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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 41488

FusionGeneSummary for VMP1_CDC42EP4

check button Fusion gene summary
Fusion gene informationFusion gene name: VMP1_CDC42EP4
Fusion gene ID: 41488
HgeneTgene
Gene symbol

VMP1

CDC42EP4

Gene ID

81671

23580

Gene namevacuole membrane protein 1CDC42 effector protein 4
SynonymsEPG3|TANGO5|TMEM49BORG4|CEP4|KAIA1777
Cytomap

17q23.1

17q25.1

Type of geneprotein-codingprotein-coding
Descriptionvacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homologcdc42 effector protein 4CDC42 effector protein (Rho GTPase binding) 4binder of Rho GTPases 4
Modification date2018052320180523
UniProtAcc

Q96GC9

Q9H3Q1

Ensembl transtripts involved in fusion geneENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
ENST00000335793, ENST00000439510, 
ENST00000581014, ENST00000582303, 
Fusion gene scores* DoF score19 X 10 X 9=17106 X 2 X 7=84
# samples 188
** MAII scorelog2(18/1710*10)=-3.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(8/84*10)=-0.070389327891398
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VMP1 [Title/Abstract] AND CDC42EP4 [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
TgeneCDC42EP4

GO:0008360

regulation of cell shape

11035016

TgeneCDC42EP4

GO:0031274

positive regulation of pseudopodium assembly

11035016


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
TCGALDBRCATCGA-C8-A275-01AVMP1chr17

57889147

+CDC42EP4chr17

71282751

-
* 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
5CDS-5UTRENST00000262291ENST00000335793VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000262291ENST00000439510VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000262291ENST00000581014VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-intronENST00000262291ENST00000582303VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000537567ENST00000335793VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000537567ENST00000439510VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000537567ENST00000581014VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-intronENST00000537567ENST00000582303VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000539763ENST00000335793VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000539763ENST00000439510VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000539763ENST00000581014VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-intronENST00000539763ENST00000582303VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000536180ENST00000335793VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000536180ENST00000439510VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000536180ENST00000581014VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-intronENST00000536180ENST00000582303VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000545362ENST00000335793VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000545362ENST00000439510VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-5UTRENST00000545362ENST00000581014VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
5CDS-intronENST00000545362ENST00000582303VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
intron-5UTRENST00000588617ENST00000335793VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
intron-5UTRENST00000588617ENST00000439510VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
intron-5UTRENST00000588617ENST00000581014VMP1chr17

57889147

+CDC42EP4chr17

71282751

-
intron-intronENST00000588617ENST00000582303VMP1chr17

57889147

+CDC42EP4chr17

71282751

-

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FusionProtFeatures for VMP1_CDC42EP4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VMP1

Q96GC9

CDC42EP4

Q9H3Q1

Stress-induced protein that, when overexpressed,promotes formation of intracellular vacuoles followed by celldeath. May be involved in the cytoplasmic vacuolization of acinarcells during the early stage of acute pancreatitis. Plays a rolein the initial stages of the autophagic process through itsinteraction with BECN1 (By similarity). Involved in cell-celladhesion. Plays an essential role in formation of cell junctions.{ECO:0000250, ECO:0000269|PubMed:17724469}. Probably involved in the organization of the actincytoskeleton. May act downstream of CDC42 to induce actin filamentassembly leading to cell shape changes. Induces pseudopodiaformation, when overexpressed in fibroblasts.

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


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FusionGeneSequence for VMP1_CDC42EP4


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).

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FusionGenePPI for VMP1_CDC42EP4


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
VMP1HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNACDC42EP4WDR6, POLR3H, CDC42, ELAVL1, LNX1, APP, VCP, SRPK2, FAM9B, RTN4IP1, SEPT4, SEPT2, SEPT7, SEPT5, SEPT6, SEPT8, SEPT11, SEPT9, SEPT3, KLHL15, SEPT10, YBEY, FHL2, CDH1, SEPT14


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


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RelatedDrugs for VMP1_CDC42EP4


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

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RelatedDiseases for VMP1_CDC42EP4


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