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TPM4 (tropomyosin)

Written2001-08Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Other alias
HGNC (Hugo) TPM4
LocusID (NCBI) 7171
Atlas_Id 359
Location 19p13.12  [Link to chromosome band 19p13]
Location_base_pair Starts at 16076325 and ends at 16103003 bp from pter ( according to hg19-Feb_2009)  [Mapping TPM4.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)
ALK (2p23.2) / TPM4 (19p13.12)AVL9 (7p14.3) / TPM4 (19p13.12)EPS15L1 (19p13.11) / TPM4 (19p13.12)
FAM32A (19p13.11) / TPM4 (19p13.12)FAM32A (19p13.12) / TPM4 (19p13.12)GSE1 (16q24.1) / TPM4 (19p13.12)
NEK6 (9q33.3) / TPM4 (19p13.12)TPM4 (19p13.12) / ALK (2p23.2)TPM4 (19p13.12) / CNNM2 (10q24.32)
TPM4 (19p13.12) / INAFM1 (19q13.32)TPM4 (19p13.12) / METRNL (17q25.3)TPM4 (19p13.12) / PROM1 (4p15.32)
TPM4 (19p13.12) / SEC62 (3q26.2)TPM4 (19p13.12) / TBL1XR1 (3q26.32)TPM4 (19p13.12) / WHAMM (15q25.2)

DNA/RNA

Transcription alternate transcripts

Protein

Description 248 amino acids, 29 kDa. Coiled-coil structure
Function Tropomyosins are actin-binding proteins; component of cytoskeletal microfilaments; tropomyosins mediate the effect of Ca2+ on the myosin-actin interaction In skeletal muscles, but their function in smooth muscles and other tissues is yet unknown
Homology Other tropomyosins: TPM1 (alpha) located in 15q22, TPM2 (beta), located in 9q13, and TPM3 located in 1q25

Implicated in

Note
  
Entity Inflammatory myofibroblastic tumors with t(2;19)(p23;p13.1)
Disease rare soft tissue tumour found in children and young adults
Prognosis good prognosis
Hybrid/Mutated Gene 5' CLTC - 3' ALK
Abnormal Protein 221 N-term amino acids from TPM4 fused to the 562 C-term amino acids from ALK (i.e. the entire cytoplasmic portion of ALK with the tyrosine kinase domain); homodimerization of the fusion protein.
Oncogenesis TPM4-ALK is contitutively activated
  

Bibliography

Deciphering the design of the tropomyosin molecule.
Brown JH, Kim KH, Jun G, Greenfield NJ, Dominguez R, Volkmann N, Hitchcock-DeGregori SE, Cohen C
Proceedings of the National Academy of Sciences of the United States of America. 2001 ; 98 (15) : 8496-8501.
PMID 11438684
 
Recurrent involvement of 2p23 in inflammatory myofibroblastic tumors.
Griffin CA, Hawkins AL, Dvorak C, Henkle C, Ellingham T, Perlman EJ
Cancer research. 1999 ; 59 (12) : 2776-2780.
PMID 10383129
 
Aberrant ALK tyrosine kinase signaling. Different cellular lineages, common oncogenic mechanisms.
Ladanyi M
The American journal of pathology. 2000 ; 157 (2) : 341-345.
PMID 10934137
 
TPM3-ALK and TPM4-ALK oncogenes in inflammatory myofibroblastic tumors.
Lawrence B, Perez-Atayde A, Hibbard MK, Rubin BP, Dal Cin P, Pinkus JL, Pinkus GS, Xiao S, Yi ES, Fletcher CD, Fletcher JA
The American journal of pathology. 2000 ; 157 (2) : 377-384.
PMID 10934142
 
Tropomyosin and actin isoforms modulate the localization of tropomyosin strands on actin filaments.
Lehman W, Hatch V, Korman V, Rosol M, Thomas L, Maytum R, Geeves MA, Van Eyk JE, Tobacman LS, Craig R
Journal of molecular biology. 2000 ; 302 (3) : 593-606.
PMID 10986121
 

Citation

This paper should be referenced as such :
Huret, JL
TPM4 (tropomyosin )
Atlas Genet Cytogenet Oncol Haematol. 2001;5(4):273-273.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TPM4ID359.html


Other Leukemias implicated (Data extracted from papers in the Atlas)

Leukemias t0219p23p13ID1549 TL_t1719q25p13ID3272


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

Solid Tumors MyofibroID5073 softissuTumID5042 t0219ID5128 TT_t1619q24p13ID102272 TT_t1919p13p13ID103137


