Atlas of Genetics and Cytogenetics in Oncology and Haematology


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GDNF (glial cell derived neurotrophic factor)

Identity

Other namesATF1
ATF2
HFB1-GDNF
HSCR3
HGNC (Hugo) GDNF
LocusID (NCBI) 2668
Atlas_Id 40705
Location 5p13.2
Location_base_pair Starts at 37812779 and ends at 37839782 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
EWSR1 (22q12.2) / GDNF (5p13.2)FUS (16p11.2) / GDNF (5p13.2)GDNF (5p13.2) / EWSR1 (22q12.2)
GDNF (5p13.2) / FUS (16p11.2)

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) [ 0 ]
  Thyroid: Papillary carcinoma with inv(10)(p12.1q11.2) ACBD5/RET

External links

Nomenclature
HGNC (Hugo)GDNF   4232
Cards
Entrez_Gene (NCBI)GDNF  2668  glial cell derived neurotrophic factor
GeneCards (Weizmann)GDNF
Ensembl hg19 (Hinxton)ENSG00000168621 [Gene_View]  chr5:37812779-37839782 [Contig_View]  GDNF [Vega]
Ensembl hg38 (Hinxton)ENSG00000168621 [Gene_View]  chr5:37812779-37839782 [Contig_View]  GDNF [Vega]
ICGC DataPortalENSG00000168621
TCGA cBioPortalGDNF
AceView (NCBI)GDNF
Genatlas (Paris)GDNF
WikiGenes2668
SOURCE (Princeton)GDNF
Genomic and cartography
GoldenPath hg19 (UCSC)GDNF  -     chr5:37812779-37839782 -  5p13.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)GDNF  -     5p13.2   [Description]    (hg38-Dec_2013)
EnsemblGDNF - 5p13.2 [CytoView hg19]  GDNF - 5p13.2 [CytoView hg38]
Mapping of homologs : NCBIGDNF [Mapview hg19]  GDNF [Mapview hg38]
OMIM171300   209880   600837   613711   
Gene and transcription
Genbank (Entrez)AF053748 AJ001897 AJ001898 AJ001899 AJ001900
RefSeq transcript (Entrez)NM_000514 NM_001190468 NM_001190469 NM_001278098 NM_199231 NM_199234
RefSeq genomic (Entrez)NC_000005 NC_018916 NG_011675 NT_006576 NW_004929321
Consensus coding sequences : CCDS (NCBI)GDNF
Cluster EST : UnigeneHs.248114 [ NCBI ]
CGAP (NCI)Hs.248114
Alternative Splicing : Fast-db (Paris)GSHG0024731
Alternative Splicing GalleryENSG00000168621
Gene ExpressionGDNF [ NCBI-GEO ]   GDNF [ EBI - ARRAY_EXPRESS ]   GDNF [ SEEK ]   GDNF [ MEM ]
Gene Expression Viewer (FireBrowse)GDNF [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)2668
Protein : pattern, domain, 3D structure
UniProt/SwissProtP39905 (Uniprot)
NextProtP39905  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP39905
Splice isoforms : SwissVarP39905 (Swissvar)
PhosPhoSitePlusP39905
Domaine pattern : Prosite (Expaxy)TGF_BETA_2 (PS51362)   
Domains : Interpro (EBI)Cystine-knot_cytokine    GDNF    TGF-b_C   
Domain families : Pfam (Sanger)TGF_beta (PF00019)   
Domain families : Pfam (NCBI)pfam00019   
Domain families : Smart (EMBL)TGFB (SM00204)  
DMDM Disease mutations2668
Blocks (Seattle)GDNF
PDB (SRS)2V5E    3FUB    4UX8   
PDB (PDBSum)2V5E    3FUB    4UX8   
PDB (IMB)2V5E    3FUB    4UX8   
PDB (RSDB)2V5E    3FUB    4UX8   
Structural Biology KnowledgeBase2V5E    3FUB    4UX8   
SCOP (Structural Classification of Proteins)2V5E    3FUB    4UX8   
CATH (Classification of proteins structures)2V5E    3FUB    4UX8   
SuperfamilyP39905
Human Protein AtlasENSG00000168621
Peptide AtlasP39905
HPRD02906
IPIIPI00026858   IPI00375525   IPI00848254   IPI00848296   IPI00903066   IPI00965059   
Protein Interaction databases
DIP (DOE-UCLA)P39905
IntAct (EBI)P39905
FunCoupENSG00000168621
BioGRIDGDNF
STRING (EMBL)GDNF
ZODIACGDNF
Ontologies - Pathways
QuickGOP39905
Ontology : AmiGOMAPK cascade  metanephros development  branching involved in ureteric bud morphogenesis  neural crest cell migration  organ induction  postsynaptic membrane organization  mesenchymal to epithelial transition involved in metanephros morphogenesis  Ras guanyl-nucleotide exchange factor activity  receptor binding  protein binding  extracellular region  extracellular region  intracellular  signal transduction  nervous system development  growth factor activity  positive regulation of cell proliferation  adult locomotory behavior  regulation of gene expression  postganglionic parasympathetic fiber development  peristalsis  neuron projection development  positive regulation of monooxygenase activity  positive regulation of dopamine secretion  protein homodimerization activity  