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TGFBRAP1 (transforming growth factor, beta receptor associated protein 1)

Written2011-04Jens U Wurthner
Translational Pharmacology, Discovery Medicine, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namestransforming growth factor
Alias_symbol (synonym)TRAP-1
TRAP1
VPS3
Other alias
HGNC (Hugo) TGFBRAP1
LocusID (NCBI) 9392
Atlas_Id 42542
Location 2q12.1  [Link to chromosome band 2q12]
Location_base_pair Starts at 105264390 and ends at 105329714 bp from pter ( according to hg19-Feb_2009)  [Mapping TGFBRAP1.png]
Fusion genes
(updated 2016)
METTL1 (12q14.1) / TGFBRAP1 (2q12.1)TGFBRAP1 (2q12.1) / AC007000.1 ()TGFBRAP1 (2q12.1) / RPLP2 (11p15.5)
TMEM131 (2q11.2) / TGFBRAP1 (2q12.1)

DNA/RNA

 
  Generated by BlastAnalyser in 2005 (unpublished). Contig: NT_022171.13 (gi: 29789878).
Description Encoded on the minus strand. 12 exons, exon number 1 is not depicted in the diagram and appears to undergo differential splicing, according to recent NCBI-AceView (accessed 17 Apr 2011).
Transcription Work by the Wurthner lab in 2003-2005 identified an 860 aa protein that could be matched with genomic sequences. Recently predicted proteins from mRNA variants describe translation products of 896, 952, 161 and 30 aminino acids (NCBI AceView, accessed 17 April 2011).

Protein

 
  CNH: Citron Homology Domain; CLH: Clathrin Homology Domain; VPS39: Vesicle Protein Sorting Protein 39 Domain.
Description A fragment of TGFBRAP1 was initially identified in a Yeast-2-Hybrid screen as a TGF-beta type I receptor interacting protein (Charng et al., 2002). Further work by Wurthner et al. demonstrated binding of the full-length molecule exclusively to either TGF-beta receptor I and TGF-beta receptor II, or to Smad4, suggesting TGFBRAP1 to be a Smad4 chaperone (Wurthner et al., 2001). Furthermore, receptor activated Smads were shown to compete for binding of TRAP1 with Smad4, suggesting only a transient association between TRAP1 and Smad4. In addition, an interaction of TRAP1 with 5-lipoxgenase in a yeast two-hybrid system was described by a different group (Provost et al., 1999). Gene inactivation of TGFBRAP1 through conventional targeting leads to early developmental arrest of murine embryos around day E 6.5 (Messler et al., 2010).
Expression Ubiquitous.
Localisation Punctate pattern suggestive of endosomal localisation.
Function Chaperone for Smad4 in the TGF-beta signal transduction cascade (Wurthner et al., 2001).
Endosomal trafficking (circumstantial evidence: domain structure and early embryonic lethality; Messler et al., 2010).
Homology hVPS39 (hVam6, hTrap-like-Protein).

Bibliography

A novel protein distinguishes between quiescent and activated forms of the type I transforming growth factor beta receptor.
Charng MJ, Zhang D, Kinnunen P, Schneider MD.
J Biol Chem. 1998 Apr 17;273(16):9365-8.
PMID 9545258
 
TLP, a novel modulator of TGF-beta signaling, has opposite effects on Smad2- and Smad3-dependent signaling.
Felici A, Wurthner JU, Parks WT, Giam LR, Reiss M, Karpova TS, McNally JG, Roberts AB.
EMBO J. 2003 Sep 1;22(17):4465-77.
PMID 12941698
 
The TGF-beta signaling modulators TRAP1/TGFBRAP1 and VPS39/Vam6/TLP are essential for early embryonic development.
Messler S, Kropp S, Episkopou V, Felici A, Wurthner J, Lemke R, Jerabek-Willemsen M, Willecke R, Scheu S, Pfeffer K, Wurthner JU.
Immunobiology. 2011 Mar;216(3):343-50. Epub 2010 Aug 19.
PMID 20961651
 