External links

Nomenclature
HGNC (Hugo)TPM4   12013
Cards
AtlasTPM4ID359
Entrez_Gene (NCBI)TPM4  7171  tropomyosin 4
AliasesHEL-S-108
GeneCards (Weizmann)TPM4
Ensembl hg19 (Hinxton)ENSG00000167460 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000167460 [Gene_View]  ENSG00000167460 [Sequence]  chr19:16076325-16103003 [Contig_View]  TPM4 [Vega]
ICGC DataPortalENSG00000167460
TCGA cBioPortalTPM4
AceView (NCBI)TPM4
Genatlas (Paris)TPM4
WikiGenes7171
SOURCE (Princeton)TPM4
Genetics Home Reference (NIH)TPM4
Genomic and cartography
GoldenPath hg38 (UCSC)TPM4  -     chr19:16076325-16103003 +  19p13.12-p13.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TPM4  -     19p13.12-p13.11   [Description]    (hg19-Feb_2009)
GoldenPathTPM4 - 19p13.12-p13.11 [CytoView hg19]  TPM4 - 19p13.12-p13.11 [CytoView hg38]
ImmunoBaseENSG00000167460
Mapping of homologs : NCBITPM4 [Mapview hg19]  TPM4 [Mapview hg38]
OMIM600317   
Gene and transcription
Genbank (Entrez)AF186109 AK023385 AK095546 AK096732 AK300136
RefSeq transcript (Entrez)NM_001145160 NM_001367836 NM_001367837 NM_001367838 NM_003290
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)TPM4
Cluster EST : UnigeneHs.665133 [ NCBI ]
CGAP (NCI)Hs.665133
Alternative Splicing GalleryENSG00000167460
Gene ExpressionTPM4 [ NCBI-GEO ]   TPM4 [ EBI - ARRAY_EXPRESS ]   TPM4 [ SEEK ]   TPM4 [ MEM ]
Gene Expression Viewer (FireBrowse)TPM4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7171
GTEX Portal (Tissue expression)TPM4
Human Protein AtlasENSG00000167460-TPM4 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP67936   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP67936  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP67936
Splice isoforms : SwissVarP67936
PhosPhoSitePlusP67936
Domaine pattern : Prosite (Expaxy)TROPOMYOSIN (PS00326)   
Domains : Interpro (EBI)Tropomyosin   
Domain families : Pfam (Sanger)Tropomyosin (PF00261)   
Domain families : Pfam (NCBI)pfam00261   
Conserved Domain (NCBI)TPM4
DMDM Disease mutations7171
Blocks (Seattle)TPM4
SuperfamilyP67936
Human Protein Atlas [tissue]ENSG00000167460-TPM4 [tissue]
Peptide AtlasP67936
HPRD11734
IPIIPI00010779   IPI00216975   IPI00910322   
Protein Interaction databases
DIP (DOE-UCLA)P67936
IntAct (EBI)P67936
FunCoupENSG00000167460
BioGRIDTPM4
STRING (EMBL)TPM4
ZODIACTPM4
Ontologies - Pathways
QuickGOP67936
Ontology : AmiGOosteoblast differentiation  stress fiber  podosome  calcium ion binding  protein binding  cytosol  cytoskeleton  muscle thin filament tropomyosin  actin filament  focal adhesion  muscle contraction  actin filament organization  structural constituent of muscle  membrane  muscle filament sliding  cortical cytoskeleton  identical protein binding  protein homodimerization activity  protein heterodimerization activity  actin filament binding  actin filament binding  extracellular exosome  
Ontology : EGO-EBIosteoblast differentiation  stress fiber  podosome  calcium ion binding  protein binding  cytosol  cytoskeleton  muscle thin filament tropomyosin  actin filament  focal adhesion  muscle contraction  actin filament organization  structural constituent of muscle  membrane  muscle filament sliding  cortical cytoskeleton  identical protein binding  protein homodimerization activity  protein heterodimerization activity  actin filament binding  actin filament binding  extracellular exosome  
Pathways : KEGGCardiac muscle contraction    Adrenergic signaling in cardiomyocytes    Hypertrophic cardiomyopathy (HCM)    Dilated cardiomyopathy   
REACTOMEP67936 [protein]
REACTOME PathwaysR-HSA-445355 [pathway]   
NDEx NetworkTPM4
Atlas of Cancer Signalling NetworkTPM4
