539
Blocks (Seattle)SLC6A12
SuperfamilyP48065
Human Protein Atlas [tissue]ENSG00000111181-SLC6A12 [tissue]
Peptide AtlasP48065
HPRD04358
IPIIPI00007647   IPI00441991   IPI01014526   IPI01014083   
Protein Interaction databases
DIP (DOE-UCLA)P48065
IntAct (EBI)P48065
FunCoupENSG00000111181
BioGRIDSLC6A12
STRING (EMBL)SLC6A12
ZODIACSLC6A12
Ontologies - Pathways
QuickGOP48065
Ontology : AmiGOamino acid transmembrane transport  gamma-aminobutyric acid:sodium symporter activity  protein binding  plasma membrane  plasma membrane  integral component of plasma membrane  amino acid transport  amino acid transmembrane transporter activity  gamma-aminobutyric acid transport  integral component of membrane  neurotransmitter binding  neuron projection  
Ontology : EGO-EBIamino acid transmembrane transport  gamma-aminobutyric acid:sodium symporter activity  protein binding  plasma membrane  plasma membrane  integral component of plasma membrane  amino acid transport  amino acid transmembrane transporter activity  gamma-aminobutyric acid transport  integral component of membrane  neurotransmitter binding  neuron projection  
NDEx NetworkSLC6A12
Atlas of Cancer Signalling NetworkSLC6A12
Wikipedia pathwaysSLC6A12
Orthology - Evolution
OrthoDB6539
GeneTree (enSembl)ENSG00000111181
Phylogenetic Trees/Animal Genes : TreeFamSLC6A12
HOGENOMP48065
Homologs : HomoloGeneSLC6A12
Homology/Alignments : Family Browser (UCSC)SLC6A12
Gene fusions - Rearrangements
Fusion : QuiverSLC6A12
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC6A12 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLC6A12
dbVarSLC6A12
ClinVarSLC6A12
1000_GenomesSLC6A12 
Exome Variant ServerSLC6A12
GNOMAD BrowserENSG00000111181
Varsome BrowserSLC6A12
Genetic variants : HAPMAP6539
Genomic Variants (DGV)SLC6A12 [DGVbeta]
DECIPHERSLC6A12 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSLC6A12 
Mutations
ICGC Data PortalSLC6A12 
TCGA Data PortalSLC6A12 
Broad Tumor PortalSLC6A12
OASIS PortalSLC6A12 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC6A12  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSLC6A12
Mutations and Diseases : HGMDSLC6A12
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch SLC6A12
DgiDB (Drug Gene Interaction Database)SLC6A12
DoCM (Curated mutations)SLC6A12 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC6A12 (select a term)
intoGenSLC6A12
Cancer3DSLC6A12(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603080   
Orphanet
DisGeNETSLC6A12
MedgenSLC6A12
Genetic Testing Registry SLC6A12
NextProtP48065 [Medical]
TSGene6539
GENETestsSLC6A12
Target ValidationSLC6A12
Huge Navigator SLC6A12 [HugePedia]
snp3D : Map Gene to Disease6539
BioCentury BCIQSLC6A12
ClinGenSLC6A12
Clinical trials, drugs, therapy
Protein Interactions : CTD6539
Pharm GKB GenePA35908
Clinical trialSLC6A12
Miscellaneous
canSAR (ICR)SLC6A12 (select the gene name)
HarmonizomeSLC6A12
DataMed IndexSLC6A12
Probes
Litterature
PubMed25 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC6A12
EVEXSLC6A12
GoPubMedSLC6A12
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Jul 16 16:28:19 CEST 2020
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