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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:97499)

Fusion Gene Summary for VKORC1-CD99

check button Fusion gene summary
Fusion gene informationFusion gene name: VKORC1-CD99
Fusion gene ID: 97499
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

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.

Q8TCZ2

Ensembl transtripts involved in fusion geneENST00000300851, ENST00000319788, 
ENST00000354895, ENST00000394975, 
ENST00000394971, ENST00000498155, 
ENST00000381192, ENST00000381187, 
ENST00000381184, ENST00000482405, 
ENST00000381180, 
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 buttonFusion gene breakpoints across VKORC1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CD99 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
Frame-shiftENST00000300851ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000300851ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000300851ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000300851ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000300851ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000319788ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000319788ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000319788ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000319788ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000319788ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000354895ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000354895ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000354895ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000354895ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000354895ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000394975ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
Frame-shiftENST00000394975ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000394975ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000394975ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
5CDS-intronENST00000394975ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000394971ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000394971ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000394971ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000394971ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000394971ENST00000381180VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000498155ENST00000381192VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-3CDSENST00000498155ENST00000381187VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000498155ENST00000381184VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000498155ENST00000482405VKORC1chr16

31105877

-CD99chrY

2606240

+
intron-intronENST00000498155ENST00000381180VKORC1chr16

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. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

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.

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Fusion Protein Features for VKORC1-CD99


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CD99

Q8TCZ2

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Plays a role in a late step of leukocyte extravasation helping cells to overcome the endothelial basement membrane. Acts at the same site as, but independently of, PECAM1 (By similarity). Homophilic adhesion molecule, but these interactions may not be required for cell aggregation (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
TgeneCD99C0206637Mesenchymal Chondrosarcoma1CTD_human