Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SLC6A1 (solute carrier family 6 member 1)

Identity

Alias_namessolute carrier family 6 (neurotransmitter transporter, GABA), member 1
solute carrier family 6 (neurotransmitter transporter), member 1
Alias_symbol (synonym)GAT1
GABATR
GABATHG
Other aliasMAE
HGNC (Hugo) SLC6A1
LocusID (NCBI) 6529
Atlas_Id 53134
Location 3p25.3  [Link to chromosome band 3p25]
Location_base_pair Starts at 10992734 and ends at 11039249 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)
SLC6A1 (3p25.3) / ARHGAP35 (19q13.32)

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)SLC6A1   11042
Cards
Entrez_Gene (NCBI)SLC6A1  6529  solute carrier family 6 member 1
AliasesGABATHG; GABATR; GAT1; MAE
GeneCards (Weizmann)SLC6A1
Ensembl hg19 (Hinxton)ENSG00000157103 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000157103 [Gene_View]  chr3:10992734-11039249 [Contig_View]  SLC6A1 [Vega]
ICGC DataPortalENSG00000157103
TCGA cBioPortalSLC6A1
AceView (NCBI)SLC6A1
Genatlas (Paris)SLC6A1
WikiGenes6529
SOURCE (Princeton)SLC6A1
Genetics Home Reference (NIH)SLC6A1
Genomic and cartography
GoldenPath hg38 (UCSC)SLC6A1  -     chr3:10992734-11039249 +  3p25.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SLC6A1  -     3p25.3   [Description]    (hg19-Feb_2009)
EnsemblSLC6A1 - 3p25.3 [CytoView hg19]  SLC6A1 - 3p25.3 [CytoView hg38]
Mapping of homologs : NCBISLC6A1 [Mapview hg19]  SLC6A1 [Mapview hg38]
OMIM137165   616421   
Gene and transcription
Genbank (Entrez)AK090958 AK295702 BC033904 BC057291 DA162953
RefSeq transcript (Entrez)NM_001348250 NM_001348251 NM_001348252 NM_001348253 NM_003042
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SLC6A1
Cluster EST : UnigeneHs.443874 [ NCBI ]
CGAP (NCI)Hs.443874
Alternative Splicing GalleryENSG00000157103
Gene ExpressionSLC6A1 [ NCBI-GEO ]   SLC6A1 [ EBI - ARRAY_EXPRESS ]   SLC6A1 [ SEEK ]   SLC6A1 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC6A1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6529
GTEX Portal (Tissue expression)SLC6A1
Human Protein AtlasENSG00000157103-SLC6A1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP30531   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP30531  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP30531
Splice isoforms : SwissVarP30531
PhosPhoSitePlusP30531
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_GABA_GAT1   
Domain families : Pfam (Sanger)SNF (PF00209)   
Domain families : Pfam (NCBI)pfam00209   
Conserved Domain (NCBI)SLC6A1
DMDM Disease mutations6529
Blocks (Seattle)SLC6A1
SuperfamilyP30531
Human Protein Atlas [tissue]ENSG00000157103-SLC6A1 [tissue]
Peptide AtlasP30531
HPRD00664
IPIIPI00026846   IPI01010873   IPI00927093   
Protein Interaction databases
DIP (DOE-UCLA)P30531
IntAct (EBI)P30531
FunCoupENSG00000157103
BioGRIDSLC6A1
STRING (EMBL)SLC6A1
ZODIACSLC6A1
Ontologies - Pathways
QuickGOP30531
Ontology : AmiGOneurotransmitter:sodium symporter activity  gamma-aminobutyric acid:sodium symporter activity  gamma-aminobutyric acid:sodium symporter activity  plasma membrane  integral component of plasma membrane  transport  neurotransmitter transport  chemical synaptic transmission  learning  response to toxic substance  response to sucrose  cell surface  response to lead ion  positive regulation of gamma-aminobutyric acid secretion  response to purine-containing compound  gamma-aminobutyric acid transport  membrane  integral component of membrane  axon  negative regulation of synaptic transmission, GABAergic  response to estradiol  response to cocaine  neuron projection  metal ion binding  protein homooligomerization  response to calcium ion  gamma-aminobutyric acid import  transmembrane transport  
Ontology : EGO-EBIneurotransmitter:sodium symporter activity  gamma-aminobutyric acid:sodium symporter activity  gamma-aminobutyric acid:sodium symporter activity  plasma membrane  integral component of plasma membrane  transport  neurotransmitter transport  chemical synaptic transmission  learning  response to toxic substance  response to sucrose  cell surface  response to lead ion  positive regulation of gamma-aminobutyric acid secretion  response to purine-containing compound  gamma-aminobutyric acid transport  membrane  integral component of membrane  axon  negative regulation of synaptic transmission, GABAergic  response to estradiol  response to cocaine  neuron projection  metal ion binding  protein homooligomerization  response to calcium ion  gamma-aminobutyric acid import  transmembrane transport  
Pathways : KEGGGABAergic synapse   
NDEx NetworkSLC6A1
Atlas of Cancer Signalling NetworkSLC6A1
Wikipedia pathwaysSLC6A1
Orthology - Evolution
OrthoDB6529
GeneTree (enSembl)ENSG00000157103
Phylogenetic Trees/Animal Genes : TreeFamSLC6A1
HOVERGENP30531
HOGENOMP30531
Homologs : HomoloGeneSLC6A1
Homology/Alignments : Family Browser (UCSC)SLC6A1
Gene fusions - Rearrangements
Tumor Fusion PortalSLC6A1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC6A1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SLC6A1
dbVarSLC6A1
ClinVarSLC6A1
1000_GenomesSLC6A1 
Exome Variant ServerSLC6A1
ExAC (Exome Aggregation Consortium)ENSG00000157103
GNOMAD BrowserENSG00000157103
Genetic variants : HAPMAP6529
Genomic Variants (DGV)SLC6A1 [DGVbeta]
DECIPHERSLC6A1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSLC6A1 
Mutations
ICGC Data PortalSLC6A1 
TCGA Data PortalSLC6A1 
Broad Tumor PortalSLC6A1
OASIS PortalSLC6A1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC6A1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSLC6A1
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 SLC6A1
DgiDB (Drug Gene Interaction Database)SLC6A1
DoCM (Curated mutations)SLC6A1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC6A1 (select a term)
intoGenSLC6A1
Cancer3DSLC6A1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM137165    616421   
Orphanet891   
DisGeNETSLC6A1
MedgenSLC6A1
Genetic Testing Registry SLC6A1
NextProtP30531 [Medical]
TSGene6529
GENETestsSLC6A1
Target ValidationSLC6A1
Huge Navigator SLC6A1 [HugePedia]
snp3D : Map Gene to Disease6529
BioCentury BCIQSLC6A1
ClinGenSLC6A1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6529
Chemical/Pharm GKB GenePA309
Clinical trialSLC6A1
Miscellaneous
canSAR (ICR)SLC6A1 (select the gene name)
Probes
Litterature
PubMed58 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC6A1
EVEXSLC6A1
GoPubMedSLC6A1
iHOPSLC6A1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 21 14:35:21 CET 2017

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