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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:ABLIM2-PPP2R2C

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ABLIM2-PPP2R2C
FusionPDB ID: 519
FusionGDB2.0 ID: 519
HgeneTgene
Gene symbol

ABLIM2

PPP2R2C

Gene ID

84448

5522

Gene nameactin binding LIM protein family member 2protein phosphatase 2 regulatory subunit Bgamma
Synonyms-B55-GAMMA|B55gamma|IMYPNO|IMYPNO1|PR52|PR55G
Cytomap

4p16.1

4p16.1

Type of geneprotein-codingprotein-coding
Descriptionactin-binding LIM protein 2abLIM-2testis tissue sperm-binding protein Li 35aprotein phosphatase 2, regulatory subunit B, gammaPP2A, subunit B, B-gamma isoformPP2A, subunit B, B55-gamma isoformPP2A, subunit B, PR55-gamma isoformPP2A, subunit B, R2-gamma isoformgamma isoform of regulatory subunit B55, protein phosphatase 2pho
Modification date2020031320200313
UniProtAcc

Q6H8Q1

Main function of 5'-partner protein: FUNCTION: May act as scaffold protein. May stimulate ABRA activity and ABRA-dependent SRF transcriptional activity. {ECO:0000269|PubMed:17194709}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000296372, ENST00000341937, 
ENST00000361581, ENST00000361737, 
ENST00000407564, ENST00000428004, 
ENST00000447017, ENST00000505872, 
ENST00000545242, ENST00000546334, 
ENST00000318888, ENST00000514025, 
ENST00000515079, 		ENST00000314348, 
ENST00000335585, ENST00000382599, 
ENST00000506140, ENST00000507294, 
ENST00000515571, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 3=486 X 6 X 5=180
# samples 46
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/180*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ABLIM2 [Title/Abstract] AND PPP2R2C [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ABLIM2 [Title/Abstract] AND PPP2R2C [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ABLIM2(8079355)-PPP2R2C(6380299), # samples:1
ABLIM2(8079355)-PPP2R2C(6382821), # samples:1
Anticipated loss of major functional domain due to fusion event.ABLIM2-PPP2R2C 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.
ABLIM2-PPP2R2C 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.
ABLIM2-PPP2R2C 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.
ABLIM2-PPP2R2C 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.
ABLIM2-PPP2R2C seems lost the major protein functional domain in Tgene 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


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/chr4:8079355/chr4:6380299)
- 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 ABLIM2 (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 PPP2R2C (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)
ENST00000361737ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2331797591972637
ENST00000361737ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2229797591972637
ENST00000361737ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2219797591972637
ENST00000361737ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2114797591972637
ENST00000545242ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2352818141993659
ENST00000545242ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2250818141993659
ENST00000545242ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2240818141993659
ENST00000545242ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2135818141993659
ENST00000546334ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2352818141993659
ENST00000546334ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2250818141993659
ENST00000546334ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2240818141993659
ENST00000546334ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2135818141993659
ENST00000296372ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2352818141993659
ENST00000296372ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2250818141993659
ENST00000296372ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2240818141993659
ENST00000296372ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2135818141993659
ENST00000447017ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2229695201870616
ENST00000447017ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2127695201870616
ENST00000447017ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2117695201870616
ENST00000447017ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2012695201870616
ENST00000361581ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-227474021915637
ENST00000361581ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-217274021915637
ENST00000361581ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-216274021915637
ENST00000361581ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-205774021915637
ENST00000341937ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-227474021915637
ENST00000341937ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-217274021915637
ENST00000341937ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-216274021915637
ENST00000341937ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-205774021915637
ENST00000407564ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2303769311944637
ENST00000407564ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2201769311944637
ENST00000407564ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2191769311944637
ENST00000407564ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2086769311944637
ENST00000505872ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-220967501850616
ENST00000505872ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-210767501850616
ENST00000505872ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-209767501850616
ENST00000505872ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-199267501850616
ENST00000428004ABLIM2chr48079355-ENST00000506140PPP2R2Cchr46380299-2352818141993659
ENST00000428004ABLIM2chr48079355-ENST00000515571PPP2R2Cchr46380299-2250818141993659
ENST00000428004ABLIM2chr48079355-ENST00000382599PPP2R2Cchr46380299-2240818141993659
ENST00000428004ABLIM2chr48079355-ENST00000507294PPP2R2Cchr46380299-2135818141993659

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
ENST00000361737ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0047287080.99527127
ENST00000361737ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0060167680.9939832
ENST00000361737ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0060322980.99396765
ENST00000361737ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.0081541160.9918459
ENST00000545242ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0046516740.9953484
ENST00000545242ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059355770.9940644
ENST00000545242ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059506010.99404943
ENST00000545242ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.007937070.99206287
ENST00000546334ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0046516740.9953484
ENST00000546334ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059355770.9940644
ENST00000546334ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059506010.99404943
ENST00000546334ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.007937070.99206287
ENST00000296372ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0046516740.9953484
ENST00000296372ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059355770.9940644
ENST00000296372ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059506010.99404943
ENST00000296372ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.007937070.99206287
ENST00000447017ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0052424060.99475765
ENST00000447017ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0068720190.99312794
ENST00000447017ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0068619080.993138
ENST00000447017ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.0090516670.9909484
ENST00000361581ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0051542360.99484575
ENST00000361581ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.006675290.9933247
ENST00000361581ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0067585350.99324155
ENST00000361581ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.008954960.9910451
ENST00000341937ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0051542360.99484575
ENST00000341937ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.006675290.9933247
ENST00000341937ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0067585350.99324155
ENST00000341937ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.008954960.9910451
ENST00000407564ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0048382120.99516183
ENST00000407564ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0062503870.9937496
ENST00000407564ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0063063810.99369365
ENST00000407564ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.0083543050.99164575
ENST00000505872ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0049305750.9950694
ENST00000505872ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0064504770.9935495
ENST00000505872ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0065053860.9934947
ENST00000505872ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.0085263350.9914737
ENST00000428004ENST00000506140ABLIM2chr48079355-PPP2R2Cchr46380299-0.0046516740.9953484
ENST00000428004ENST00000515571ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059355770.9940644
ENST00000428004ENST00000382599ABLIM2chr48079355-PPP2R2Cchr46380299-0.0059506010.99404943
ENST00000428004ENST00000507294ABLIM2chr48079355-PPP2R2Cchr46380299-0.007937070.99206287

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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C 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 ABLIM2-PPP2R2C 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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C

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 ABLIM2-PPP2R2C

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