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

PDGFD (platelet derived growth factor D)

Identity

Alias_symbol (synonym)SCDGF-B
MSTP036
IEGF
Other aliasSCDGFB
HGNC (Hugo) PDGFD
LocusID (NCBI) 80310
Atlas_Id 46596
Location 11q22.3  [Link to chromosome band 11q22]
Location_base_pair Starts at 103907186 and ends at 104164299 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
L2HGDH (14q21.3) / PDGFD (11q22.3)PDGFD (11q22.3) / NCCRP1 (19q13.2)PDGFD (11q22.3) / PDGFD (11q22.3)

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 Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(5;11)(q33;q13) NUMA1/PDGFRB a novel fusion


External links

Nomenclature
HGNC (Hugo)PDGFD   30620
Cards
Entrez_Gene (NCBI)PDGFD  80310  platelet derived growth factor D
AliasesIEGF; MSTP036; SCDGF-B; SCDGFB
GeneCards (Weizmann)PDGFD
Ensembl hg19 (Hinxton)ENSG00000170962 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000170962 [Gene_View]  chr11:103907186-104164299 [Contig_View]  PDGFD [Vega]
ICGC DataPortalENSG00000170962
TCGA cBioPortalPDGFD
AceView (NCBI)PDGFD
Genatlas (Paris)PDGFD
WikiGenes80310
SOURCE (Princeton)PDGFD
Genetics Home Reference (NIH)PDGFD
Genomic and cartography
GoldenPath hg38 (UCSC)PDGFD  -     chr11:103907186-104164299 -  11q22.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDGFD  -     11q22.3   [Description]    (hg19-Feb_2009)
EnsemblPDGFD - 11q22.3 [CytoView hg19]  PDGFD - 11q22.3 [CytoView hg38]
Mapping of homologs : NCBIPDGFD [Mapview hg19]  PDGFD [Mapview hg38]
OMIM609673   
Gene and transcription
Genbank (Entrez)AB033832 AF113216 AF335584 AF336376 AI962915
RefSeq transcript (Entrez)NM_025208 NM_033135
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PDGFD
Cluster EST : UnigeneHs.352298 [ NCBI ]
CGAP (NCI)Hs.352298
Alternative Splicing GalleryENSG00000170962
Gene ExpressionPDGFD [ NCBI-GEO ]   PDGFD [ EBI - ARRAY_EXPRESS ]   PDGFD [ SEEK ]   PDGFD [ MEM ]
Gene Expression Viewer (FireBrowse)PDGFD [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)80310
GTEX Portal (Tissue expression)PDGFD
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9GZP0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9GZP0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9GZP0
Splice isoforms : SwissVarQ9GZP0
PhosPhoSitePlusQ9GZP0
Domaine pattern : Prosite (Expaxy)CUB (PS01180)    PDGF_2 (PS50278)   
Domains : Interpro (EBI)CUB_dom    Cystine-knot_cytokine    PDGF/VEGF_dom    PDGFD   
Domain families : Pfam (Sanger)CUB (PF00431)    PDGF (PF00341)   
Domain families : Pfam (NCBI)pfam00431    pfam00341   
Domain families : Smart (EMBL)CUB (SM00042)  
Conserved Domain (NCBI)PDGFD
DMDM Disease mutations80310
Blocks (Seattle)PDGFD
SuperfamilyQ9GZP0
Human Protein AtlasENSG00000170962
Peptide AtlasQ9GZP0
HPRD17830
IPIIPI00018822   IPI00011865   IPI00985313   
Protein Interaction databases
DIP (DOE-UCLA)Q9GZP0
IntAct (EBI)Q9GZP0
FunCoupENSG00000170962
BioGRIDPDGFD
STRING (EMBL)PDGFD
ZODIACPDGFD
Ontologies - Pathways
QuickGOQ9GZP0
Ontology : AmiGOGolgi membrane  platelet-derived growth factor receptor binding  extracellular region  extracellular space  endoplasmic reticulum lumen  multicellular organism development  blood coagulation  growth factor activity  positive regulation of cell proliferation  positive regulation of phosphatidylinositol 3-kinase signaling  positive regulation of cell migration  positive regulation of protein autophosphorylation  cellular response to platelet-derived growth factor stimulus  positive regulation of MAP kinase activity  platelet-derived growth factor receptor signaling pathway  positive regulation of fibroblast proliferation  positive regulation of smooth muscle cell proliferation  regulation of peptidyl-tyrosine phosphorylation  positive regulation of cell division  extracellular exosome  cellular response to hydrogen peroxide  positive regulation of ERK1 and ERK2 cascade  cellular response to amino acid stimulus  cellular response to transforming growth factor beta stimulus  positive regulation of smooth muscle cell chemotaxis  positive regulation of glomerular mesangial cell proliferation  positive regulation of monocyte extravasation  
