Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SDC2 (syndecan 2)

Identity

Alias_namesHSPG
HSPG1
heparan sulfate proteoglycan 1, cell surface-associated
Alias_symbol (synonym)fibroglycan
SYND2
CD362
Other alias
HGNC (Hugo) SDC2
LocusID (NCBI) 6383
Atlas_Id 42224
Location 8q22.1  [Link to chromosome band 8q22]
Location_base_pair Starts at 96493813 and ends at 96611790 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)
FRZB (2q32.1) / SDC2 (8q22.1)FZD6 (8q22.3) / SDC2 (8q22.1)GRPR (Xp22.2) / SDC2 (8q22.1)
SDC2 (8q22.1) / CTD-3025N20.2 ()SDC2 (8q22.1) / GRPR (Xp22.2)SDC2 (8q22.1) / SDC2 (8q22.1)
SDC2 8q22.1 CTD-3025N20.2

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 ]
  FZD6/SDC2 (8q22)

External links

Nomenclature
HGNC (Hugo)SDC2   10659
Cards
Entrez_Gene (NCBI)SDC2  6383  syndecan 2
AliasesCD362; HSPG; HSPG1; SYND2
GeneCards (Weizmann)SDC2
Ensembl hg19 (Hinxton)ENSG00000169439 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000169439 [Gene_View]  ENSG00000169439 [Sequence]  chr8:96493813-96611790 [Contig_View]  SDC2 [Vega]
ICGC DataPortalENSG00000169439
TCGA cBioPortalSDC2
AceView (NCBI)SDC2
Genatlas (Paris)SDC2
WikiGenes6383
SOURCE (Princeton)SDC2
Genetics Home Reference (NIH)SDC2
Genomic and cartography
GoldenPath hg38 (UCSC)SDC2  -     chr8:96493813-96611790 +  8q22.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SDC2  -     8q22.1   [Description]    (hg19-Feb_2009)
GoldenPathSDC2 - 8q22.1 [CytoView hg19]  SDC2 - 8q22.1 [CytoView hg38]
Genome Data Viewer NCBISDC2 [Mapview hg19]  
OMIM142460   
Gene and transcription
Genbank (Entrez)AA114891 AK025488 AK074530 AK097839 AK130131
RefSeq transcript (Entrez)NM_002998
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SDC2
Alternative Splicing GalleryENSG00000169439
Gene ExpressionSDC2 [ NCBI-GEO ]   SDC2 [ EBI - ARRAY_EXPRESS ]   SDC2 [ SEEK ]   SDC2 [ MEM ]
Gene Expression Viewer (FireBrowse)SDC2 [ Firebrowse - Broad ]
GenevisibleExpression of SDC2 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6383
GTEX Portal (Tissue expression)SDC2
Human Protein AtlasENSG00000169439-SDC2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP34741   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP34741  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP34741
Splice isoforms : SwissVarP34741
PhosPhoSitePlusP34741
Domaine pattern : Prosite (Expaxy)SYNDECAN (PS00964)   
Domains : Interpro (EBI)Neurexin-like    Syndecan    Syndecan-2    Syndecan/Neurexin_dom    Syndecan_CS   
Domain families : Pfam (Sanger)Syndecan (PF01034)   
Domain families : Pfam (NCBI)pfam01034   
Domain families : Smart (EMBL)4.1m (SM00294)  
Conserved Domain (NCBI)SDC2
DMDM Disease mutations6383
PDB (RSDB)6ITH   
PDB Europe6ITH   
PDB (PDBSum)6ITH   
PDB (IMB)6ITH   
Structural Biology KnowledgeBase6ITH   
SCOP (Structural Classification of Proteins)6ITH   
CATH (Classification of proteins structures)6ITH   
SuperfamilyP34741
Human Protein Atlas [tissue]ENSG00000169439-SDC2 [tissue]
Peptide AtlasP34741
HPRD00803
IPIIPI00300407   IPI01013696   IPI00976274   IPI00794290   IPI01015202   
Protein Interaction databases
DIP (DOE-UCLA)P34741
IntAct (EBI)P34741
FunCoupENSG00000169439
BioGRIDSDC2
STRING (EMBL)SDC2
ZODIACSDC2
Ontologies - Pathways
QuickGOP34741
Ontology : AmiGOretinoid metabolic process  protein binding  endoplasmic reticulum lumen  Golgi lumen  plasma membrane  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  biological_process  cell surface  integral component of membrane  cell migration  PDZ domain binding  identical protein binding  lysosomal lumen  post-translational protein modification  cellular protein metabolic process  ephrin receptor signaling pathway  dendrite morphogenesis  regulation of dendrite morphogenesis  leukocyte migration  collagen-containing extracellular matrix  
Ontology : EGO-EBIretinoid metabolic process  protein binding  endoplasmic reticulum lumen  Golgi lumen  plasma membrane  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  biological_process  cell surface  integral component of membrane  cell migration  PDZ domain binding  identical protein binding  lysosomal lumen  post-translational protein modification  cellular protein metabolic process  ephrin receptor signaling pathway  dendrite morphogenesis  regulation of dendrite morphogenesis  leukocyte migration  collagen-containing extracellular matrix  
Pathways : KEGGCell adhesion molecules (CAMs)    Malaria    Proteoglycans in cancer   
NDEx NetworkSDC2
Atlas of Cancer Signalling NetworkSDC2
Wikipedia pathwaysSDC2
Orthology - Evolution
OrthoDB6383
GeneTree (enSembl)ENSG00000169439
Phylogenetic Trees/Animal Genes : TreeFamSDC2
HOGENOMP34741
Homologs : HomoloGeneSDC2
Homology/Alignments : Family Browser (UCSC)SDC2
Gene fusions - Rearrangements
Fusion : MitelmanFZD6/SDC2 [8q22.3/8q22.1]  
Fusion PortalSDC2 8q22.1 CTD-3025N20.2 LUAD
Fusion : QuiverSDC2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSDC2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SDC2
dbVarSDC2
ClinVarSDC2
1000_GenomesSDC2 
Exome Variant ServerSDC2
GNOMAD BrowserENSG00000169439
Varsome BrowserSDC2
Genetic variants : HAPMAP6383
Genomic Variants (DGV)SDC2 [DGVbeta]
DECIPHERSDC2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSDC2 
Mutations
ICGC Data PortalSDC2 
TCGA Data PortalSDC2 
Broad Tumor PortalSDC2
OASIS PortalSDC2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSDC2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSDC2
Mutations and Diseases : HGMDSDC2
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
BioMutaselect SDC2
DgiDB (Drug Gene Interaction Database)SDC2
DoCM (Curated mutations)SDC2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SDC2 (select a term)
intoGenSDC2
Cancer3DSDC2 (select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM142460   
Orphanet
DisGeNETSDC2
MedgenSDC2
Genetic Testing Registry SDC2
NextProtP34741 [Medical]
TSGene6383
GENETestsSDC2
Open Targets GeneticsENSG00000169439  [validation]
snp3D : Map Gene to Disease6383
BioCentury BCIQSDC2
ClinGenSDC2
Clinical trials, drugs, therapy
Protein Interactions : CTD6383
Pharm GKB GenePA35589
Clinical trialSDC2
Miscellaneous
canSAR (ICR)SDC2 (select the gene name)
HarmonizomeSDC2
DataMed IndexSDC2
Probes
Litterature
PubMed147 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSDC2
EVEXSDC2
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 : Sat Jul 11 20:10:28 CEST 2020
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