Interaction of 5-lipoxygenase with cellular proteins.
Provost P, Samuelsson B, Radmark O.
Proc Natl Acad Sci U S A. 1999 Mar 2;96(5):1881-5.
PMID 10051563
 
Transforming growth factor-beta receptor-associated protein 1 is a Smad4 chaperone.
Wurthner JU, Frank DB, Felici A, Green HM, Cao Z, Schneider MD, McNally JG, Lechleider RJ, Roberts AB.
J Biol Chem. 2001 Jun 1;276(22):19495-502. Epub 2001 Feb 20.
PMID 11278302
 

Citation

This paper should be referenced as such :
Wurthner, JU
TGFBRAP1 (transforming growth factor, beta receptor associated protein 1)
Atlas Genet Cytogenet Oncol Haematol. 2011;15(11):931-932.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/TGFBRAP1ID42542ch2q12.html


External links

Nomenclature
HGNC (Hugo)TGFBRAP1   16836
Cards
AtlasTGFBRAP1ID42542ch2q12
Entrez_Gene (NCBI)TGFBRAP1  9392  transforming growth factor beta receptor associated protein 1
AliasesTRAP-1; TRAP1; VPS3
GeneCards (Weizmann)TGFBRAP1
Ensembl hg19 (Hinxton)ENSG00000135966 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000135966 [Gene_View]  chr2:105264390-105329714 [Contig_View]  TGFBRAP1 [Vega]
ICGC DataPortalENSG00000135966
TCGA cBioPortalTGFBRAP1
AceView (NCBI)TGFBRAP1
Genatlas (Paris)TGFBRAP1
WikiGenes9392
SOURCE (Princeton)TGFBRAP1
Genetics Home Reference (NIH)TGFBRAP1
Genomic and cartography
GoldenPath hg38 (UCSC)TGFBRAP1  -     chr2:105264390-105329714 -  2q12.1-q12.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TGFBRAP1  -     2q12.1-q12.2   [Description]    (hg19-Feb_2009)
EnsemblTGFBRAP1 - 2q12.1-q12.2 [CytoView hg19]  TGFBRAP1 - 2q12.1-q12.2 [CytoView hg38]
Mapping of homologs : NCBITGFBRAP1 [Mapview hg19]  TGFBRAP1 [Mapview hg38]
OMIM606237   
Gene and transcription
Genbank (Entrez)AF022795 AK021697 AK291382 BC011136 BC019841
RefSeq transcript (Entrez)NM_001142621 NM_001328646 NM_004257
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)TGFBRAP1
Cluster EST : UnigeneHs.592796 [ NCBI ]
CGAP (NCI)Hs.592796
Alternative Splicing GalleryENSG00000135966
Gene ExpressionTGFBRAP1 [ NCBI-GEO ]   TGFBRAP1 [ EBI - ARRAY_EXPRESS ]   TGFBRAP1 [ SEEK ]   TGFBRAP1 [ MEM ]
Gene Expression Viewer (FireBrowse)TGFBRAP1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9392
GTEX Portal (Tissue expression)TGFBRAP1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8WUH2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8WUH2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8WUH2
Splice isoforms : SwissVarQ8WUH2
PhosPhoSitePlusQ8WUH2
Domaine pattern : Prosite (Expaxy)CHCR (PS50236)    CNH (PS50219)   
Domains : Interpro (EBI)Clathrin_H-chain/VPS_repeat    CNH_dom    VPS39/TGF_beta_rcpt-assoc_1    VPS39/TGF_beta_rcpt-assoc_2   
Domain families : Pfam (Sanger)Clathrin (PF00637)    CNH (PF00780)    Vps39_1 (PF10366)    Vps39_2 (PF10367)   
Domain families : Pfam (NCBI)pfam00637    pfam00780    pfam10366    pfam10367   
Conserved Domain (NCBI)TGFBRAP1
DMDM Disease mutations9392
Blocks (Seattle)TGFBRAP1
SuperfamilyQ8WUH2
Human Protein AtlasENSG00000135966
Peptide AtlasQ8WUH2
HPRD06948
IPIIPI00550891   IPI01013444   IPI00302717   
Protein Interaction databases
