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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PPP4R1-ITGB6

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPP4R1-ITGB6
FusionPDB ID: 68186
FusionGDB2.0 ID: 68186
HgeneTgene
Gene symbol

PPP4R1

ITGB6

Gene ID

9989

3694

Gene nameprotein phosphatase 4 regulatory subunit 1integrin subunit beta 6
SynonymsMEG1|PP4(Rmeg)|PP4R1AI1H
Cytomap

18p11.22

2q24.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 4 regulatory subunit 1serine/threonine phosphatase 4integrin beta-6integrin, beta 6
Modification date2020031320200313
UniProtAcc.

P18564

Ensembl transtripts involved in fusion geneENST idsENST00000400555, ENST00000400556, 
ENST00000580583, 		ENST00000409872, 
ENST00000409967, ENST00000428609, 
ENST00000485635, ENST00000283249, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 13 X 9=15218 X 6 X 8=384
# samples 1410
** MAII scorelog2(14/1521*10)=-3.44152142077953
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/384*10)=-1.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PPP4R1 [Title/Abstract] AND ITGB6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP4R1(9614224)-ITGB6(160968710), # samples:1
Anticipated loss of major functional domain due to fusion event.PPP4R1-ITGB6 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP4R1-ITGB6 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP4R1-ITGB6 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP4R1-ITGB6 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame 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
TgeneITGB6

GO:0033627

cell adhesion mediated by integrin

17158881

TgeneITGB6

GO:1901388

regulation of transforming growth factor beta activation

22278742


check buttonFusion gene breakpoints across PPP4R1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across ITGB6 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-CancerERR315472PPP4R1chr18

9614224

-ITGB6chr2

160968710

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000400556PPP4R1chr189614224-ENST00000283249ITGB6chr2160968710-258212674511145
ENST00000400555PPP4R1chr189614224-ENST00000283249ITGB6chr2160968710-259313785522145

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
ENST00000400556ENST00000283249PPP4R1chr189614224-ITGB6chr2160968710-0.0046551630.9953448
ENST00000400555ENST00000283249PPP4R1chr189614224-ITGB6chr2160968710-0.0056918810.9943082

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>68186_68186_1_PPP4R1-ITGB6_PPP4R1_chr18_9614224_ENST00000400555_ITGB6_chr2_160968710_ENST00000283249_length(amino acids)=145AA_BP=18
MADLSLLQEDLQEDADGYFSKDGSVSCSLQGENECLITFLITTDNEGKTIIHSINEKDCPKPPNIPMIMLGVSLAILLIGVVLLCIWKLL

--------------------------------------------------------------

>68186_68186_2_PPP4R1-ITGB6_PPP4R1_chr18_9614224_ENST00000400556_ITGB6_chr2_160968710_ENST00000283249_length(amino acids)=145AA_BP=18
MADLSLLQEDLQEDADGYFSKDGSVSCSLQGENECLITFLITTDNEGKTIIHSINEKDCPKPPNIPMIMLGVSLAILLIGVVLLCIWKLL

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Fusion Protein Functional Features


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/chr18:9614224/chr2:160968710)
- 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
.ITGB6

P18564

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: Integrin alpha-V:beta-6 (ITGAV:ITGB6) is a receptor for fibronectin and cytotactin (PubMed:17545607, PubMed:17158881). It recognizes the sequence R-G-D in its ligands (PubMed:17545607, PubMed:17158881). Internalisation of integrin alpha-V/beta-6 via clathrin-mediated endocytosis promotes carcinoma cell invasion (PubMed:17545607, PubMed:17158881). ITGAV:ITGB6 acts as a receptor for fibrillin-1 (FBN1) and mediates R-G-D-dependent cell adhesion to FBN1 (PubMed:17158881). Integrin alpha-V:beta-6 (ITGAV:ITGB6) mediates R-G-D-dependent release of transforming growth factor beta-1 (TGF-beta-1) from regulatory Latency-associated peptide (LAP), thereby playing a key role in TGF-beta-1 activation (PubMed:15184403, PubMed:22278742, PubMed:28117447). {ECO:0000269|PubMed:15184403, ECO:0000269|PubMed:17158881, ECO:0000269|PubMed:17545607, ECO:0000269|PubMed:22278742, ECO:0000269|PubMed:28117447}.; FUNCTION: (Microbial infection) Integrin ITGAV:ITGB6 acts as a receptor for Coxsackievirus A9 and Coxsackievirus B1. {ECO:0000269|PubMed:15194773, ECO:0000269|PubMed:9426447}.; FUNCTION: (Microbial infection) Integrin ITGAV:ITGB6 acts as a receptor for Herpes simplex virus-1/HHV-1 (PubMed:24367260). {ECO:0000269|PubMed:24367260}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115731_788660.3333333333334789.0Topological domainCytoplasmic
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216731_788660.3333333333334789.0Topological domainCytoplasmic
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115710_730660.3333333333334789.0TransmembraneHelical
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216710_730660.3333333333334789.0TransmembraneHelical

