Atlas of Genetics and Cytogenetics in Oncology and Haematology

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   
X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SLC5A7 (solute carrier family 5 member 7)

Identity

Alias (NCBI)CHT
CHT1
CMS20
HMN7A
HGNC (Hugo) SLC5A7
HGNC Alias symbhCHT
CHT1
HGNC Previous namesolute carrier family 5 (choline transporter), member 7
 solute carrier family 5 (sodium/choline cotransporter), member 7
LocusID (NCBI) 60482
Atlas_Id 73465
Location 2q12.3  [Link to chromosome band 2q12]
Location_base_pair Starts at 107986514 and ends at 108013987 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)SLC5A7   14025
Cards
Entrez_Gene (NCBI)SLC5A7    solute carrier family 5 member 7
AliasesCHT; CHT1; CMS20; HMN7A
GeneCards (Weizmann)SLC5A7
Ensembl hg19 (Hinxton)ENSG00000115665 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000115665 [Gene_View]  ENSG00000115665 [Sequence]  chr2:107986514-108013987 [Contig_View]  SLC5A7 [Vega]
ICGC DataPortalENSG00000115665
TCGA cBioPortalSLC5A7
AceView (NCBI)SLC5A7
Genatlas (Paris)SLC5A7
SOURCE (Princeton)SLC5A7
Genetics Home Reference (NIH)SLC5A7
Genomic and cartography
GoldenPath hg38 (UCSC)SLC5A7  -     chr2:107986514-108013987 +  2q12.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SLC5A7  -     2q12.3   [Description]    (hg19-Feb_2009)
GoldenPathSLC5A7 - 2q12.3 [CytoView hg19]  SLC5A7 - 2q12.3 [CytoView hg38]
ImmunoBaseENSG00000115665
genome Data Viewer NCBISLC5A7 [Mapview hg19]  
OMIM158580   608761   617143   
Gene and transcription
Genbank (Entrez)AB043997 AB084377 AF276871 AJ401466 AK300801
RefSeq transcript (Entrez)NM_001305005 NM_001305006 NM_001305007 NM_021815
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SLC5A7
Alternative Splicing GalleryENSG00000115665
Gene ExpressionSLC5A7 [ NCBI-GEO ]   SLC5A7 [ EBI - ARRAY_EXPRESS ]   SLC5A7 [ SEEK ]   SLC5A7 [ MEM ]
Gene Expression Viewer (FireBrowse)SLC5A7 [ Firebrowse - Broad ]
GenevisibleExpression of SLC5A7 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)60482
GTEX Portal (Tissue expression)SLC5A7
Human Protein AtlasENSG00000115665-SLC5A7 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9GZV3   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9GZV3  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9GZV3
Splice isoforms : SwissVarQ9GZV3
PhosPhoSitePlusQ9GZV3
Domaine pattern : Prosite (Expaxy)NA_SOLUT_SYMP_3 (PS50283)   
Domains : Interpro (EBI)Na/Glc_symporter_sf    Na/solute_symporter   
Domain families : Pfam (Sanger)SSF (PF00474)   
Domain families : Pfam (NCBI)pfam00474   
Conserved Domain (NCBI)SLC5A7
Blocks (Seattle)SLC5A7
SuperfamilyQ9GZV3
Human Protein Atlas [tissue]ENSG00000115665-SLC5A7 [tissue]
Peptide AtlasQ9GZV3
HPRD12294
IPIIPI00029180   IPI01009671   
Protein Interaction databases
DIP (DOE-UCLA)Q9GZV3
IntAct (EBI)Q9GZV3
BioGRIDSLC5A7
STRING (EMBL)SLC5A7
ZODIACSLC5A7
Ontologies - Pathways
QuickGOQ9GZV3
Ontology : AmiGOin utero embryonic development  choline:sodium symporter activity  choline:sodium symporter activity  plasma membrane  plasma membrane  sodium ion transport  neurotransmitter secretion  synaptic transmission, cholinergic  neuromuscular synaptic transmission  acetylcholine biosynthetic process  acetylcholine biosynthetic process  choline transmembrane transporter activity  choline transmembrane transporter activity  choline transport  integral component of membrane  cell junction  axon  dendrite  neuromuscular junction  choline binding  perikaryon  synapse  transmembrane transport  presynapse  
Ontology : EGO-EBIin utero embryonic development  choline:sodium symporter activity  choline:sodium symporter activity  plasma membrane  plasma membrane  sodium ion transport  neurotransmitter secretion  synaptic transmission, cholinergic  neuromuscular synaptic transmission  acetylcholine biosynthetic process  acetylcholine biosynthetic process  choline transmembrane transporter activity  choline transmembrane transporter activity  choline transport  integral component of membrane  cell junction  axon  dendrite  neuromuscular junction  choline binding  perikaryon  synapse  transmembrane transport  presynapse  
NDEx NetworkSLC5A7
Atlas of Cancer Signalling NetworkSLC5A7
Wikipedia pathwaysSLC5A7
Orthology - Evolution
OrthoDB60482
GeneTree (enSembl)ENSG00000115665
Phylogenetic Trees/Animal Genes : TreeFamSLC5A7
HOGENOMQ9GZV3
Homologs : HomoloGeneSLC5A7
Homology/Alignments : Family Browser (UCSC)SLC5A7
Gene fusions - Rearrangements
Fusion : QuiverSLC5A7
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSLC5A7 [hg38]
dbVarSLC5A7
ClinVarSLC5A7
MonarchSLC5A7
1000_GenomesSLC5A7 
Exome Variant ServerSLC5A7
GNOMAD BrowserENSG00000115665
Varsome BrowserSLC5A7
Genomic Variants (DGV)SLC5A7 [DGVbeta]
DECIPHERSLC5A7 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSLC5A7 
Mutations
ICGC Data PortalSLC5A7 
TCGA Data PortalSLC5A7 
Broad Tumor PortalSLC5A7
OASIS PortalSLC5A7 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSLC5A7  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSLC5A7
Mutations and Diseases : HGMDSLC5A7
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 SLC5A7
DgiDB (Drug Gene Interaction Database)SLC5A7
DoCM (Curated mutations)SLC5A7 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SLC5A7 (select a term)
intoGenSLC5A7
Cancer3DSLC5A7(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM158580    608761    617143   
Orphanet16924   
DisGeNETSLC5A7
MedgenSLC5A7
Genetic Testing Registry SLC5A7
NextProtQ9GZV3 [Medical]
GENETestsSLC5A7
Target ValidationSLC5A7
Huge Navigator SLC5A7 [HugePedia]
ClinGenSLC5A7
Clinical trials, drugs, therapy
MyCancerGenomeSLC5A7
Protein Interactions : CTD
Pharm GKB GenePA37838
Clinical trialSLC5A7
Miscellaneous
canSAR (ICR)SLC5A7 (select the gene name)
HarmonizomeSLC5A7
DataMed IndexSLC5A7
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSLC5A7
EVEXSLC5A7
GoPubMedSLC5A7
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sat Dec 5 17:27:22 CET 2020
Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.