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PDE4DIP (phosphodiesterase 4D interacting protein (myomegalin))

Written2006-05Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers; CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesCMYA2
cardiomyopathy associated 2
Alias_symbol (synonym)KIAA0477
KIAA0454
MMGL
Other aliasMyomegalin
HGNC (Hugo) PDE4DIP
LocusID (NCBI) 9659
Atlas_Id 180
Location 1q21.1  [Link to chromosome band 1q21]
Location_base_pair Starts at 148808181 and ends at 148932728 bp from pter ( according to hg19-Feb_2009)  [Mapping PDE4DIP.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)
E2F5 (8q21.2) / PDE4DIP (1q21.1)EFTUD2 (17q21.31) / PDE4DIP (1q21.1)KCNK5 (6p21.2) / PDE4DIP (1q21.1)
MPZL1 (1q24.2) / PDE4DIP (1q21.1)PDE4DIP (1q21.1) / C1orf186 (1q32.1)PDE4DIP (1q21.1) / PDGFRB (5q32)
PDE4DIP (1q21.1) / TTC28 (22q12.1)PDGFRB (5q32) / PDE4DIP (1q21.1)TRPS1 (8q23.3) / PDE4DIP (1q21.1)
VANGL2 (1q23.2) / PDE4DIP (1q21.1)

DNA/RNA

Transcription Various splicing forms, in particular KIAA0477 and KIAA0454

Protein

Note The protein encoded by PDE4DIP is called myomegalin
Description Large protein; some isoforms having more than 2300 aminoacids (62 kDa and 230-250 kDa proteins in the rat ortholog); mainly composed of alpha-helical and coiled-coil structures; includes a leucine zipper in N-term, a dynactin-centractin binding domain, and a helix-loop-helix.
Expression in heart and skeletal muscles; little expression in other tissues
Localisation Cytoplasm in the Golgi/centrosomal area in non muscle cells and nucleus; in the sarcomeres of muscle cells
Function Interacts with the cyclic nucleotide phosphodiesterase PDE4D, enzymes that degrade and inactivate cAMP; may oligomerize
Homology With the Drosophila centrosomin (a component of the centrosome and the mitotic spindle)

Implicated in

Note
  
Entity t(1;5)(q22;q33) in chronic eosinophilic leukemia --> PDE4DIP - PDGFRB
Note KIAA0477 isoforms was found involved in the hybrid gene / fusion protein.
Disease Rare disease mainly found in infants.
Prognosis Treatment with imatinib may be relevant.
  

Bibliography

Isolation of novel heart-specific genes using the BodyMap database.
Soejima H, Kawamoto S, Akai J, Miyoshi O, Arai Y, Morohka T, Matsuo S, Niikawa N, Kimura A, Okubo K, Mukai T
Genomics. 2001 ; 74 (1) : 115-120.
PMID 11374908
 
Myomegalin is a novel protein of the golgi/centrosome that interacts with a cyclic nucleotide phosphodiesterase.
Verde I, Pahlke G, Salanova M, Zhang G, Wang S, Coletti D, Onuffer J, Jin SL, Conti M
The Journal of biological chemistry. 2001 ; 276 (14) : 11189-11198.
PMID 11134006
 
Cloning of the t(1;5)(q23;q33) in a myeloproliferative disorder associated with eosinophilia: involvement of PDGFRB and response to imatinib.
Wilkinson K, Velloso ER, Lopes LF, Lee C, Aster JC, Shipp MA, Aguiar RC
Blood. 2003 ; 102 (12) : 4187-4190.
PMID 12907457
 

Citation

This paper should be referenced as such :
Huret, JL
PDE4DIP (phosphodiesterase 4D interacting protein (myomegalin))
Atlas Genet Cytogenet Oncol Haematol. 2006;10(4):227-227.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PDE4DIP01q22ID180.html

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  der(5)t(1;5)(q12-q25;q13-q35)
t(1;5)(q21;q32) PDE4DIP/PDGFRB::t(1;5)(q21-23;q32) TPM3/PDGFRB::t(1;5)(q21-23;q31-33)
t(1;5)(q21;q32) PDE4DIP/PDGFRB

