Atlas of Genetics and Cytogenetics in Oncology and Haematology


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CHSY1 (chondroitin sulfate synthase 1)

Identity

Alias (NCBI)CHSY
CSS1
ChSy-1
TPBS
HGNC (Hugo) CHSY1
HGNC Alias symbKIAA0990
CSS1
HGNC Previous namecarbohydrate (chondroitin) synthase 1
LocusID (NCBI) 22856
Atlas_Id 52320
Location 15q26.3  [Link to chromosome band 15q26]
Location_base_pair Starts at 101175727 and ends at 101252048 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)
CHSY1 (15q26.3) / SPOCK2 (10q22.1)CHSY1 (15q26.3) / SRCAP (16p11.2)LPP (3q28) / CHSY1 (15q26.3)
VRK2 (2p16.1) / CHSY1 (15q26.3)CHSY1 15q26.3 / SPOCK2 10q22.1VRK2 2p16.1 / CHSY1 15q26.3

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) [ 2 ]
  t(2;15)(p16;q26) VRK2/CHSY1
t(10;15)(q22;q26) CHSY1/SPOCK2


External links

Nomenclature
HGNC (Hugo)CHSY1   17198
Cards
Entrez_Gene (NCBI)CHSY1  22856  chondroitin sulfate synthase 1
AliasesCHSY; CSS1; ChSy-1; TPBS
GeneCards (Weizmann)CHSY1
Ensembl hg19 (Hinxton)ENSG00000131873 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000131873 [Gene_View]  ENSG00000131873 [Sequence]  chr15:101175727-101252048 [Contig_View]  CHSY1 [Vega]
ICGC DataPortalENSG00000131873
TCGA cBioPortalCHSY1
AceView (NCBI)CHSY1
Genatlas (Paris)CHSY1
WikiGenes22856
SOURCE (Princeton)CHSY1
Genetics Home Reference (NIH)CHSY1
Genomic and cartography
GoldenPath hg38 (UCSC)CHSY1  -     chr15:101175727-101252048 -  15q26.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)CHSY1  -     15q26.3   [Description]    (hg19-Feb_2009)
GoldenPathCHSY1 - 15q26.3 [CytoView hg19]  CHSY1 - 15q26.3 [CytoView hg38]
ImmunoBaseENSG00000131873
genome Data Viewer NCBICHSY1 [Mapview hg19]  
OMIM605282   608183   
Gene and transcription
Genbank (Entrez)AB023207 AB071402 AK075096 AK296943 AL137409
RefSeq transcript (Entrez)NM_014918
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)CHSY1
Alternative Splicing GalleryENSG00000131873
Gene ExpressionCHSY1 [ NCBI-GEO ]   CHSY1 [ EBI - ARRAY_EXPRESS ]   CHSY1 [ SEEK ]   CHSY1 [ MEM ]
Gene Expression Viewer (FireBrowse)CHSY1 [ Firebrowse - Broad ]
GenevisibleExpression of CHSY1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)22856
GTEX Portal (Tissue expression)CHSY1
Human Protein AtlasENSG00000131873-CHSY1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ86X52   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ86X52  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ86X52
Splice isoforms : SwissVarQ86X52
Catalytic activity : Enzyme2.4.1.175 [ Enzyme-Expasy ]   2.4.1.1752.4.1.175 [ IntEnz-EBI ]   2.4.1.175 [ BRENDA ]   2.4.1.175 [ KEGG ]   [ MEROPS ]
PhosPhoSitePlusQ86X52
Domains : Interpro (EBI)Chond_GalNAc    Nucleotide-diphossugar_trans   
Domain families : Pfam (Sanger)CHGN (PF05679)   
Domain families : Pfam (NCBI)pfam05679   
Conserved Domain (NCBI)CHSY1
DMDM Disease mutations22856
Blocks (Seattle)CHSY1
SuperfamilyQ86X52
Human Protein Atlas [tissue]ENSG00000131873-CHSY1 [tissue]
Peptide AtlasQ86X52
HPRD10493
IPIIPI00329141   IPI00852578   
Protein Interaction databases
DIP (DOE-UCLA)Q86X52
IntAct (EBI)Q86X52
FunCoupENSG00000131873
BioGRIDCHSY1
STRING (EMBL)CHSY1
ZODIACCHSY1
Ontologies - Pathways
QuickGOQ86X52