Ontology : EGO-EBIGolgi membrane  platelet-derived growth factor receptor binding  extracellular region  extracellular space  endoplasmic reticulum lumen  multicellular organism development  blood coagulation  growth factor activity  positive regulation of cell proliferation  positive regulation of phosphatidylinositol 3-kinase signaling  positive regulation of cell migration  positive regulation of protein autophosphorylation  cellular response to platelet-derived growth factor stimulus  positive regulation of MAP kinase activity  platelet-derived growth factor receptor signaling pathway  positive regulation of fibroblast proliferation  positive regulation of smooth muscle cell proliferation  regulation of peptidyl-tyrosine phosphorylation  positive regulation of cell division  extracellular exosome  cellular response to hydrogen peroxide  positive regulation of ERK1 and ERK2 cascade  cellular response to amino acid stimulus  cellular response to transforming growth factor beta stimulus  positive regulation of smooth muscle cell chemotaxis  positive regulation of glomerular mesangial cell proliferation  positive regulation of monocyte extravasation  
Pathways : KEGGRas signaling pathway    Rap1 signaling pathway    PI3K-Akt signaling pathway    Focal adhesion    Gap junction    Regulation of actin cytoskeleton    Prostate cancer    Melanoma   
NDEx NetworkPDGFD
Atlas of Cancer Signalling NetworkPDGFD
Wikipedia pathwaysPDGFD
Orthology - Evolution
OrthoDB80310
GeneTree (enSembl)ENSG00000170962
Phylogenetic Trees/Animal Genes : TreeFamPDGFD
HOVERGENQ9GZP0
HOGENOMQ9GZP0
Homologs : HomoloGenePDGFD
Homology/Alignments : Family Browser (UCSC)PDGFD
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDGFD [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDGFD
dbVarPDGFD
ClinVarPDGFD
1000_GenomesPDGFD 
Exome Variant ServerPDGFD
ExAC (Exome Aggregation Consortium)PDGFD (select the gene name)
Genetic variants : HAPMAP80310
Genomic Variants (DGV)PDGFD [DGVbeta]
DECIPHERPDGFD [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDGFD 
Mutations
ICGC Data PortalPDGFD 
TCGA Data PortalPDGFD 
Broad Tumor PortalPDGFD
OASIS PortalPDGFD [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDGFD  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDGFD
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PDGFD
DgiDB (Drug Gene Interaction Database)PDGFD
DoCM (Curated mutations)PDGFD (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDGFD (select a term)
intoGenPDGFD
Cancer3DPDGFD(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM609673   
Orphanet
MedgenPDGFD
Genetic Testing Registry PDGFD
NextProtQ9GZP0 [Medical]
TSGene80310
GENETestsPDGFD
Target ValidationPDGFD
Huge Navigator PDGFD [HugePedia]
snp3D : Map Gene to Disease80310
BioCentury BCIQPDGFD
ClinGenPDGFD
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD80310
Chemical/Pharm GKB GenePA134892327
Clinical trialPDGFD
Miscellaneous
canSAR (ICR)PDGFD (select the gene name)
Probes
Litterature
PubMed57 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDGFD
EVEXPDGFD
GoPubMedPDGFD
iHOPPDGFD
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 : Mon Sep 25 19:24:13 CEST 2017

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.