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 5 ]
  t(1;1)(q21;q23) VANGL2/PDE4DIP
t(1;1)(q21;q24) MPZL1/PDE4DIP
t(1;6)(q21;p21) KCNK5/PDE4DIP
t(1;8)(q21;q23) TRPS1/PDE4DIP
t(1;22)(q21;q12) PDE4DIP/TTC28

External links

Nomenclature
HGNC (Hugo)PDE4DIP   15580
Cards
AtlasPDE4DIP01q22ID180
Entrez_Gene (NCBI)PDE4DIP  9659  phosphodiesterase 4D interacting protein
AliasesCMYA2; MMGL
GeneCards (Weizmann)PDE4DIP
Ensembl hg19 (Hinxton)ENSG00000178104 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000178104 [Gene_View]  ENSG00000178104 [Sequence]  chr1:148808181-148932728 [Contig_View]  PDE4DIP [Vega]
ICGC DataPortalENSG00000178104
TCGA cBioPortalPDE4DIP
AceView (NCBI)PDE4DIP
Genatlas (Paris)PDE4DIP
WikiGenes9659
SOURCE (Princeton)PDE4DIP
Genetics Home Reference (NIH)PDE4DIP
Genomic and cartography
GoldenPath hg38 (UCSC)PDE4DIP  -     chr1:148808181-148932728 +  1q21.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDE4DIP  -     1q21.2   [Description]    (hg19-Feb_2009)
EnsemblPDE4DIP - 1q21.2 [CytoView hg19]  PDE4DIP - 1q21.2 [CytoView hg38]
Mapping of homologs : NCBIPDE4DIP [Mapview hg19]  PDE4DIP [Mapview hg38]
OMIM608117   
Gene and transcription
Genbank (Entrez)AA025132 AA434604 AA707296 AB007923 AB007946
RefSeq transcript (Entrez)NM_001002810 NM_001002811 NM_001002812 NM_001195260 NM_001195261 NM_001198832 NM_001198834 NM_001350520 NM_001350521 NM_001350522 NM_001350523 NM_014644 NM_022359
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PDE4DIP
Cluster EST : UnigeneHs.731111 [ NCBI ]
CGAP (NCI)Hs.731111
Alternative Splicing GalleryENSG00000178104
Gene ExpressionPDE4DIP [ NCBI-GEO ]   PDE4DIP [ EBI - ARRAY_EXPRESS ]   PDE4DIP [ SEEK ]   PDE4DIP [ MEM ]
Gene Expression Viewer (FireBrowse)PDE4DIP [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9659
GTEX Portal (Tissue expression)PDE4DIP
Human Protein AtlasENSG00000178104-PDE4DIP [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ5VU43   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ5VU43  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ5VU43
Splice isoforms : SwissVarQ5VU43
PhosPhoSitePlusQ5VU43
Domaine pattern : Prosite (Expaxy)NBPF (PS51316)   
Domains : Interpro (EBI)Cnn_1N    NBPF_dom   
Domain families : Pfam (Sanger)Cnn_1N (PF07989)    DUF1220 (PF06758)   
Domain families : Pfam (NCBI)pfam07989    pfam06758   
Domain families : Smart (EMBL)DUF1220 (SM01148)  
Conserved Domain (NCBI)PDE4DIP
DMDM Disease mutations9659
Blocks (Seattle)PDE4DIP
SuperfamilyQ5VU43
Human Protein Atlas [tissue]ENSG00000178104-PDE4DIP [tissue]
Peptide AtlasQ5VU43
HPRD10482
IPI###############################################################################################################################################################################################################################################################   
Protein Interaction databases
DIP (DOE-UCLA)Q5VU43
IntAct (EBI)Q5VU43
FunCoupENSG00000178104
BioGRIDPDE4DIP
STRING (EMBL)PDE4DIP
ZODIACPDE4DIP
Ontologies - Pathways
QuickGOQ5VU43
Ontology : AmiGOprotein binding  nucleus  cytoplasm  Golgi apparatus  Golgi apparatus  centrosome  centrosome  enzyme binding  myofibril  protein-containing complex scaffold activity  cellular protein-containing complex assembly  regulation of Golgi organization  
