FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 30428

FusionGeneSummary for RAPGEF1_WDR83

check button Fusion gene summary
Fusion gene informationFusion gene name: RAPGEF1_WDR83
Fusion gene ID: 30428
HgeneTgene
Gene symbol

RAPGEF1

WDR83

Gene ID

2889

84292

Gene nameRap guanine nucleotide exchange factor 1WD repeat domain 83
SynonymsC3G|GRF2MORG1
Cytomap

9q34.13

19p13.13

Type of geneprotein-codingprotein-coding
Descriptionrap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)WD repeat domain-containing protein 83MAPK organizer 1mitogen-activated protein kinase organizer 1
Modification date2018052220180519
UniProtAcc

Q13905

Q9BRX9

Ensembl transtripts involved in fusion geneENST00000372189, ENST00000372195, 
ENST00000372190, ENST00000481260, 
ENST00000418543, ENST00000242796, 
Fusion gene scores* DoF score17 X 14 X 10=23802 X 2 X 2=8
# samples 212
** MAII scorelog2(21/2380*10)=-3.50250034052918
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: RAPGEF1 [Title/Abstract] AND WDR83 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneRAPGEF1

GO:0038180

nerve growth factor signaling pathway

17724123

HgeneRAPGEF1

GO:0043547

positive regulation of GTPase activity

10548487

HgeneRAPGEF1

GO:0071320

cellular response to cAMP

21840392

HgeneRAPGEF1

GO:1990090

cellular response to nerve growth factor stimulus

17724123

TgeneWDR83

GO:0000375

RNA splicing, via transesterification reactions

11991638

TgeneWDR83

GO:0000398

mRNA splicing, via spliceosome

11991638


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVSTADTCGA-BR-7716-01ARAPGEF1chr9

134615157

-WDR83chr19

12783661

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000372189ENST00000418543RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
intron-3CDSENST00000372189ENST00000242796RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
Frame-shitENST00000372195ENST00000418543RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
Frame-shitENST00000372195ENST00000242796RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
intron-3CDSENST00000372190ENST00000418543RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
intron-3CDSENST00000372190ENST00000242796RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
intron-3CDSENST00000481260ENST00000418543RAPGEF1chr9

134615157

-WDR83chr19

12783661

+
intron-3CDSENST00000481260ENST00000242796RAPGEF1chr9

134615157

-WDR83chr19

12783661

+

Top

FusionProtFeatures for RAPGEF1_WDR83


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAPGEF1

Q13905

WDR83

Q9BRX9

Guanine nucleotide-releasing protein that binds to SH3domain of CRK and GRB2/ASH. Transduces signals from CRK toactivate RAS. Plays a role in the establishment of basalendothelial barrier function. Plays a role in nerve growth factor(NGF)-induced sustained activation of Rap1 and neurite outgrowth.{ECO:0000269|PubMed:17724123, ECO:0000269|PubMed:21840392,ECO:0000269|PubMed:7806500}. Molecular scaffold protein for various multimericprotein complexes. Acts as a module in the assembly of amulticomponent scaffold for the ERK pathway, linking ERK responsesto specific agonists. At low concentrations it enhances ERKactivation, whereas high concentrations lead to the inhibition ofERK activation. Also involved in response to hypoxia by acting asa negative regulator of HIF1A/HIF-1-alpha via its interaction withEGLN3/PHD3. May promote degradation of HIF1A. May act byrecruiting signaling complexes to a specific upstream activator(By similarity). May also be involved in pre-mRNA splicing.{ECO:0000250}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

.

* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


Top

FusionGeneSequence for RAPGEF1_WDR83


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

Top

FusionGenePPI for RAPGEF1_WDR83


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
RAPGEF1BCAR1, HCK, CRKL, NEDD9, GRB2, CRK, SHC1, CBL, ATXN1, MBIP, RPS15, SLC20A1, MOV10, NXF1, ABL1, EGFR, SPATS2L, RAP1A, RAP2BWDR83LAMTOR3, MAP2K1, MAP2K2, RAF1, MAPK3, MAPK1, SNRPC, SF3B4, SF1, PRPF8, LSM3, PPIL1, AQR, HSPB1, UBL5, SAP30BP, HNRNPH2, PCBP2, BAG2, TOE1, GPKOW, GNB2L1, KDM1A, PARD6A, PARD6B, PARD6G, CRB3, KEAP1, TSSC4, USB1, EAPP, PPIE, CCT7, UBB, KIAA1671, NUMA1, CCT3, RBM15B, CWF19L2, CCT6B, CCT6A, CCT2, CCT8, XAB2, GPATCH1, CCT4, DHX35, CRNKL1, CUX1, NEK1, CDC5L, TCP1, PIKFYVE, DPYSL2, EIF4E2, PPP1R13L, SGOL2, SNW1, GIGYF2, ZHX1, DCAF13, SLIRP, PSMG2, ARHGEF2, PRKAG2, EXO1, ISY1, CDC40, KCTD3, SHKBP1, RNF187, SYF2, SIPA1L1, RIMS4, SIPA1L3, FRMD4A, FAM122B, ZNF140, MPRIP, SH2B2, CCDC12, GPSM1, ARHGEF17, CYTH3, BUD31, NET1, CCDC84, CCDC94, TBC1D3, KRAS, CRK, SSX2IP, OFD1, PCM1, CC2D2A, CEP97, KIAA0753, CEP104, CEP162, CEP290, CEP120, CEP152, FGFR1OP, CEP128, CEP135, CEP44, CEP89, CNTRL, FBF1, NINL, NIN, NPHP1, ODF2, RPGRIP1L, CEP19, LCA5, RPGRIP1, STIL, BAG6, PRPF19, GIGYF1, AURKAIP1, SNRPG, SNRPF, SNRPE, KIAA1143, ECD, C11orf57, DVL3, ZC3H18, SNRPN, DACH1, CCT5, RP2


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


Top

RelatedDrugs for RAPGEF1_WDR83


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

RelatedDiseases for RAPGEF1_WDR83


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource