Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SDC4 (syndecan 4)

Identity

Alias (NCBI)SYND4
HGNC (Hugo) SDC4
HGNC Alias symbSYND4
amphiglycan
ryudocan
HGNC Alias namesyndecan proteoglycan 4
HGNC Previous namesyndecan 4 (amphiglycan, ryudocan)
LocusID (NCBI) 6385
Atlas_Id 42226
Location 20q13.12  [Link to chromosome band 20q13]
Location_base_pair Starts at 45325289 and ends at 45348424 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)
ARHGEF3 (3p14.3) / SDC4 (20q13.12)KMT2E (7q22.3) / SDC4 (20q13.12)ROS1 (6q22.1) / SDC4 (20q13.12)
SDC4 (20q13.12) / AP1G2 (14q11.2)SDC4 (20q13.12) / BIN1 (2q14.3)SDC4 (20q13.12) / NRG1 (8p12)
SDC4 (20q13.12) / ROS1 (6q22.1)SDC4 (20q13.12) / SDC4 (20q13.12)SDC4 (20q13.12) / SPCS1 (3p21.1)
SDC4 (20q13.12) / TSHZ2 (20q13.2)SDC4 (20q13.12) / YWHAB (20q13.12)SDC4 20q13.12 / ROS1 6q22.1
SDC4 20q13.12 / AP1G2 14q11.2SDC4 20q13.12 / NRG1 8p12SDC4 20q13.12 / SPCS1 3p21.1
SDC4 20q13.12 / TSHZ2 20q13.2SDC4 20q13.12 / YWHAB 20q13.12

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) [ 6 ]
  Lung: Translocations in Adenocarcinoma
t(3;20)(p21;q12) SDC4/SPCS1
t(6;20)(q22;q12) SDC4/ROS1
t(14;20)(q11;q12) SDC4/AP1G2
t(20;20)(q12;q13) SDC4/TSHZ2
t(20;20)(q12;q13) SDC4/YWHAB