negative regulation of apoptotic process  negative regulation of neuron apoptotic process  positive regulation of GTPase activity  positive regulation of cell differentiation  positive regulation of transcription from RNA polymerase II promoter  mRNA stabilization  enteric nervous system development  sympathetic nervous system development  regulation of dopamine uptake involved in synaptic transmission  ureteric bud formation  regulation of morphogenesis of a branching structure  positive regulation of ureteric bud formation  positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis  positive regulation of branching involved in ureteric bud morphogenesis  regulation of stem cell differentiation  negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  
Ontology : EGO-EBIMAPK cascade  metanephros development  branching involved in ureteric bud morphogenesis  neural crest cell migration  organ induction  postsynaptic membrane organization  mesenchymal to epithelial transition involved in metanephros morphogenesis  Ras guanyl-nucleotide exchange factor activity  receptor binding  protein binding  extracellular region  extracellular region  intracellular  signal transduction  nervous system development  growth factor activity  positive regulation of cell proliferation  adult locomotory behavior  regulation of gene expression  postganglionic parasympathetic fiber development  peristalsis  neuron projection development  positive regulation of monooxygenase activity  positive regulation of dopamine secretion  protein homodimerization activity  negative regulation of apoptotic process  negative regulation of neuron apoptotic process  positive regulation of GTPase activity  positive regulation of cell differentiation  positive regulation of transcription from RNA polymerase II promoter  mRNA stabilization  enteric nervous system development  sympathetic nervous system development  regulation of dopamine uptake involved in synaptic transmission  ureteric bud formation  regulation of morphogenesis of a branching structure  positive regulation of ureteric bud formation  positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis  positive regulation of branching involved in ureteric bud morphogenesis  regulation of stem cell differentiation  negative regulation of extrinsic apoptotic signaling pathway in absence of ligand  
NDEx Network
Atlas of Cancer Signalling NetworkGDNF
Wikipedia pathwaysGDNF
Orthology - Evolution
OrthoDB2668
GeneTree (enSembl)ENSG00000168621
Phylogenetic Trees/Animal Genes : TreeFamGDNF
Homologs : HomoloGeneGDNF
Homology/Alignments : Family Browser (UCSC)GDNF
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerGDNF [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)GDNF
dbVarGDNF
ClinVarGDNF
1000_GenomesGDNF 
Exome Variant ServerGDNF
ExAC (Exome Aggregation Consortium)GDNF (select the gene name)
SNP (GeneSNP Utah)GDNF
SNP : HGBaseGDNF
Genetic variants : HAPMAPGDNF
Genomic Variants (DGV)GDNF [DGVbeta]
Mutations
ICGC Data PortalGDNF 
TCGA Data PortalGDNF 
Broad Tumor PortalGDNF
OASIS PortalGDNF [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICGDNF 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch GDNF
DgiDB (Drug Gene Interaction Database)GDNF
DoCM (Curated mutations)GDNF (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)GDNF (select a term)
intoGenGDNF
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)5:37812779-37839782
CONAN: Copy Number AnalysisGDNF 
Mutations and Diseases : HGMDGDNF
OMIM171300    209880    600837    613711   
MedgenGDNF
Genetic Testing Registry GDNF
NextProtP39905 [Medical]
TSGene2668
GENETestsGDNF
Huge Navigator GDNF [HugePedia]  GDNF [HugeCancerGEM]
snp3D : Map Gene to Disease2668
BioCentury BCIQGDNF
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD2668
Chemical/Pharm GKB GenePA28644
Clinical trialGDNF
Miscellaneous
canSAR (ICR)GDNF (select the gene name)
Probes
Litterature
PubMed172 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineGDNF
GoPubMedGDNF
iHOPGDNF
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 Apr 16 17:45:59 CEST 2016

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