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SYNPO2 (synaptopodin 2)

Written2003-12Jian-Hua Luo
Gene Array Laboratory, Univeristy of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_symbol (synonym)MYOPODIN
Other aliasMyopodin
synaptopodin 2
HGNC (Hugo) SYNPO2
LocusID (NCBI) 171024
Atlas_Id 488
Location 4q26  [Link to chromosome band 4q26]
Location_base_pair Starts at 118888841 and ends at 119038520 bp from pter ( according to hg19-Feb_2009)  [Mapping SYNPO2.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ADD3 (10q25.1) / SYNPO2 (4q26)GABRE (Xq28) / SYNPO2 (4q26)PTGS1 (9q33.2) / SYNPO2 (4q26)
SNRNP70 (19q13.33) / SYNPO2 (4q26)SYNPO2 (4q26) / SYNPO2 (4q26)
Note Myopodin probably represents an alternative splicing variant of synaptopodin 2. The predicted synaptopodin 2 contains 1021 amino acid and myopodin 698. The extra 323 amino acid in synaptopodin 2 is located at the N-terminus.

DNA/RNA

 
  Genome structure of myopodin and synaptopodin 2. Green represents exons of myopodin, and orange synaptopodin 2. Introns are indicated with lines.
Description The genome sequence of myopodin contains 6.8 Kb, while synaptopodin 2 38 kb.
Transcription A typical messenger RNA of myopodin is 4.2-4.4 kb, and synaptopodin 2 6.7 kb.
Pseudogene Unknown

Protein

 
  Protein structure of myopodin and synaptopodin 2. Orange represents sequence unique to synaptopodin 2, Green myopodin. Black stripe represents sequence homologous to synaptopodin 1.
Description A nuclear localization signal is identified in N-terminus region of myopodin. Myopodin also contains six stretches of homologous sequences with synaptopodin 1.
Expression Skeletal muscle, prostate, large and small intestine.
Localisation Nucleus, cytoplasm.
Function Actin bundling.
Homology Synaptopodin

Mutations

Germinal Not known
Somatic Deletion

Implicated in

Note
Disease Prostate cancer and urothelial cell carcinoma.
Prognosis Deletion preferentially occurs in aggressive type of prostate cancer. Loss of expression in nucleus in urothelial cell carcinoma is predictive of poor clinical outcome.
Cytogenetics Not known
  

Bibliography

Myopodin, a synaptopodin homologue, is frequently deleted in invasive prostate cancers.
Lin F, Yu YP, Woods J, Cieply K, Gooding B, Finkelstein P, Dhir R, Krill D, Becich MJ, Michalopoulos G, Finkelstein S, Luo JH
The American journal of pathology. 2001 ; 159 (5) : 1603-1612.
PMID 11696420
 
Tumor suppressor role for myopodin in bladder cancer: loss of nuclear expression of myopodin is cell-cycle dependent and predicts clinical outcome.
Sanchez-Carbayo M, Schwarz K, Charytonowicz E, Cordon-Cardo C, Mundel P
Oncogene. 2003 ; 22 (34) : 5298-5305.
PMID 12917631
 
Differentiation- and stress-dependent nuclear cytoplasmic redistribution of myopodin, a novel actin-bundling protein.
Weins A, Schwarz K, Faul C, Barisoni L, Linke WA, Mundel P
The Journal of cell biology. 2001 ; 155 (3) : 393-404.
PMID 11673475
 

Citation

This paper should be referenced as such :
Luo, JH
SYNPO2 (synaptopodin 2)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(1):14-15.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/SYNPO2ID488.html


