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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)

Leukemias t0105q22q33ID1115 TL_t0105q21q32ID3381

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 5 ]

Solid Tumors TT_t0101q21q23ID103918 TT_t0101q21q24ID103920 TT_t0106q21p21ID104474 TT_t0108q21q23ID104528 TT_t0122q21q12ID104362

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)
GoldenPathPDE4DIP - 1q21.2 [CytoView hg19]  PDE4DIP - 1q21.2 [CytoView hg38]
ImmunoBaseENSG00000178104
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
IPIIPI00470939   IPI00869196   IPI00479644   IPI00337544   IPI00456484   IPI00642902   IPI00869114   IPI00643207   IPI00401276   IPI00868730   IPI00376888   IPI00982145   IPI00455448   IPI00979642   IPI00152241   IPI00977575   IPI00980240   IPI00975830   IPI00978568   IPI00976851   IPI00741084   IPI00976529   IPI00869124   IPI00982999   IPI00980385   IPI00975860   IPI00979020   IPI00983681   IPI00979892   IPI00984416   IPI00983066   IPI00982262   IPI00981690   
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  cellular protein-containing complex assembly  molecular adaptor activity  regulation of Golgi organization  
Ontology : EGO-EBIprotein binding  nucleus  cytoplasm  Golgi apparatus  Golgi apparatus  centrosome  centrosome  enzyme binding  myofibril  cellular protein-containing complex assembly  molecular adaptor activity  regulation of Golgi organization  
NDEx NetworkPDE4DIP
Atlas of Cancer Signalling NetworkPDE4DIP
Wikipedia pathwaysPDE4DIP
Orthology - Evolution
OrthoDB9659
GeneTree (enSembl)ENSG00000178104
Phylogenetic Trees/Animal Genes : TreeFamPDE4DIP
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 : FusionGDB18286    20741    22409    26395    26396    39690    41336   
Fusion : Fusion_HubANKRD13C--PDE4DIP    CH17-472G23.4--PDE4DIP    CNN3--PDE4DIP    CRTC2--PDE4DIP    CUX1--PDE4DIP    E2F5--PDE4DIP    EFTUD2--PDE4DIP    EIF1AX--PDE4DIP    EPS15L1--PDE4DIP    ETV6--PDE4DIP    FAM213A--PDE4DIP    FN1--PDE4DIP    GFRA2--PDE4DIP    KCNK5--PDE4DIP    LINC01719--PDE4DIP   
LOC653513--PDE4DIP    LPL--PDE4DIP    MAN1A2--PDE4DIP    MPZL1--PDE4DIP    MYO18A--PDE4DIP    NBPF13P--PDE4DIP    OGDH--PDE4DIP    PDE4DIP--ABCD3    PDE4DIP--ACTN2    PDE4DIP--ADD1    PDE4DIP--ARL6IP5    PDE4DIP--ART3    PDE4DIP--ATP1A1    PDE4DIP--ATP2B1    PDE4DIP--ATP5J   
PDE4DIP--BCAS1    PDE4DIP--BCAS2    PDE4DIP--C1ORF186    PDE4DIP--CHMP1A    PDE4DIP--COPA    PDE4DIP--CRY1    PDE4DIP--DAP3    PDE4DIP--EIF1AX    PDE4DIP--EIF4G3    PDE4DIP--GBP2    PDE4DIP--GPSM2    PDE4DIP--HSA-MIR-6723    PDE4DIP--ING1    PDE4DIP--IPO9    PDE4DIP--LOC728989   
PDE4DIP--MYL1    PDE4DIP--NAV1    PDE4DIP--NEB    PDE4DIP--NEXN    PDE4DIP--NPPA    PDE4DIP--NUDC    PDE4DIP--NUP214    PDE4DIP--OBSCN    PDE4DIP--PCCB    PDE4DIP--PDGFRB    PDE4DIP--RPS6KC1    PDE4DIP--RSRC1    PDE4DIP--SAFB    PDE4DIP--SGSM3    PDE4DIP--SH3KBP1   
PDE4DIP--SMYD3    PDE4DIP--SPG21    PDE4DIP--SVIL    PDE4DIP--TBC1D23    PDE4DIP--TPM3    PDE4DIP--TTC27    PDE4DIP--UBR5    PDE4DIP--WI2-1896O14.1    PDE4DIP--YLPM1    PDE4DIP--ZNF644    PDGFRB--PDE4DIP    PPP6R2--PDE4DIP    SH3BP5L--PDE4DIP    SH3GL1--PDE4DIP    STIM1--PDE4DIP   
TNNT3--PDE4DIP    TRPS1--PDE4DIP    TTN--PDE4DIP    VANGL2--PDE4DIP    ZMYM4--PDE4DIP   
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]
Somatic Mutations in Cancer : COSMICPDE4DIP  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPDE4DIP
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)
DataMed IndexPDE4DIP
Probes
Litterature
PubMed50 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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