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Center for Computational Systems Medicine level2
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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 Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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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:RB1CC1-PTPN3

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RB1CC1-PTPN3
FusionPDB ID: 72551
FusionGDB2.0 ID: 72551
HgeneTgene
Gene symbol

RB1CC1

PTPN3

Gene ID

9821

5774

Gene nameRB1 inducible coiled-coil 1protein tyrosine phosphatase non-receptor type 3
SynonymsATG17|CC1|FIP200|PPP1R131PTP-H1|PTPH1
Cytomap

8q11.23

9q31.3

Type of geneprotein-codingprotein-coding
DescriptionRB1-inducible coiled-coil protein 1200 kDa FAK family kinase-interacting proteinFAK family kinase-interacting protein of 200 kDaphosphatase 1, regulatory subunit 131tyrosine-protein phosphatase non-receptor type 3cytoskeletal-associated protein tyrosine phosphataseprotein-tyrosine phosphatase H1
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000025008, ENST00000435644, 
ENST00000539297, ENST00000521611, 
ENST00000497739, ENST00000262539, 
ENST00000374541, ENST00000394827, 
ENST00000412145, ENST00000446349, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 6 X 6=2887 X 7 X 7=343
# samples 910
** MAII scorelog2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/343*10)=-1.77820857639809
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: RB1CC1 [Title/Abstract] AND PTPN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RB1CC1(53580581)-PTPN3(112153841), # samples:3
Anticipated loss of major functional domain due to fusion event.RB1CC1-PTPN3 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.
RB1CC1-PTPN3 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.
RB1CC1-PTPN3 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.
RB1CC1-PTPN3 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.
RB1CC1-PTPN3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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
TgenePTPN3

GO:0006470

protein dephosphorylation

10364224

TgenePTPN3

GO:0045930

negative regulation of mitotic cell cycle

10364224

TgenePTPN3

GO:0098902

regulation of membrane depolarization during action potential

16930557

TgenePTPN3

GO:2000649

regulation of sodium ion transmembrane transporter activity

16930557


check buttonFusion gene breakpoints across RB1CC1 (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 PTPN3 (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
ChimerDB4PRADTCGA-KK-A8IJ-01ARB1CC1chr8

53580581

-PTPN3chr9

112153841

-
ChimerDB4PRADTCGA-KK-A8IJRB1CC1chr8

53580581

-PTPN3chr9

112153841

-


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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)
ENST00000539297RB1CC1chr853580581-ENST00000412145PTPN3chr9112153841-5824117301961653
ENST00000539297RB1CC1chr853580581-ENST00000446349PTPN3chr9112153841-5824117301961653
ENST00000539297RB1CC1chr853580581-ENST00000374541PTPN3chr9112153841-5818117301961653
ENST00000539297RB1CC1chr853580581-ENST00000262539PTPN3chr9112153841-2146117301961653
ENST00000539297RB1CC1chr853580581-ENST00000394827PTPN3chr9112153841-2431117301961653

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
ENST00000539297ENST00000412145RB1CC1chr853580581-PTPN3chr9112153841-0.0002327330.99976724
ENST00000539297ENST00000446349RB1CC1chr853580581-PTPN3chr9112153841-0.0002327330.99976724
ENST00000539297ENST00000374541RB1CC1chr853580581-PTPN3chr9112153841-0.0002328560.9997671
ENST00000539297ENST00000262539RB1CC1chr853580581-PTPN3chr9112153841-0.0007625510.9992374
ENST00000539297ENST00000394827RB1CC1chr853580581-PTPN3chr9112153841-0.000624150.9993759

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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

>72551_72551_1_RB1CC1-PTPN3_RB1CC1_chr8_53580581_ENST00000539297_PTPN3_chr9_112153841_ENST00000262539_length(amino acids)=653AA_BP=386
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVCTYSAGTDTNPIFLFNKEMILCDRPPAIPKT
TFSTENDMEIKVEESLMMPAVFHTVASRTQLALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTELVLSPDMPRTTNESLLTSFPKSVEHVSPDTA
DAESGKEIRESCQSTVHQQDETTIDTKDGDLPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANL
VNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHT
VTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQ

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

>72551_72551_2_RB1CC1-PTPN3_RB1CC1_chr8_53580581_ENST00000539297_PTPN3_chr9_112153841_ENST00000374541_length(amino acids)=653AA_BP=386
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVCTYSAGTDTNPIFLFNKEMILCDRPPAIPKT
TFSTENDMEIKVEESLMMPAVFHTVASRTQLALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTELVLSPDMPRTTNESLLTSFPKSVEHVSPDTA
DAESGKEIRESCQSTVHQQDETTIDTKDGDLPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANL
VNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHT
VTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQ

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

>72551_72551_3_RB1CC1-PTPN3_RB1CC1_chr8_53580581_ENST00000539297_PTPN3_chr9_112153841_ENST00000394827_length(amino acids)=653AA_BP=386
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVCTYSAGTDTNPIFLFNKEMILCDRPPAIPKT
TFSTENDMEIKVEESLMMPAVFHTVASRTQLALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTELVLSPDMPRTTNESLLTSFPKSVEHVSPDTA
DAESGKEIRESCQSTVHQQDETTIDTKDGDLPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANL
VNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHT
VTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQ

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

>72551_72551_4_RB1CC1-PTPN3_RB1CC1_chr8_53580581_ENST00000539297_PTPN3_chr9_112153841_ENST00000412145_length(amino acids)=653AA_BP=386
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVCTYSAGTDTNPIFLFNKEMILCDRPPAIPKT
TFSTENDMEIKVEESLMMPAVFHTVASRTQLALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTELVLSPDMPRTTNESLLTSFPKSVEHVSPDTA
DAESGKEIRESCQSTVHQQDETTIDTKDGDLPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANL
VNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHT
VTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQ

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

>72551_72551_5_RB1CC1-PTPN3_RB1CC1_chr8_53580581_ENST00000539297_PTPN3_chr9_112153841_ENST00000446349_length(amino acids)=653AA_BP=386
MKLYVFLVNTGTTLTFDTELTVQTVADLKHAIQSKYKIAIQHQVLVVNGGECMAADRRVCTYSAGTDTNPIFLFNKEMILCDRPPAIPKT
TFSTENDMEIKVEESLMMPAVFHTVASRTQLALEMYEVAKKLCSFCEGLVHDEHLQHQGWAAIMANLEDCSNSYQKLLFKFESIYSNYLQ
SIEDIKLKLTHLGTAVSVMAKIPLLECLTRHSYRECLGRLDSLPEHEDSEKAEMKRSTELVLSPDMPRTTNESLLTSFPKSVEHVSPDTA
DAESGKEIRESCQSTVHQQDETTIDTKDGDLPFFNVSLLDWINVQDRPNDVESLVRKCFDSMSRLDPRIIRPFIAECRQTIAKLDNQNMK
AIKGLEDRLYALDQMIASCGRLVNEQKELAQQLYRKKPGLAITFAKLPQNLDKNRYKDVLPYDTTRVLLQGNEDYINASYVNMEIPAANL
VNKYIATQGPLPHTCAQFWQVVWDQKLSLIVMLTTLTERGRTKCHQYWPDPPDVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHT
VTHLQYVAWPDHGVPDDSSDFLEFVNYVRSLRVDSEPVLVHCSAGIGRTGVLVTMETAMCLTERNLPIYPLDIVRKMRDQRAMMVQTSSQ

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

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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/chr8:53580581/chr9:112153841)
- 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: 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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgenePTPN3chr8:53580581chr9:112153841ENST000004121451321646_901520.0783.0DomainTyrosine-protein phosphatase
TgenePTPN3chr8:53580581chr9:112153841ENST000004463491220510_582475.0738.0DomainPDZ
TgenePTPN3chr8:53580581chr9:112153841ENST000004463491220646_901475.0738.0DomainTyrosine-protein phosphatase
TgenePTPN3chr8:53580581chr9:112153841ENST000003745411826842_848651.0914.0RegionSubstrate binding
TgenePTPN3chr8:53580581chr9:112153841ENST000004121451321842_848520.0783.0RegionSubstrate binding
TgenePTPN3chr8:53580581chr9:112153841ENST000004463491220842_848475.0738.0RegionSubstrate binding

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000025008-8241438_1485391.01595.0Coiled coilOntology_term=ECO:0000255
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000025008-824859_1397391.01595.0Coiled coilOntology_term=ECO:0000255
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000435644-8241438_1485391.01592.0Coiled coilOntology_term=ECO:0000255
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000435644-824859_1397391.01592.0Coiled coilOntology_term=ECO:0000255
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000539297-6221438_1485391.01592.0Coiled coilOntology_term=ECO:0000255
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000539297-622859_1397391.01592.0Coiled coilOntology_term=ECO:0000255
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000025008-824663_666391.01595.0Compositional biasNote=Poly-Thr
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000435644-824663_666391.01592.0Compositional biasNote=Poly-Thr
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000539297-622663_666391.01592.0Compositional biasNote=Poly-Thr
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000025008-824566_569391.01595.0MotifNuclear localization signal
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000435644-824566_569391.01592.0MotifNuclear localization signal
HgeneRB1CC1chr8:53580581chr9:112153841ENST00000539297-622566_569391.01592.0MotifNuclear localization signal
TgenePTPN3chr8:53580581chr9:112153841ENST00000374541182629_312651.0914.0DomainFERM
TgenePTPN3chr8:53580581chr9:112153841ENST000003745411826510_582651.0914.0DomainPDZ
TgenePTPN3chr8:53580581chr9:112153841ENST000003745411826646_901651.0914.0DomainTyrosine-protein phosphatase
TgenePTPN3chr8:53580581chr9:112153841ENST00000412145132129_312520.0783.0DomainFERM
TgenePTPN3chr8:53580581chr9:112153841ENST000004121451321510_582520.0783.0DomainPDZ
TgenePTPN3chr8:53580581chr9:112153841ENST00000446349122029_312475.0738.0DomainFERM


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
RB1CC1_pLDDT.png
all structure
all structure
PTPN3_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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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
RB1CC1
PTPN3


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 RB1CC1-PTPN3


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 RB1CC1-PTPN3


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