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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:PTK2-CHMP4A (FusionGDB2 ID:70030)

Fusion Gene Summary for PTK2-CHMP4A

check button Fusion gene summary
Fusion gene informationFusion gene name: PTK2-CHMP4A
Fusion gene ID: 70030
HgeneTgene
Gene symbol

PTK2

CHMP4A

Gene ID

5747

128866

Gene nameprotein tyrosine kinase 2charged multivesicular body protein 4B
SynonymsFADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAKC20orf178|CHMP4A|CTPP3|CTRCT31|SNF7|SNF7-2|Shax1|VPS32B|Vps32-2|dJ553F4.4
Cytomap

8q24.3

20q11.22

Type of geneprotein-codingprotein-coding
Descriptionfocal adhesion kinase 1FADK 1FAK-related non-kinase polypeptidePTK2 protein tyrosine kinase 2focal adhesion kinase isoform FAK-Del33focal adhesion kinase-related nonkinaseprotein phosphatase 1 regulatory subunit 71charged multivesicular body protein 4bSNF7 homolog associated with Alix 1Snf7 homologue associated with Alix 1chromatin modifying protein 4Bchromatin-modifying protein 4bhSnf7-2hVps32-2vacuolar protein-sorting-associated protein 32-2
Modification date2020032720200313
UniProtAcc.

Q9BY43

Ensembl transtripts involved in fusion geneENST00000340930, ENST00000395218, 
ENST00000430260, ENST00000517712, 
ENST00000517887, ENST00000519419, 
ENST00000519465, ENST00000519635, 
ENST00000519881, ENST00000520151, 
ENST00000520892, ENST00000521059, 
ENST00000522684, ENST00000522950, 
ENST00000535192, ENST00000538769, 
ENST00000347519, ENST00000530996, 
ENST00000542700, ENST00000609024, 
Fusion gene scores* DoF score39 X 32 X 15=187204 X 3 X 3=36
# samples 574
** MAII scorelog2(57/18720*10)=-5.03747470541866
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PTK2 [Title/Abstract] AND CHMP4A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTK2(141789334)-CHMP4A(24678821), # samples:1
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
HgenePTK2

GO:0007179

transforming growth factor beta receptor signaling pathway

24036928

HgenePTK2

GO:0007229

integrin-mediated signaling pathway

24036928

HgenePTK2

GO:0010763

positive regulation of fibroblast migration

26763945

HgenePTK2

GO:0018108

peptidyl-tyrosine phosphorylation

10655584|11331870

HgenePTK2

GO:0022408

negative regulation of cell-cell adhesion

21703394

HgenePTK2

GO:0030335

positive regulation of cell migration

11331870|21703394

HgenePTK2

GO:0033628

regulation of cell adhesion mediated by integrin

10655584

HgenePTK2

GO:0046777

protein autophosphorylation

10655584|11331870

HgenePTK2

GO:0048013

ephrin receptor signaling pathway

10655584

HgenePTK2

GO:0060396

growth hormone receptor signaling pathway

10925297

HgenePTK2

GO:0090303

positive regulation of wound healing

26763945

TgeneCHMP4A

GO:0039702

viral budding via host ESCRT complex

24878737

TgeneCHMP4A

GO:0051258

protein polymerization

18209100


check buttonFusion gene breakpoints across PTK2 (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 CHMP4A (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
ChiTaRS5.0N/AAA642576PTK2chr8

141789334

-CHMP4Achr14

24678821

+


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Fusion Gene ORF analysis for PTK2-CHMP4A

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-3UTRENST00000340930ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000395218ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000430260ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000517712ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000517887ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000519419ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000519465ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000519635ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000519881ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000520151ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000520892ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000521059ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000522684ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000522950ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000535192ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-3UTRENST00000538769ENST00000347519PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000340930ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000340930ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000340930ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000395218ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000395218ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000395218ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000430260ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000430260ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000430260ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000517712ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000517712ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000517712ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000517887ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000517887ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000517887ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519419ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519419ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519419ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519465ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519465ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519465ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519635ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519635ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519635ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519881ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519881ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000519881ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000520151ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000520151ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000520151ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000520892ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000520892ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000520892ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000521059ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000521059ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000521059ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000522684ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000522684ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000522684ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000522950ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000522950ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000522950ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000535192ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000535192ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000535192ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000538769ENST00000530996PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000538769ENST00000542700PTK2chr8

141789334

-CHMP4Achr14

24678821

+
intron-intronENST00000538769ENST00000609024PTK2chr8

141789334

-CHMP4Achr14

24678821

+

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 PTK2-CHMP4A


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)

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 PTK2-CHMP4A


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/:141789334/:24678821)
- 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
.CHMP4A

Q9BY43

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: Probable core component of the endosomal sorting required for transport complex III (ESCRT-III) which is involved in multivesicular bodies (MVBs) formation and sorting of endosomal cargo proteins into MVBs. MVBs contain intraluminal vesicles (ILVs) that are generated by invagination and scission from the limiting membrane of the endosome and mostly are delivered to lysosomes enabling degradation of membrane proteins, such as stimulated growth factor receptors, lysosomal enzymes and lipids. The MVB pathway appears to require the sequential function of ESCRT-O, -I,-II and -III complexes. ESCRT-III proteins mostly dissociate from the invaginating membrane before the ILV is released. The ESCRT machinery also functions in topologically equivalent membrane fission events, such as the terminal stages of cytokinesis and the budding of enveloped viruses (HIV-1 and other lentiviruses). ESCRT-III proteins are believed to mediate the necessary vesicle extrusion and/or membrane fission activities, possibly in conjunction with the AAA ATPase VPS4. When overexpressed, membrane-assembled circular arrays of CHMP4A filaments can promote or stabilize negative curvature and outward budding. Via its interaction with PDCD6IP involved in HIV-1 p6- and p9-dependent virus release. CHMP4A/B/C are required for the exosomal release of SDCBP, CD63 and syndecan (PubMed:22660413). {ECO:0000269|PubMed:12860994, ECO:0000269|PubMed:14505569, ECO:0000269|PubMed:14519844, ECO:0000269|PubMed:14583093, ECO:0000269|PubMed:18209100, ECO:0000269|PubMed:22660413}.

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 PTK2-CHMP4A


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 PTK2-CHMP4A


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 PTK2-CHMP4A


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 PTK2-CHMP4A


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