Ontology : EGO-EBIprotein binding  nucleus  cytoplasm  Golgi apparatus  Golgi apparatus  centrosome  centrosome  enzyme binding  myofibril  protein-containing complex scaffold activity  cellular protein-containing complex assembly  regulation of Golgi organization  
NDEx NetworkPDE4DIP
Atlas of Cancer Signalling NetworkPDE4DIP
Wikipedia pathwaysPDE4DIP
Orthology - Evolution
OrthoDB9659
GeneTree (enSembl)ENSG00000178104
Phylogenetic Trees/Animal Genes : TreeFamPDE4DIP
HOVERGENQ5VU43
HOGENOMQ5VU43
Homologs : HomoloGenePDE4DIP
Homology/Alignments : Family Browser (UCSC)PDE4DIP
Gene fusions - Rearrangements
Fusion : MitelmanKCNK5/PDE4DIP [6p21.2/1q21.1]  [t(1;6)(q21;p21)]  
Fusion : MitelmanMPZL1/PDE4DIP [1q24.2/1q21.1]  [t(1;1)(q21;q24)]  
Fusion : MitelmanPDE4DIP/C1orf186 [1q21.1/1q32.1]  [t(1;1)(q21;q32)]  
Fusion : MitelmanPDE4DIP/PDGFRB [1q21.1/5q32]  [t(1;5)(q21;q32)]  
Fusion : MitelmanPDE4DIP/TTC28 [1q21.1/22q12.1]  [t(1;22)(q21;q12)]  
Fusion : MitelmanTRPS1/PDE4DIP [8q23.3/1q21.1]  [t(1;8)(q21;q23)]  
Fusion : MitelmanVANGL2/PDE4DIP [1q23.2/1q21.1]  [t(1;1)(q21;q23)]  
Fusion PortalKCNK5 6p21.2 PDE4DIP 1q21.1 LUAD
Fusion PortalMPZL1 1q24.2 PDE4DIP 1q21.1 BRCA
Fusion PortalPDE4DIP 1q21.1 C1orf186 1q32.1 BRCA
Fusion PortalTRPS1 8q23.3 PDE4DIP 1q21.1 BRCA
Fusion PortalVANGL2 1q23.2 PDE4DIP 1q21.1 LUAD
Fusion : TICdbPDE4DIP [1q21.1]  -  PDGFRB [5q32]
Fusion : QuiverPDE4DIP
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDE4DIP [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDE4DIP
dbVarPDE4DIP
ClinVarPDE4DIP
1000_GenomesPDE4DIP 
Exome Variant ServerPDE4DIP
ExAC (Exome Aggregation Consortium)ENSG00000178104
GNOMAD BrowserENSG00000178104
Varsome BrowserPDE4DIP
Genetic variants : HAPMAP9659
Genomic Variants (DGV)PDE4DIP [DGVbeta]
DECIPHERPDE4DIP [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDE4DIP 
Mutations
ICGC Data PortalPDE4DIP 
TCGA Data PortalPDE4DIP 
Broad Tumor PortalPDE4DIP
OASIS PortalPDE4DIP [ Somatic mutations - Copy number]
Cancer Gene: CensusPDE4DIP 
Somatic Mutations in Cancer : COSMICPDE4DIP  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDE4DIP
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 PDE4DIP
DgiDB (Drug Gene Interaction Database)PDE4DIP
DoCM (Curated mutations)PDE4DIP (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDE4DIP (select a term)
intoGenPDE4DIP
NCG5 (London)PDE4DIP
Cancer3DPDE4DIP(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM608117   
Orphanet
DisGeNETPDE4DIP
MedgenPDE4DIP
Genetic Testing Registry PDE4DIP
NextProtQ5VU43 [Medical]
TSGene9659
GENETestsPDE4DIP
Target ValidationPDE4DIP
Huge Navigator PDE4DIP [HugePedia]
snp3D : Map Gene to Disease9659
BioCentury BCIQPDE4DIP
ClinGenPDE4DIP
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9659
Chemical/Pharm GKB GenePA33131
Clinical trialPDE4DIP
Miscellaneous
canSAR (ICR)PDE4DIP (select the gene name)
Probes
Litterature
PubMed45 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDE4DIP
EVEXPDE4DIP
GoPubMedPDE4DIP
iHOPPDE4DIP
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 3 16:01:26 CEST 2018
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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.