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220127_16417.333333333333332934.0RepeatNote=HEAT 5
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220168_20617.333333333333332934.0RepeatNote=HEAT 6
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-2201_2517.333333333333332934.0RepeatNote=HEAT 1
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220208_24617.333333333333332934.0RepeatNote=HEAT 7
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220248_28517.333333333333332934.0RepeatNote=HEAT 8
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-22026_6317.333333333333332934.0RepeatNote=HEAT 2
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220287_32417.333333333333332934.0RepeatNote=HEAT 9
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220505_54217.333333333333332934.0RepeatNote=HEAT 10
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220568_60617.333333333333332934.0RepeatNote=HEAT 11
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-22065_8117.333333333333332934.0RepeatNote=HEAT 3
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220698_73417.333333333333332934.0RepeatNote=HEAT 12
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220799_83717.333333333333332934.0RepeatNote=HEAT 13
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-22082_11917.333333333333332934.0RepeatNote=HEAT 4
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400555-220861_89817.333333333333332934.0RepeatNote=HEAT 14
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220127_16417.333333333333332951.0RepeatNote=HEAT 5
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220168_20617.333333333333332951.0RepeatNote=HEAT 6
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-2201_2517.333333333333332951.0RepeatNote=HEAT 1
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220208_24617.333333333333332951.0RepeatNote=HEAT 7
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220248_28517.333333333333332951.0RepeatNote=HEAT 8
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-22026_6317.333333333333332951.0RepeatNote=HEAT 2
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220287_32417.333333333333332951.0RepeatNote=HEAT 9
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220505_54217.333333333333332951.0RepeatNote=HEAT 10
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220568_60617.333333333333332951.0RepeatNote=HEAT 11
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-22065_8117.333333333333332951.0RepeatNote=HEAT 3
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220698_73417.333333333333332951.0RepeatNote=HEAT 12
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220799_83717.333333333333332951.0RepeatNote=HEAT 13
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-22082_11917.333333333333332951.0RepeatNote=HEAT 4
HgenePPP4R1chr18:9614224chr2:160968710ENST00000400556-220861_89817.333333333333332951.0RepeatNote=HEAT 14
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115131_371660.3333333333334789.0DomainNote=VWFA
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216131_371660.3333333333334789.0DomainNote=VWFA
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115456_619660.3333333333334789.0RegionNote=Cysteine-rich tandem repeats
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216456_619660.3333333333334789.0RegionNote=Cysteine-rich tandem repeats
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115456_501660.3333333333334789.0RepeatNote=I
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115502_543660.3333333333334789.0RepeatNote=II
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115544_582660.3333333333334789.0RepeatNote=III
TgeneITGB6chr18:9614224chr2:160968710ENST000002832491115583_619660.3333333333334789.0RepeatNote=IV
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216456_501660.3333333333334789.0RepeatNote=I
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216502_543660.3333333333334789.0RepeatNote=II
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216544_582660.3333333333334789.0RepeatNote=III
TgeneITGB6chr18:9614224chr2:160968710ENST000004098721216583_619660.3333333333334789.0RepeatNote=IV
TgeneITGB6chr18:9614224chr2:160968710ENST00000283249111522_709660.3333333333334789.0Topological domainExtracellular
TgeneITGB6chr18:9614224chr2:160968710ENST00000409872121622_709660.3333333333334789.0Topological domainExtracellular


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PPP4R1
ITGB6


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to PPP4R1-ITGB6


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to PPP4R1-ITGB6


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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