Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SLC46A2 (solute carrier family 46 member 2)

Identity

Alias (NCBI)Ly110
TSCOT
HGNC (Hugo) SLC46A2
HGNC Alias symbLy110
HGNC Previous nameTSCOT
HGNC Previous namethymic stromal co-transporter
 solute carrier family 46, member 2
LocusID (NCBI) 57864
Atlas_Id 50168
Location 9q32  [Link to chromosome band 9q32]
Location_base_pair Starts at 112878920 and ends at 112890876 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)
USP42 (7p22.1) / SLC46A2 (9q32)USP42 7p22.1 / SLC46A2 9q32

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(7;9)(p22;q32) USP42/SLC46A2

External links

Nomenclature
HGNC (Hugo)SLC46A2   16055
Cards
Entrez_Gene (NCBI)SLC46A2    solute carrier family 46 member 2
AliasesLy110; TSCOT
GeneCards (Weizmann)SLC46A2
Ensembl hg19 (Hinxton)ENSG00000119457 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000119457 [Gene_View]  ENSG00000119457 [Sequence]  chr9:112878920-112890876 [Contig_View]  SLC46A2 [Vega]
ICGC DataPortalENSG00000119457
TCGA cBioPortalSLC46A2
AceView (NCBI)SLC46A2
Genatlas (Paris)SLC46A2
SOURCE (Princeton)SLC46A2
Genetics Home Reference (NIH)SLC46A2
Genomic and cartography
GoldenPath hg38 (UCSC)SLC46A2  -     chr9:112878920-112890876 -  9q32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SLC46A2  -     9q32   [Description]    (hg19-Feb_2009)
GoldenPathSLC46A2 - 9q32 [CytoView hg19]  SLC46A2 - 9q32 [CytoView hg38]
ImmunoBaseENSG00000119457
genome Data Viewer NCBISLC46A2 [Mapview hg19]  
OMIM608956   
Gene and transcription
Genbank (Entrez)AF242557 AK055571 AK314414 BC048285 DA593062
RefSeq transcript (Entrez)NM_033051
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SLC46A2
Alternative Splicing GalleryENSG00000119457
Gene ExpressionSLC46A2 [ NCBI-GEO ]   SLC46A2 [ EBI - ARRAY_EXPRESS ]   SLC46A2 [ SEEK ]   SLC46A2 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC46A2 [ Firebrowse - Broad ]
GenevisibleExpression of SLC46A2 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)57864
GTEX Portal (Tissue expression)SLC46A2
Human Protein AtlasENSG00000119457-SLC46A2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BY10   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BY10  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BY10
Splice isoforms : SwissVarQ9BY10
PhosPhoSitePlusQ9BY10
Domains : Interpro (EBI)MFS    MFS_trans_sf    Tet-R_TetA/multi-R_MdtG   
Domain families : Pfam (Sanger)MFS_1 (PF07690)   
Domain families : Pfam (NCBI)pfam07690   
Conserved Domain (NCBI)SLC46A2
Blocks (Seattle)SLC46A2
SuperfamilyQ9BY10
Human Protein Atlas [tissue]ENSG00000119457-SLC46A2 [tissue]
Peptide AtlasQ9BY10
HPRD16411
IPIIPI00011465   
Protein Interaction databases
DIP (DOE-UCLA)Q9BY10
IntAct (EBI)Q9BY10
BioGRIDSLC46A2
STRING (EMBL)SLC46A2
ZODIACSLC46A2
Ontologies - Pathways
QuickGOQ9BY10
Ontology : AmiGOplasma membrane  cell surface  symporter activity  integral component of membrane  T cell homeostasis  regulation of T cell differentiation  thymus development  transmembrane transport  negative regulation of T cell apoptotic process  positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway  
Ontology : EGO-EBIplasma membrane  cell surface  symporter activity  integral component of membrane  T cell homeostasis  regulation of T cell differentiation  thymus development  transmembrane transport  negative regulation of T cell apoptotic process  positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway  
NDEx NetworkSLC46A2
Atlas of Cancer Signalling NetworkSLC46A2
Wikipedia pathwaysSLC46A2
Orthology - Evolution
OrthoDB57864
GeneTree (enSembl)ENSG00000119457
Phylogenetic Trees/Animal Genes : TreeFamSLC46A2
HOGENOMQ9BY10
Homologs : HomoloGeneSLC46A2
Homology/Alignments : Family Browser (UCSC)SLC46A2
Gene fusions - Rearrangements
Fusion : MitelmanUSP42/SLC46A2 [7p22.1/9q32]  
Fusion PortalUSP42 7p22.1 SLC46A2 9q32 BRCA
Fusion : QuiverSLC46A2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC46A2 [hg38]
dbVarSLC46A2
ClinVarSLC46A2
MonarchSLC46A2
1000_GenomesSLC46A2 
Exome Variant ServerSLC46A2
GNOMAD BrowserENSG00000119457
Varsome BrowserSLC46A2
Genomic Variants (DGV)SLC46A2 [DGVbeta]
DECIPHERSLC46A2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSLC46A2 
Mutations
ICGC Data PortalSLC46A2 
TCGA Data PortalSLC46A2 
Broad Tumor PortalSLC46A2
OASIS PortalSLC46A2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC46A2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSLC46A2
Mutations and Diseases : HGMDSLC46A2
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 SLC46A2
DgiDB (Drug Gene Interaction Database)SLC46A2
DoCM (Curated mutations)SLC46A2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC46A2 (select a term)
intoGenSLC46A2
Cancer3DSLC46A2(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608956   
Orphanet
DisGeNETSLC46A2
MedgenSLC46A2
Genetic Testing Registry SLC46A2
NextProtQ9BY10 [Medical]
GENETestsSLC46A2
Target ValidationSLC46A2
Huge Navigator SLC46A2 [HugePedia]
ClinGenSLC46A2
Clinical trials, drugs, therapy
MyCancerGenomeSLC46A2
Protein Interactions : CTD
Pharm GKB GenePA162403790
PharosQ9BY10
Clinical trialSLC46A2
Miscellaneous
canSAR (ICR)SLC46A2 (select the gene name)
HarmonizomeSLC46A2
DataMed IndexSLC46A2
Probes
Litterature
PubMed10 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSLC46A2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jan 1 18:37:59 CET 2021
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