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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: 41625

FusionGeneSummary for VPS53_F7

check button Fusion gene summary
Fusion gene informationFusion gene name: VPS53_F7
Fusion gene ID: 41625
HgeneTgene
Gene symbol

VPS53

F7

Gene ID

55275

2155

Gene nameVPS53, GARP complex subunitcoagulation factor VII
SynonymsHCCS1|PCH2E|hVps53L|pp13624SPCA
Cytomap

17p13.3

13q34

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 53 homologcoagulation factor VIIFVII coagulation proteincoagulation factor VII (serum prothrombin conversion accelerator)eptacog alfaproconvertin
Modification date2018052320180523
UniProtAcc

Q5VIR6

P08709

Ensembl transtripts involved in fusion geneENST00000437048, ENST00000574029, 
ENST00000576149, ENST00000446250, 
ENST00000291074, ENST00000571805, 
ENST00000401468, 
ENST00000541084, 
ENST00000346342, ENST00000375581, 
ENST00000473085, 
Fusion gene scores* DoF score10 X 5 X 10=5004 X 3 X 4=48
# samples 134
** MAII scorelog2(13/500*10)=-1.94341647163363
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VPS53 [Title/Abstract] AND F7 [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
TgeneF7

GO:0002690

positive regulation of leukocyte chemotaxis

17991872

TgeneF7

GO:0007596

blood coagulation

8632006|24998411

TgeneF7

GO:0010641

positive regulation of platelet-derived growth factor receptor signaling pathway

17991872

TgeneF7

GO:0016485

protein processing

24998411

TgeneF7

GO:0050927

positive regulation of positive chemotaxis

17991872

TgeneF7

GO:0051897

positive regulation of protein kinase B signaling

18612547


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
TCGALDTHCATCGA-EL-A3CR-01AVPS53chr17

600658

-F7chr13

113768066

+
* 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-intronENST00000437048ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000437048ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000437048ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
5CDS-3UTRENST00000437048ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+
intron-intronENST00000574029ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
intron-intronENST00000574029ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
intron-intronENST00000574029ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
intron-3UTRENST00000574029ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+
intron-intronENST00000576149ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
intron-intronENST00000576149ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
intron-intronENST00000576149ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
intron-3UTRENST00000576149ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+
5UTR-intronENST00000446250ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
5UTR-intronENST00000446250ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
5UTR-intronENST00000446250ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
5UTR-3UTRENST00000446250ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000291074ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000291074ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000291074ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
5CDS-3UTRENST00000291074ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000571805ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000571805ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000571805ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
5CDS-3UTRENST00000571805ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000401468ENST00000541084VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000401468ENST00000346342VPS53chr17

600658

-F7chr13

113768066

+
5CDS-intronENST00000401468ENST00000375581VPS53chr17

600658

-F7chr13

113768066

+
5CDS-3UTRENST00000401468ENST00000473085VPS53chr17

600658

-F7chr13

113768066

+

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FusionProtFeatures for VPS53_F7


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VPS53

Q5VIR6

F7

P08709

Acts as component of the GARP complex that is involvedin retrograde transport from early and late endosomes to thetrans-Golgi network (TGN). The GARP complex is required for themaintenance of the cycling of mannose 6-phosphate receptorsbetween the TGN and endosomes, this cycling is necessary forproper lysosomal sorting of acid hydrolases such as CTSD(PubMed:15878329, PubMed:18367545). Acts as component of the EARPcomplex that is involved in endocytic recycling. The EARP complexassociates with Rab4-positive endosomes and promotes recycling ofinternalized transferrin receptor (TFRC) to the plasma membrane(PubMed:25799061). {ECO:0000269|PubMed:15878329,ECO:0000269|PubMed:18367545, ECO:0000269|PubMed:25799061}. Initiates the extrinsic pathway of blood coagulation.Serine protease that circulates in the blood in a zymogen form.Factor VII is converted to factor VIIa by factor Xa, factor XIIa,factor IXa, or thrombin by minor proteolysis. In the presence oftissue factor and calcium ions, factor VIIa then converts factor Xto factor Xa by limited proteolysis. Factor VIIa will also convertfactor IX to factor IXa in the presence of tissue factor andcalcium.

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 VPS53_F7


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 VPS53_F7


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
VPS53VPS52, VPS51, EXOC2, VPS53, VPS54, STX6, VAMP4, THOC2, THOC1, USP7, TXNDC9, VCP, SNAP29, BSG, PSMD7, CCDC132, DTNBP1, TSSC1, C10orf76, PTAR1, RAB1A, CCDC40, EXOC1, EXOC6, SYCE3, PRAF2, CEP170, PKN3, NCKAP5L, TFPT, CCHCR1, YEATS4, TUFT1, RABGAP1L, GOLGA5, CLOCK, PSMD9, DZIP3, GRIPAP1, RCOR1, HMG20A, CCDC93, OIP5, PHF21A, PTRF, PHLDB3, HAUS6, GIT2, RPRD1A, ARNTL, MAX, RABGEF1, NUF2, THAP11, KDM1A, RABEP1, TRIM25F7F3, F10, USP49, UIMC1, DMWD, ALB, RCHY1, CEP250, CEP76, VCP, FUS, USP7, C1QL1, NMU, CRELD2


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 VPS53_F7


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneF7P08709DB00036Coagulation factor VIIa Recombinant HumanCoagulation factor VIIbiotechapproved
TgeneF7P08709DB00100Coagulation Factor IX (Recombinant)Coagulation factor VIIbiotechapproved|investigational
TgeneF7P08709DB13151Anti-inhibitor coagulant complexCoagulation factor VIIbiotechapproved|investigational
TgeneF7P08709DB00170MenadioneCoagulation factor VIIsmall moleculeapproved|nutraceutical

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RelatedDiseases for VPS53_F7


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVPS53C4014488PONTOCEREBELLAR HYPOPLASIA, TYPE 2E1UNIPROT
TgeneF7C0015503Factor VII Deficiency16CTD_human;HPO;ORPHANET;UNIPROT
TgeneF7C0151699Intracranial Hemorrhages5CTD_human;HPO
TgeneF7C0019080Hemorrhage3CTD_human
TgeneF7C2937358Cerebral Hemorrhage2CTD_human
TgeneF7C0012739Disseminated Intravascular Coagulation1CTD_human
TgeneF7C0018965Hematuria1CTD_human
TgeneF7C0019087Hemorrhagic Disorders1CTD_human
TgeneF7C0032787Postoperative Complications1CTD_human
TgeneF7C0040038Thromboembolism1CTD_human
TgeneF7C0042487Venous Thrombosis1CTD_human
TgeneF7C0273058Traumatic intracranial hemorrhage1CTD_human
TgeneF7C0749098Hematoma, Subdural, Acute1CTD_human