Ontology : AmiGOGolgi membrane  chondrocyte development  extracellular region  proximal/distal pattern formation  membrane  integral component of membrane  chondroitin sulfate biosynthetic process  chondroitin sulfate biosynthetic process  negative regulation of ossification  response to nutrient levels  Golgi cisterna membrane  positive regulation of smoothened signaling pathway  metal ion binding  glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity  N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity  sulfation  bone morphogenesis  
Ontology : EGO-EBIGolgi membrane  chondrocyte development  extracellular region  proximal/distal pattern formation  membrane  integral component of membrane  chondroitin sulfate biosynthetic process  chondroitin sulfate biosynthetic process  negative regulation of ossification  response to nutrient levels  Golgi cisterna membrane  positive regulation of smoothened signaling pathway  metal ion binding  glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity  N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity  sulfation  bone morphogenesis  
Pathways : KEGGGlycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate   
NDEx NetworkCHSY1
Atlas of Cancer Signalling NetworkCHSY1
Wikipedia pathwaysCHSY1
Orthology - Evolution
OrthoDB22856
GeneTree (enSembl)ENSG00000131873
Phylogenetic Trees/Animal Genes : TreeFamCHSY1
HOGENOMQ86X52
Homologs : HomoloGeneCHSY1
Homology/Alignments : Family Browser (UCSC)CHSY1
Gene fusions - Rearrangements
Fusion : MitelmanCHSY1/SPOCK2 [15q26.3/10q22.1]  
Fusion : MitelmanVRK2/CHSY1 [2p16.1/15q26.3]  
Fusion PortalCHSY1 15q26.3 SPOCK2 10q22.1 BRCA
Fusion PortalVRK2 2p16.1 CHSY1 15q26.3 BRCA
Fusion : QuiverCHSY1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerCHSY1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CHSY1
dbVarCHSY1
ClinVarCHSY1
1000_GenomesCHSY1 
Exome Variant ServerCHSY1
GNOMAD BrowserENSG00000131873
Varsome BrowserCHSY1
Genetic variants : HAPMAP22856
Genomic Variants (DGV)CHSY1 [DGVbeta]
DECIPHERCHSY1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisCHSY1 
Mutations
ICGC Data PortalCHSY1 
TCGA Data PortalCHSY1 
Broad Tumor PortalCHSY1
OASIS PortalCHSY1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICCHSY1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DCHSY1
Mutations and Diseases : HGMDCHSY1
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 CHSY1
DgiDB (Drug Gene Interaction Database)CHSY1
DoCM (Curated mutations)CHSY1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CHSY1 (select a term)
intoGenCHSY1
Cancer3DCHSY1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605282    608183   
Orphanet22298   
DisGeNETCHSY1
MedgenCHSY1
Genetic Testing Registry CHSY1
NextProtQ86X52 [Medical]
TSGene22856
GENETestsCHSY1
Target ValidationCHSY1
Huge Navigator CHSY1 [HugePedia]
snp3D : Map Gene to Disease22856
BioCentury BCIQCHSY1
ClinGenCHSY1
Clinical trials, drugs, therapy
Protein Interactions : CTD22856
Pharm GKB GenePA26509
Clinical trialCHSY1
Miscellaneous
canSAR (ICR)CHSY1 (select the gene name)
HarmonizomeCHSY1
DataMed IndexCHSY1
Probes
Litterature
PubMed26 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCHSY1
EVEXCHSY1
GoPubMedCHSY1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Thu Jul 16 15:07:52 CEST 2020

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