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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:PTPRC-BCAS3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTPRC-BCAS3
FusionPDB ID: 70328
FusionGDB2.0 ID: 70328
HgeneTgene
Gene symbol

PTPRC

BCAS3

Gene ID

5788

54828

Gene nameprotein tyrosine phosphatase receptor type CBCAS3 microtubule associated cell migration factor
SynonymsB220|CD45|CD45R|GP180|L-CA|LCA|LY5|T200GAOB1|MAAB
Cytomap

1q31.3-q32.1

17q23.2

Type of geneprotein-codingprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase CCD45 antigenT200 glycoproteinT200 leukocyte common antigenprotein tyrosine phosphatase, receptor type, c polypeptidebreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1
Modification date2020032720200313
UniProtAcc.

Q9H6U6

Main function of 5'-partner protein: FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.
Ensembl transtripts involved in fusion geneENST idsENST00000348564, ENST00000352140, 
ENST00000367364, ENST00000367376, 
ENST00000413409, ENST00000442510, 
ENST00000594404, ENST00000598951, 
ENST00000391970, 
ENST00000585812, 
ENST00000407086, ENST00000408905, 
ENST00000585744, ENST00000588462, 
ENST00000588874, ENST00000390652, 
ENST00000589222, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 6 X 3=10845 X 32 X 19=27360
# samples 653
** MAII scorelog2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(53/27360*10)=-5.6899320603227
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PTPRC [Title/Abstract] AND BCAS3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PTPRC [Title/Abstract] AND BCAS3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PTPRC(198608471)-BCAS3(59469337), # samples:1
Anticipated loss of major functional domain due to fusion event.PTPRC-BCAS3 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.
PTPRC-BCAS3 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.
PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PTPRC-BCAS3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PTPRC-BCAS3 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgenePTPRC

GO:0006469

negative regulation of protein kinase activity

9197241

HgenePTPRC

GO:0032677

regulation of interleukin-8 production

12100025

HgenePTPRC

GO:0050764

regulation of phagocytosis

12100025

HgenePTPRC

GO:0050852

T cell receptor signaling pathway

10358156

HgenePTPRC

GO:0061097

regulation of protein tyrosine kinase activity

12100025

TgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

TgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

TgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058



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/chr1:198608471/chr17:59469337)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across PTPRC (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 BCAS3 (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 Amino Acid Sequences


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)
ENST00000352140PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1093238313687124
ENST00000352140PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1100238313687124
ENST00000594404PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1093238313687124
ENST00000594404PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1100238313687124
ENST00000367376PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1093238313687124
ENST00000367376PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1100238313687124
ENST00000442510PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1069214289663124
ENST00000442510PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1076214289663124
ENST00000348564PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1014159234608124
ENST00000348564PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1021159234608124
ENST00000598951PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1093238313687124
ENST00000598951PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1100238313687124
ENST00000367364PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1012157232606124
ENST00000367364PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1019157232606124
ENST00000413409PTPRCchr1198608471+ENST00000589222BCAS3chr1759469337+1012157232606124
ENST00000413409PTPRCchr1198608471+ENST00000390652BCAS3chr1759469337+1019157232606124

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
ENST00000352140ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.86889530.13110468
ENST00000352140ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.87038320.12961678
ENST00000594404ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.86889530.13110468
ENST00000594404ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.87038320.12961678
ENST00000367376ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.86889530.13110468
ENST00000367376ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.87038320.12961678
ENST00000442510ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.858258660.1417413
ENST00000442510ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.86566560.1343344
ENST00000348564ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.927731750.072268225
ENST00000348564ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.925937830.074062094
ENST00000598951ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.86889530.13110468
ENST00000598951ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.87038320.12961678
ENST00000367364ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.92197590.07802412
ENST00000367364ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.921198670.078801356
ENST00000413409ENST00000589222PTPRCchr1198608471+BCAS3chr1759469337+0.92197590.07802412
ENST00000413409ENST00000390652PTPRCchr1198608471+BCAS3chr1759469337+0.921198670.078801356

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for PTPRC-BCAS3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide

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Potential FusionNeoAntigen Information of PTPRC-BCAS3 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of PTPRC-BCAS3 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of PTPRC-BCAS3

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRC-BCAS3

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of PTPRC-BCAS3

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of PTPRC-BCAS3

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for PTPRC-BCAS3

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to PTPRC-BCAS3

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 PTPRC-BCAS3

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