External links

Nomenclature
HGNC (Hugo)SYNPO2   17732
Cards
AtlasSYNPO2ID488
Entrez_Gene (NCBI)SYNPO2  171024  synaptopodin 2
Aliases
GeneCards (Weizmann)SYNPO2
Ensembl hg19 (Hinxton)ENSG00000172403 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000172403 [Gene_View]  chr4:118888841-119038520 [Contig_View]  SYNPO2 [Vega]
ICGC DataPortalENSG00000172403
TCGA cBioPortalSYNPO2
AceView (NCBI)SYNPO2
Genatlas (Paris)SYNPO2
WikiGenes171024
SOURCE (Princeton)SYNPO2
Genetics Home Reference (NIH)SYNPO2
Genomic and cartography
GoldenPath hg38 (UCSC)SYNPO2  -     chr4:118888841-119038520 +  4q26   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SYNPO2  -     4q26   [Description]    (hg19-Feb_2009)
EnsemblSYNPO2 - 4q26 [CytoView hg19]  SYNPO2 - 4q26 [CytoView hg38]
Mapping of homologs : NCBISYNPO2 [Mapview hg19]  SYNPO2 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AA043349 AF177291 AJ010482 AK000774 AK296962
RefSeq transcript (Entrez)NM_001128933 NM_001128934 NM_001286754 NM_001286755 NM_133477
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SYNPO2
Cluster EST : UnigeneHs.655519 [ NCBI ]
CGAP (NCI)Hs.655519
Alternative Splicing GalleryENSG00000172403
Gene ExpressionSYNPO2 [ NCBI-GEO ]   SYNPO2 [ EBI - ARRAY_EXPRESS ]   SYNPO2 [ SEEK ]   SYNPO2 [ MEM ]
Gene Expression Viewer (FireBrowse)SYNPO2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)171024
GTEX Portal (Tissue expression)SYNPO2
Human Protein AtlasENSG00000172403-SYNPO2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UMS6   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UMS6  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UMS6
Splice isoforms : SwissVarQ9UMS6
PhosPhoSitePlusQ9UMS6
Domaine pattern : Prosite (Expaxy)PDZ (PS50106)   
Domains : Interpro (EBI)PDZ   
Domain families : Pfam (Sanger)PDZ (PF00595)   
Domain families : Pfam (NCBI)pfam00595   
Domain families : Smart (EMBL)PDZ (SM00228)  
Conserved Domain (NCBI)SYNPO2
DMDM Disease mutations171024
Blocks (Seattle)SYNPO2
SuperfamilyQ9UMS6
Human Protein Atlas [tissue]ENSG00000172403-SYNPO2 [tissue]
Peptide AtlasQ9UMS6
HPRD15456
IPIIPI00900324   IPI00173549   IPI00900276   IPI00910033   IPI00966171   
Protein Interaction databases
DIP (DOE-UCLA)Q9UMS6
IntAct (EBI)Q9UMS6
FunCoupENSG00000172403
BioGRIDSYNPO2
STRING (EMBL)SYNPO2
ZODIACSYNPO2
Ontologies - Pathways
QuickGOQ9UMS6
Ontology : AmiGOautophagosome assembly  stress fiber  actin binding  protein binding  nucleus  nucleus  cytosol  focal adhesion  actin cytoskeleton  actin cytoskeleton  Z disc  Z disc  Z disc  filamin binding  positive regulation of actin filament bundle assembly  intracellular membrane-bounded organelle  muscle alpha-actinin binding  alpha-actinin binding  14-3-3 protein binding  tethering complex  
Ontology : EGO-EBIautophagosome assembly  stress fiber  actin binding  protein binding  nucleus  nucleus  cytosol  focal adhesion  actin cytoskeleton  actin cytoskeleton  Z disc  Z disc  Z disc  filamin binding  positive regulation of actin filament bundle assembly  intracellular membrane-bounded organelle  muscle alpha-actinin binding  alpha-actinin binding  14-3-3 protein binding  tethering complex  
NDEx NetworkSYNPO2
Atlas of Cancer Signalling NetworkSYNPO2
Wikipedia pathwaysSYNPO2
Orthology - Evolution
OrthoDB171024
GeneTree (enSembl)ENSG00000172403
Phylogenetic Trees/Animal Genes : TreeFamSYNPO2
HOVERGENQ9UMS6
HOGENOMQ9UMS6
Homologs : HomoloGeneSYNPO2
Homology/Alignments : Family Browser (UCSC)SYNPO2
Gene fusions - Rearrangements
Tumor Fusion PortalSYNPO2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSYNPO2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SYNPO2
dbVarSYNPO2
ClinVarSYNPO2
1000_GenomesSYNPO2 
Exome Variant ServerSYNPO2
ExAC (Exome Aggregation Consortium)ENSG00000172403
GNOMAD BrowserENSG00000172403
Genetic variants : HAPMAP171024
Genomic Variants (DGV)SYNPO2 [DGVbeta]
DECIPHERSYNPO2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSYNPO2 
Mutations
ICGC Data PortalSYNPO2 
TCGA Data PortalSYNPO2 
Broad Tumor PortalSYNPO2
OASIS PortalSYNPO2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSYNPO2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSYNPO2
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 SYNPO2
DgiDB (Drug Gene Interaction Database)SYNPO2
DoCM (Curated mutations)SYNPO2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SYNPO2 (select a term)
intoGenSYNPO2
NCG5 (London)SYNPO2
Cancer3DSYNPO2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM
Orphanet
DisGeNETSYNPO2
MedgenSYNPO2
Genetic Testing Registry SYNPO2
NextProtQ9UMS6 [Medical]
TSGene171024
GENETestsSYNPO2
Target ValidationSYNPO2
Huge Navigator SYNPO2 [HugePedia]
snp3D : Map Gene to Disease171024
BioCentury BCIQSYNPO2
ClinGenSYNPO2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD171024
Chemical/Pharm GKB GenePA38244
Clinical trialSYNPO2
Miscellaneous
canSAR (ICR)SYNPO2 (select the gene name)
Probes
Litterature
PubMed33 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSYNPO2
EVEXSYNPO2
GoPubMedSYNPO2
iHOPSYNPO2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Nov 15 12:36:16 CET 2017

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