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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:VKORC1-CD99 (FusionGDB2 ID:HG79001TG4267)

Fusion Gene Summary for VKORC1-CD99

check button Fusion gene summary
Fusion gene informationFusion gene name: VKORC1-CD99
Fusion gene ID: hg79001tg4267
HgeneTgene
Gene symbol

VKORC1

CD99

Gene ID

79001

4267

Gene namevitamin K epoxide reductase complex subunit 1CD99 molecule (Xg blood group)
SynonymsEDTP308|MST134|MST576|VKCFD2|VKORHBA71|MIC2|MIC2X|MIC2Y|MSK5X
Cytomap('VKORC1')('CD99')

16p11.2

Xp22.33 and Yp11.2

Type of geneprotein-codingprotein-coding
Descriptionvitamin K epoxide reductase complex subunit 1phylloquinone epoxide reductasevitamin K dependent clotting factors deficiency 2vitamin K1 2,3-epoxide reductase subunit 1vitamin K1 epoxide reductase (warfarin-sensitive)CD99 antigenE2 antigenMIC2 (monoclonal antibody 12E7)T-cell surface glycoprotein E2antigen identified by monoclonal 12E7, Y homologantigen identified by monoclonal antibodies 12E7, F21 and O13cell surface antigen 12E7cell surface antigen HBA-71cel
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000300851, ENST00000319788, 
ENST00000354895, ENST00000394975, 
ENST00000394971, ENST00000498155, 
Fusion gene scores* DoF score6 X 6 X 4=14427 X 20 X 5=2700
# samples 629
** MAII scorelog2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(29/2700*10)=-3.21883460192326
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VKORC1 [Title/Abstract] AND CD99 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVKORC1(31105877)-CD99(2606240), # samples:1
Anticipated loss of major functional domain due to fusion event.VKORC1-CD99 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
VKORC1-CD99 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
HgeneVKORC1

GO:0042373

vitamin K metabolic process

16270630



check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4Non-Cancer43NVKORC1chr16

31105877

-CD99chrY

2606240

+


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Fusion Gene ORF analysis for VKORC1-CD99

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-intronENST00000300851ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000300851ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000300851ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000319788ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000319788ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000319788ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000354895ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000354895ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000354895ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000394975ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000394975ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000394975ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000300851ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000300851ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000319788ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000319788ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000354895ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000354895ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000394975ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000394975ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000394971ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000394971ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000498155ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000498155ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000394971ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000394971ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000394971ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000498155ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000498155ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000498155ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for VKORC1-CD99


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
VKORC1chr1631105877-CD99chrY2606240+1.50E-111
VKORC1chr1631105877-CD99chrY2606240+1.50E-111


check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for VKORC1-CD99


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:31105877/:2606240)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {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


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Fusion Gene Sequence for VKORC1-CD99


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for VKORC1-CD99


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


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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Related Drugs for VKORC1-CD99


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for VKORC1-CD99


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVKORC1C1843832VITAMIN K-DEPENDENT CLOTTING FACTORS, COMBINED DEFICIENCY OF, 23CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneVKORC1C0019080Hemorrhage2CTD_human
HgeneVKORC1C0750384Coumarin Resistance2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneVKORC1C0003496Aortic Rupture1CTD_human
HgeneVKORC1C0005779Blood Coagulation Disorders1CTD_human
HgeneVKORC1C0010068Coronary heart disease1CTD_human
HgeneVKORC1C0013221Drug toxicity1CTD_human
HgeneVKORC1C0038454Cerebrovascular accident1CTD_human
HgeneVKORC1C0040053Thrombosis1CTD_human
HgeneVKORC1C0041755Adverse reaction to drug1CTD_human
HgeneVKORC1C0042373Vascular Diseases1CTD_human
HgeneVKORC1C0087086Thrombus1CTD_human
HgeneVKORC1C0741160Aortic Aneurysm, Ruptured1CTD_human
HgeneVKORC1C0751956Acute Cerebrovascular Accidents1CTD_human
HgeneVKORC1C1848534VITAMIN K-DEPENDENT CLOTTING FACTORS, COMBINED DEFICIENCY OF, 11ORPHANET
TgeneC0206637Mesenchymal Chondrosarcoma1CTD_human