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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:VAMP7-TGFB2 (FusionGDB2 ID:97199)

Fusion Gene Summary for VAMP7-TGFB2

check button Fusion gene summary
Fusion gene informationFusion gene name: VAMP7-TGFB2
Fusion gene ID: 97199
HgeneTgene
Gene symbol

VAMP7

TGFB2

Gene ID

6845

7042

Gene namevesicle associated membrane protein 7transforming growth factor beta 2
SynonymsSYBL1|TI-VAMP|TIVAMP|VAMP-7G-TSF|LDS4|TGF-beta2
Cytomap

Xq28 and Yq12

1q41

Type of geneprotein-codingprotein-coding
Descriptionvesicle-associated membrane protein 7synaptobrevin-like 1synaptobrevin-like protein 1tetanus neurotoxin-insensitive VAMPtetanus-insensitive VAMPtransforming growth factor beta-2 proproteinBSC-1 cell growth inhibitorceterminglioblastoma-derived T-cell suppressor factorpolyerginprepro-transforming growth factor beta-2
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000286448, ENST00000479687, 
ENST00000262640, ENST00000460621, 
ENST00000366930, ENST00000366929, 
ENST00000479322, 
Fusion gene scores* DoF score3 X 3 X 3=271 X 1 X 1=1
# samples 31
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(1/1*10)=3.32192809488736
Context

PubMed: VAMP7 [Title/Abstract] AND TGFB2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVAMP7(155130251)-TGFB2(218578511), # samples:2
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneVAMP7