Wikipedia pathwaysTPM4
Orthology - Evolution
OrthoDB7171
GeneTree (enSembl)ENSG00000167460
Phylogenetic Trees/Animal Genes : TreeFamTPM4
HOGENOMP67936
Homologs : HomoloGeneTPM4
Homology/Alignments : Family Browser (UCSC)TPM4
Gene fusions - Rearrangements
Fusion : MitelmanFAM32A/TPM4 [19p13.12/19p13.12]  [t(19;19)(p13;p13)]  
Fusion : MitelmanGSE1/TPM4 [16q24.1/19p13.12]  [t(16;19)(q24;p13)]  
Fusion : MitelmanTPM4/ALK [19p13.12/2p23.2]  [t(2;19)(p23;p13)]  
Fusion : COSMICTPM4 [19p13.12]  -  ALK [2p23.2]  [fusion_441]  [fusion_442]  
Fusion PortalFAM32A 19p13.12 TPM4 19p13.12 OV
Fusion : TICdbTPM4 [19p13.12]  -  ALK [2p23.2]
Fusion : FusionGDB12792    24011    29596    30088    3646    39238    39239    39240    39241    39242    39243    39244    39245    39246    39247   
Fusion : Fusion_HubAC007956.1--TPM4    ACTN1--TPM4    ALK--TPM4    ATL3--TPM4    AVL9--TPM4    CAMKMT--TPM4    CASC4--TPM4    CERCAM--TPM4    COL1A2--TPM4    CRTAP--TPM4    DLC1--TPM4    DLST--TPM4    EHD2--TPM4    EIF2S3--TPM4    EPS15L1--TPM4   
FAM32A--TPM4    KLF2--TPM4    LYZ--TPM4    NEK6--TPM4    NXN--TPM4    PELI1--TPM4    PRKCA--TPM4    RHPN2--TPM4    S1PR2--TPM4    SCD5--TPM4    SFXN3--TPM4    SLC35F6--TPM4    TGM4--TPM4    TMEM18--TPM4    TNFAIP8L1--TPM4   
TPM4--ACTG1    TPM4--ADAM8    TPM4--ADARB1    TPM4--AGAP3    TPM4--AKT2    TPM4--ALDOA    TPM4--ALK    TPM4--BMP1    TPM4--BRD4    TPM4--CERS4    TPM4--CNNM2    TPM4--DAZAP1    TPM4--DDX5    TPM4--GPC1    TPM4--HNRNPL   
TPM4--HSPB6    TPM4--IGFL2    TPM4--ILF3    TPM4--INPPL1    TPM4--KLF2    TPM4--KRT13    TPM4--LPAR2    TPM4--LRRC25    TPM4--LTBP1    TPM4--METRNL    TPM4--NPEPPS    TPM4--NTRK1    TPM4--PIP5K1C    TPM4--PPP1R12C    TPM4--PPP2CB   
TPM4--PROM1    TPM4--PRR24    TPM4--PTMA    TPM4--RAC2    TPM4--RNH1    TPM4--SAMD1    TPM4--SEC62    TPM4--SF3B2    TPM4--SNX27    TPM4--TBL1XR1    TPM4--TGIF1    TPM4--TMC8    TPM4--TPM3    TPM4--TRABD    TPM4--UBXN2B   
TPM4--WHAMM    TPM4--ZNF652   
Fusion : QuiverTPM4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTPM4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TPM4
dbVarTPM4
ClinVarTPM4
1000_GenomesTPM4 
Exome Variant ServerTPM4
ExAC (Exome Aggregation Consortium)ENSG00000167460
GNOMAD BrowserENSG00000167460
Varsome BrowserTPM4
Genetic variants : HAPMAP7171
Genomic Variants (DGV)TPM4 [DGVbeta]
DECIPHERTPM4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTPM4 
Mutations
ICGC Data PortalTPM4 
TCGA Data PortalTPM4 
Broad Tumor PortalTPM4
OASIS PortalTPM4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICTPM4  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DTPM4
Mutations and Diseases : HGMDTPM4
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 TPM4
DgiDB (Drug Gene Interaction Database)TPM4
DoCM (Curated mutations)TPM4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TPM4 (select a term)
intoGenTPM4
NCG5 (London)TPM4
Cancer3DTPM4(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM600317   
Orphanet18017   
DisGeNETTPM4
MedgenTPM4
Genetic Testing Registry TPM4
NextProtP67936 [Medical]
TSGene7171
GENETestsTPM4
Target ValidationTPM4
Huge Navigator TPM4 [HugePedia]
snp3D : Map Gene to Disease7171
BioCentury BCIQTPM4
ClinGenTPM4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7171
Chemical/Pharm GKB GenePA36693
Clinical trialTPM4
Miscellaneous
canSAR (ICR)TPM4 (select the gene name)
DataMed IndexTPM4
Probes
Litterature
PubMed75 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTPM4
EVEXTPM4
GoPubMedTPM4
iHOPTPM4
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Aug 26 19:33:23 CEST 2019

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jlhuret@AtlasGeneticsOncology.org.