External links

Nomenclature
HGNC (Hugo)SDC4   10661
Cards
Entrez_Gene (NCBI)SDC4    syndecan 4
AliasesSYND4
GeneCards (Weizmann)SDC4
Ensembl hg19 (Hinxton)ENSG00000124145 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000124145 [Gene_View]  ENSG00000124145 [Sequence]  chr20:45325289-45348424 [Contig_View]  SDC4 [Vega]
ICGC DataPortalENSG00000124145
TCGA cBioPortalSDC4
AceView (NCBI)SDC4
Genatlas (Paris)SDC4
SOURCE (Princeton)SDC4
Genetics Home Reference (NIH)SDC4
Genomic and cartography
GoldenPath hg38 (UCSC)SDC4  -     chr20:45325289-45348424 -  20q13.12   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SDC4  -     20q13.12   [Description]    (hg19-Feb_2009)
GoldenPathSDC4 - 20q13.12 [CytoView hg19]  SDC4 - 20q13.12 [CytoView hg38]
ImmunoBaseENSG00000124145
genome Data Viewer NCBISDC4 [Mapview hg19]  
OMIM600017   
Gene and transcription
Genbank (Entrez)AK222695 AK223243 AK303964 AK312507 BC030805
RefSeq transcript (Entrez)NM_002999
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SDC4
Alternative Splicing GalleryENSG00000124145
Gene ExpressionSDC4 [ NCBI-GEO ]   SDC4 [ EBI - ARRAY_EXPRESS ]   SDC4 [ SEEK ]   SDC4 [ MEM ]
Gene Expression Viewer (FireBrowse)SDC4 [ Firebrowse - Broad ]
GenevisibleExpression of SDC4 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6385
GTEX Portal (Tissue expression)SDC4
Human Protein AtlasENSG00000124145-SDC4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP31431   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP31431  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP31431
Splice isoforms : SwissVarP31431
PhosPhoSitePlusP31431
Domaine pattern : Prosite (Expaxy)SYNDECAN (PS00964)   
Domains : Interpro (EBI)Neurexin-like    Syndecan    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)SDC4
Blocks (Seattle)SDC4
PDB (RSDB)1EJP    1EJQ    1OBY    1YBO   
PDB Europe1EJP    1EJQ    1OBY    1YBO   
PDB (PDBSum)1EJP    1EJQ    1OBY    1YBO   
PDB (IMB)1EJP    1EJQ    1OBY    1YBO   
Structural Biology KnowledgeBase1EJP    1EJQ    1OBY    1YBO   
SCOP (Structural Classification of Proteins)1EJP    1EJQ    1OBY    1YBO   
CATH (Classification of proteins structures)1EJP    1EJQ    1OBY    1YBO   
SuperfamilyP31431
Human Protein Atlas [tissue]ENSG00000124145-SDC4 [tissue]
Peptide AtlasP31431
HPRD08366
IPIIPI00011564   IPI01012616   
Protein Interaction databases
DIP (DOE-UCLA)P31431
IntAct (EBI)P31431
BioGRIDSDC4
STRING (EMBL)SDC4
ZODIACSDC4
Ontologies - Pathways
QuickGOP31431
Ontology : AmiGOretinoid metabolic process  ureteric bud development  neural tube closure  fibronectin binding  protein kinase C binding  protein binding  Golgi lumen  plasma membrane  integral component of plasma membrane  focal adhesion  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  cell surface  regulation of fibroblast migration  cell migration  wound healing  negative regulation of T cell proliferation  identical protein binding  costamere  lysosomal lumen  membrane raft  positive regulation of protein kinase activity  leukocyte migration  positive regulation of stress fiber assembly  positive regulation of focal adhesion assembly  inner ear receptor cell stereocilium organization  thrombospondin receptor activity  extracellular exosome  positive regulation of exosomal secretion  positive regulation of extracellular exosome assembly  
Ontology : EGO-EBIretinoid metabolic process  ureteric bud development  neural tube closure  fibronectin binding  protein kinase C binding  protein binding  Golgi lumen  plasma membrane  integral component of plasma membrane  focal adhesion  glycosaminoglycan biosynthetic process  glycosaminoglycan catabolic process  cell surface  regulation of fibroblast migration  cell migration  wound healing  negative regulation of T cell proliferation  identical protein binding  costamere  lysosomal lumen  membrane raft  positive regulation of protein kinase activity  leukocyte migration  positive regulation of stress fiber assembly  positive regulation of focal adhesion assembly  inner ear receptor cell stereocilium organization  thrombospondin receptor activity  extracellular exosome  positive regulation of exosomal secretion  positive regulation of extracellular exosome assembly  
Pathways : KEGGECM-receptor interaction    Cell adhesion molecules (CAMs)    Proteoglycans in cancer   
NDEx NetworkSDC4
Atlas of Cancer Signalling NetworkSDC4
Wikipedia pathwaysSDC4
Orthology - Evolution
OrthoDB6385
GeneTree (enSembl)ENSG00000124145
Phylogenetic Trees/Animal Genes : TreeFamSDC4
HOGENOMP31431
Homologs : HomoloGeneSDC4
Homology/Alignments : Family Browser (UCSC)SDC4
Gene fusions - Rearrangements
Fusion : MitelmanSDC4/AP1G2 [20q13.12/14q11.2]  
Fusion : MitelmanSDC4/ROS1 [20q13.12/6q22.1]  
Fusion : MitelmanSDC4/SPCS1 [20q13.12/3p21.1]  
Fusion : MitelmanSDC4/TSHZ2 [20q13.12/20q13.2]  
Fusion : MitelmanSDC4/YWHAB [20q13.12/20q13.12]  
Fusion PortalSDC4 20q13.12 AP1G2 14q11.2 LUAD
Fusion PortalSDC4 20q13.12 NRG1 8p12 LUAD
Fusion PortalSDC4 20q13.12 SPCS1 3p21.1 GBM
Fusion PortalSDC4 20q13.12 TSHZ2 20q13.2 LUAD
Fusion PortalSDC4 20q13.12 YWHAB 20q13.12 LUAD
Fusion : QuiverSDC4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSDC4 [hg38]
dbVarSDC4
ClinVarSDC4
MonarchSDC4
1000_GenomesSDC4 
Exome Variant ServerSDC4
GNOMAD BrowserENSG00000124145
Varsome BrowserSDC4
Genomic Variants (DGV)SDC4 [DGVbeta]
DECIPHERSDC4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSDC4 
Mutations
ICGC Data PortalSDC4 
TCGA Data PortalSDC4 
Broad Tumor PortalSDC4
OASIS PortalSDC4 [ Somatic mutations - Copy number]
Cancer Gene: CensusSDC4 
Somatic Mutations in Cancer : COSMICSDC4  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DSDC4
Mutations and Diseases : HGMDSDC4
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 SDC4
DgiDB (Drug Gene Interaction Database)SDC4
DoCM (Curated mutations)SDC4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SDC4 (select a term)
intoGenSDC4
Cancer3DSDC4(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600017   
Orphanet
DisGeNETSDC4
MedgenSDC4
Genetic Testing Registry SDC4
NextProtP31431 [Medical]
GENETestsSDC4
Target ValidationSDC4
Huge Navigator SDC4 [HugePedia]
ClinGenSDC4
Clinical trials, drugs, therapy
MyCancerGenomeSDC4
Protein Interactions : CTD
Pharm GKB GenePA35591
PharosP31431
Clinical trialSDC4
Miscellaneous
canSAR (ICR)SDC4 (select the gene name)
HarmonizomeSDC4
DataMed IndexSDC4
Probes
Litterature
PubMed154 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXSDC4
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 : Fri Jan 1 18:36:29 CET 2021
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