GO:0006906

vesicle fusion

10888671

HgeneVAMP7

GO:0008333

endosome to lysosome transport

10888671

HgeneVAMP7

GO:0016192

vesicle-mediated transport

10888671

TgeneTGFB2

GO:0000902

cell morphogenesis

15896309

TgeneTGFB2

GO:0001654

eye development

15944186

TgeneTGFB2

GO:0001837

epithelial to mesenchymal transition

10092230|18223299

TgeneTGFB2

GO:0001942

hair follicle development

10433821

TgeneTGFB2

GO:0003007

heart morphogenesis

10092230

TgeneTGFB2

GO:0006468

protein phosphorylation

18358889

TgeneTGFB2

GO:0007050

cell cycle arrest

18223299

TgeneTGFB2

GO:0007179

transforming growth factor beta receptor signaling pathway

11157754|18358889

TgeneTGFB2

GO:0007507

heart development

15896309

TgeneTGFB2

GO:0008219

cell death

16227582

TgeneTGFB2

GO:0008284

positive regulation of cell proliferation

15896309

TgeneTGFB2

GO:0008285

negative regulation of cell proliferation

15944186

TgeneTGFB2

GO:0008347

glial cell migration

18431253

TgeneTGFB2

GO:0010002

cardioblast differentiation

15896309

TgeneTGFB2

GO:0010629

negative regulation of gene expression

25217442

TgeneTGFB2

GO:0010634

positive regulation of epithelial cell migration

17960115

TgeneTGFB2

GO:0010693

negative regulation of alkaline phosphatase activity

18358889

TgeneTGFB2

GO:0010718

positive regulation of epithelial to mesenchymal transition

17999987|18505915

TgeneTGFB2

GO:0010936

negative regulation of macrophage cytokine production

20875417

TgeneTGFB2

GO:0014068

positive regulation of phosphatidylinositol 3-kinase signaling

18223299

TgeneTGFB2

GO:0016477

cell migration

10092230

TgeneTGFB2

GO:0016525

negative regulation of angiogenesis

25217442|28977001

TgeneTGFB2

GO:0030199

collagen fibril organization

16891397

TgeneTGFB2

GO:0030307

positive regulation of cell growth

15896309|20573232

TgeneTGFB2

GO:0030308

negative regulation of cell growth

18358889

TgeneTGFB2

GO:0032147

activation of protein kinase activity

17192487|17960115

TgeneTGFB2

GO:0032570

response to progesterone

18039789

TgeneTGFB2

GO:0032874

positive regulation of stress-activated MAPK cascade

17192487

TgeneTGFB2

GO:0033630

positive regulation of cell adhesion mediated by integrin

17960115|18223299

TgeneTGFB2

GO:0042493

response to drug

20573232

TgeneTGFB2

GO:0043525

positive regulation of neuron apoptotic process

16227582

TgeneTGFB2

GO:0045216

cell-cell junction organization

18505915

TgeneTGFB2

GO:0045726

positive regulation of integrin biosynthetic process

17960115

TgeneTGFB2

GO:0045747

positive regulation of Notch signaling pathway

25217442

TgeneTGFB2

GO:0045823

positive regulation of heart contraction

15896309

TgeneTGFB2

GO:0050680

negative regulation of epithelial cell proliferation

17217916

TgeneTGFB2

GO:0050714

positive regulation of protein secretion

18505915

TgeneTGFB2

GO:0051794

regulation of timing of catagen

15955085

TgeneTGFB2

GO:0051795

positive regulation of timing of catagen

15955085

TgeneTGFB2

GO:0051891

positive regulation of cardioblast differentiation

15896309

TgeneTGFB2

GO:0060038

cardiac muscle cell proliferation

15896309

TgeneTGFB2

GO:0060317

cardiac epithelial to mesenchymal transition

10092230

TgeneTGFB2

GO:0060389

pathway-restricted SMAD protein phosphorylation

11157754|18358889

TgeneTGFB2

GO:0060395

SMAD protein signal transduction

17192487

TgeneTGFB2

GO:0097191

extrinsic apoptotic signaling pathway

17217916

TgeneTGFB2

GO:1902895

positive regulation of pri-miRNA transcription by RNA polymerase II

25217442


check buttonFusion gene breakpoints across VAMP7 (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 TGFB2 (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
ChimerDB4BRCATCGA-A2-A0D0-01AVAMP7chrX

155130251

+TGFB2chr1

218578511

+
ChimerDB4BRCATCGA-A2-A0D0-01AVAMP7chrX

155130251

+TGFB2chr1

218578511

+


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Fusion Gene ORF analysis for VAMP7-TGFB2

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-3CDSENST00000286448ENST00000366930VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000286448ENST00000366929VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-intronENST00000286448ENST00000479322VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000479687ENST00000366930VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000479687ENST00000366929VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-intronENST00000479687ENST00000479322VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000262640ENST00000366930VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000262640ENST00000366929VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-intronENST00000262640ENST00000479322VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000460621ENST00000366930VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-3CDSENST00000460621ENST00000366929VAMP7chrX

155130251

+TGFB2chr1

218578511

+
intron-intronENST00000460621ENST00000479322VAMP7chrX

155130251

+TGFB2chr1

218578511

+

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 VAMP7-TGFB2


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)
VAMP7chrX155130251+TGFB2chr1218578510+5.12E-050.99994886
VAMP7chrX155130251+TGFB2chr1218578510+5.12E-050.99994886

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 VAMP7-TGFB2


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
..
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: 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.

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 VAMP7-TGFB2


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 VAMP7-TGFB2


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 VAMP7-TGFB2


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 VAMP7-TGFB2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVAMP7C0343641Human papilloma virus infection1CTD_human
HgeneVAMP7C1168401Squamous cell carcinoma of the head and neck1CTD_human
HgeneVAMP7C451074446,XY partial gonadal dysgenesis1ORPHANET
TgeneTGFB2C3553762LOEYS-DIETZ SYNDROME 44GENOMICS_ENGLAND;UNIPROT
TgeneTGFB2C4707243Familial thoracic aortic aneurysm and aortic dissection3CLINGEN;GENOMICS_ENGLAND;ORPHANET
TgeneTGFB2C0162872Aortic Aneurysm, Thoracic2CTD_human
TgeneTGFB2C0340630Aortic Aneurysm, Thoracoabdominal2CTD_human
TgeneTGFB2C2697932Loeys-Dietz Syndrome2CTD_human;GENOMICS_ENGLAND
TgeneTGFB2C0003504Aortic Valve Insufficiency1CTD_human
TgeneTGFB2C0004364Autoimmune Diseases1CTD_human
TgeneTGFB2C0005941Bone Diseases, Developmental1CTD_human
TgeneTGFB2C0008311Cholangitis1CTD_human
TgeneTGFB2C0008925Cleft Palate1CTD_human
TgeneTGFB2C0010520Cyanosis1CTD_human
TgeneTGFB2C0014175Endometriosis1CTD_human
TgeneTGFB2C0015393Eye Abnormalities1CTD_human
TgeneTGFB2C0017601Glaucoma1CTD_human
TgeneTGFB2C0018798Congenital Heart Defects1CTD_human
TgeneTGFB2C0034067Pulmonary Emphysema1GENOMICS_ENGLAND
TgeneTGFB2C0035238Congenital abnormality of respiratory system1CTD_human
TgeneTGFB2C0041956Ureteral obstruction1CTD_human
TgeneTGFB2C0042063Urogenital Abnormalities1CTD_human
TgeneTGFB2C0151491Congenital musculoskeletal anomalies1CTD_human
TgeneTGFB2C0206762Limb Deformities, Congenital1CTD_human
TgeneTGFB2C0269102Endometrioma1CTD_human
TgeneTGFB2C0345967Malignant mesothelioma1CTD_human
TgeneTGFB2C0376634Craniofacial Abnormalities1CTD_human
TgeneTGFB2C1836635Loeys-Dietz Aortic Aneurysm Syndrome1CTD_human
TgeneTGFB2C1837218Cleft palate, isolated1CTD_human
TgeneTGFB2C4551955Loeys-Dietz Syndrome, Type 1a1CTD_human