DIP (DOE-UCLA)Q8WUH2
IntAct (EBI)Q8WUH2
FunCoupENSG00000135966
BioGRIDTGFBRAP1
STRING (EMBL)TGFBRAP1
ZODIACTGFBRAP1
Ontologies - Pathways
QuickGOQ8WUH2
Ontology : AmiGOtransforming growth factor beta receptor binding  protein binding  early endosome  regulation of transcription, DNA-templated  intracellular protein transport  signal transduction  transforming growth factor beta receptor signaling pathway  endosome to lysosome transport  membrane  CORVET complex  endosomal vesicle fusion  intracellular membrane-bounded organelle  SMAD binding  
Ontology : EGO-EBItransforming growth factor beta receptor binding  protein binding  early endosome  regulation of transcription, DNA-templated  intracellular protein transport  signal transduction  transforming growth factor beta receptor signaling pathway  endosome to lysosome transport  membrane  CORVET complex  endosomal vesicle fusion  intracellular membrane-bounded organelle  SMAD binding  
NDEx NetworkTGFBRAP1
Atlas of Cancer Signalling NetworkTGFBRAP1
Wikipedia pathwaysTGFBRAP1
Orthology - Evolution
OrthoDB9392
GeneTree (enSembl)ENSG00000135966
Phylogenetic Trees/Animal Genes : TreeFamTGFBRAP1
HOVERGENQ8WUH2
HOGENOMQ8WUH2
Homologs : HomoloGeneTGFBRAP1
Homology/Alignments : Family Browser (UCSC)TGFBRAP1
Gene fusions - Rearrangements
Fusion : MitelmanTMEM131/TGFBRAP1 [2q11.2/2q12.1]  [t(2;2)(q11;q12)]  
Fusion: TCGATGFBRAP1 2q12.1 AC007000.1 HNSC
Fusion: TCGATMEM131 2q11.2 TGFBRAP1 2q12.1 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTGFBRAP1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TGFBRAP1
dbVarTGFBRAP1
ClinVarTGFBRAP1
1000_GenomesTGFBRAP1 
Exome Variant ServerTGFBRAP1
ExAC (Exome Aggregation Consortium)TGFBRAP1 (select the gene name)
Genetic variants : HAPMAP9392
Genomic Variants (DGV)TGFBRAP1 [DGVbeta]
DECIPHERTGFBRAP1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTGFBRAP1 
Mutations
ICGC Data PortalTGFBRAP1 
TCGA Data PortalTGFBRAP1 
Broad Tumor PortalTGFBRAP1
OASIS PortalTGFBRAP1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICTGFBRAP1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTGFBRAP1
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 TGFBRAP1
DgiDB (Drug Gene Interaction Database)TGFBRAP1
DoCM (Curated mutations)TGFBRAP1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TGFBRAP1 (select a term)
intoGenTGFBRAP1
NCG5 (London)TGFBRAP1
Cancer3DTGFBRAP1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606237   
Orphanet
MedgenTGFBRAP1
Genetic Testing Registry TGFBRAP1
NextProtQ8WUH2 [Medical]
TSGene9392
GENETestsTGFBRAP1
Target ValidationTGFBRAP1
Huge Navigator TGFBRAP1 [HugePedia]
snp3D : Map Gene to Disease9392
BioCentury BCIQTGFBRAP1
ClinGenTGFBRAP1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9392
Chemical/Pharm GKB GenePA134963946
Clinical trialTGFBRAP1
Miscellaneous
canSAR (ICR)TGFBRAP1 (select the gene name)
Probes
Litterature
PubMed20 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTGFBRAP1
EVEXTGFBRAP1
GoPubMedTGFBRAP1
iHOPTGFBRAP1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:16:27 CEST 2017

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