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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:PCCA-MBNL2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PCCA-MBNL2
FusionPDB ID: 63156
FusionGDB2.0 ID: 63156
HgeneTgene
Gene symbol

PCCA

MBNL2

Gene ID

5095

10150

Gene namepropionyl-CoA carboxylase subunit alphamuscleblind like splicing regulator 2
Synonyms-MBLL|MBLL39|PRO2032
Cytomap

13q32.3

13q32.1

Type of geneprotein-codingprotein-coding
Descriptionpropionyl-CoA carboxylase alpha chain, mitochondrialPCCase alpha subunitpccA complementation grouppropanoyl-CoA:carbon dioxide ligase alpha subunitpropionyl CoA carboxylase, alpha polypeptidepropionyl Coenzyme A carboxylase, alpha polypeptidepropionmuscleblind-like protein 2muscleblind-like 2muscleblind-like protein 1muscleblind-like protein-like 39
Modification date2020031320200313
UniProtAcc.

Q5VZF2

Main function of 5'-partner protein: FUNCTION: Mediates pre-mRNA alternative splicing regulation. Acts either as activator or repressor of splicing on specific pre-mRNA targets. Inhibits cardiac troponin-T (TNNT2) pre-mRNA exon inclusion but induces insulin receptor (IR) pre-mRNA exon inclusion in muscle. Antagonizes the alternative splicing activity pattern of CELF proteins. RNA-binding protein that binds to 5'ACACCC-3' core sequence, termed zipcode, within the 3'UTR of ITGA3. Binds to CUG triplet repeat expansion in myotonic dystrophy muscle cells by sequestering the target RNAs. Seems to regulate expression and localization of ITGA3 by transporting it from the nucleus to cytoplasm at adhesion plaques. May play a role in myotonic dystrophy pathophysiology (DM). {ECO:0000269|PubMed:15257297, ECO:0000269|PubMed:16273094, ECO:0000269|PubMed:16946708}.
Ensembl transtripts involved in fusion geneENST idsENST00000485946, ENST00000376279, 
ENST00000376285, ENST00000376286, 
ENST00000343600, ENST00000345429, 
ENST00000376673, ENST00000397601, 
ENST00000445661, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score20 X 16 X 12=38407 X 8 X 5=280
# samples 259
** MAII scorelog2(25/3840*10)=-3.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/280*10)=-1.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PCCA [Title/Abstract] AND MBNL2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PCCA [Title/Abstract] AND MBNL2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PCCA(100861717)-MBNL2(97986530), # samples:3
Anticipated loss of major functional domain due to fusion event.PCCA-MBNL2 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.
PCCA-MBNL2 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.
PCCA-MBNL2 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.
PCCA-MBNL2 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.
PCCA-MBNL2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PCCA-MBNL2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PCCA-MBNL2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
PCCA-MBNL2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
TgeneMBNL2

GO:0043484

regulation of RNA splicing

15257297|16946708



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/chr13:100861717/chr13:97986530)
- 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 PCCA (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 MBNL2 (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)
ENST00000376279PCCAchr13100809594+ENST00000343600MBNL2chr1398043576+337257464588174
ENST00000376279PCCAchr13100809594+ENST00000345429MBNL2chr1398043576+337357464588174
ENST00000376286PCCAchr13100809594+ENST00000343600MBNL2chr1398043576+329449664510148
ENST00000376286PCCAchr13100809594+ENST00000345429MBNL2chr1398043576+329549664510148
ENST00000376285PCCAchr13100809594+ENST00000343600MBNL2chr1398043576+330450638520160
ENST00000376285PCCAchr13100809594+ENST00000345429MBNL2chr1398043576+330550638520160
ENST00000376279PCCAchr13100861717+ENST00000397601MBNL2chr1397986530+4289706641617517
ENST00000376279PCCAchr13100861717+ENST00000343600MBNL2chr1397986530+4288706641617517
ENST00000376279PCCAchr13100861717+ENST00000345429MBNL2chr1397986530+4420706641635523
ENST00000376279PCCAchr13100861717+ENST00000376673MBNL2chr1397986530+4325706641653529
ENST00000376279PCCAchr13100861717+ENST00000445661MBNL2chr1397986530+1317706641152362
ENST00000376286PCCAchr13100861717+ENST00000397601MBNL2chr1397986530+4211628641539491
ENST00000376286PCCAchr13100861717+ENST00000343600MBNL2chr1397986530+4210628641539491
ENST00000376286PCCAchr13100861717+ENST00000345429MBNL2chr1397986530+4342628641557497
ENST00000376286PCCAchr13100861717+ENST00000376673MBNL2chr1397986530+4247628641575503
ENST00000376286PCCAchr13100861717+ENST00000445661MBNL2chr1397986530+1239628641074336
ENST00000376285PCCAchr13100861717+ENST00000397601MBNL2chr1397986530+4221638381549503
ENST00000376285PCCAchr13100861717+ENST00000343600MBNL2chr1397986530+4220638381549503
ENST00000376285PCCAchr13100861717+ENST00000345429MBNL2chr1397986530+4352638381567509
ENST00000376285PCCAchr13100861717+ENST00000376673MBNL2chr1397986530+4257638381585515
ENST00000376285PCCAchr13100861717+ENST00000445661MBNL2chr1397986530+1249638381084348
ENST00000376279PCCAchr13100861717+ENST00000397601MBNL2chr1397986529+4289706641617517
ENST00000376279PCCAchr13100861717+ENST00000343600MBNL2chr1397986529+4288706641617517
ENST00000376279PCCAchr13100861717+ENST00000345429MBNL2chr1397986529+4420706641635523
ENST00000376279PCCAchr13100861717+ENST00000376673MBNL2chr1397986529+4325706641653529
ENST00000376279PCCAchr13100861717+ENST00000445661MBNL2chr1397986529+1317706641152362
ENST00000376286PCCAchr13100861717+ENST00000397601MBNL2chr1397986529+4211628641539491
ENST00000376286PCCAchr13100861717+ENST00000343600MBNL2chr1397986529+4210628641539491
ENST00000376286PCCAchr13100861717+ENST00000345429MBNL2chr1397986529+4342628641557497
ENST00000376286PCCAchr13100861717+ENST00000376673MBNL2chr1397986529+4247628641575503
ENST00000376286PCCAchr13100861717+ENST00000445661MBNL2chr1397986529+1239628641074336
ENST00000376285PCCAchr13100861717+ENST00000397601MBNL2chr1397986529+4221638381549503
ENST00000376285PCCAchr13100861717+ENST00000343600MBNL2chr1397986529+4220638381549503
ENST00000376285PCCAchr13100861717+ENST00000345429MBNL2chr1397986529+4352638381567509
ENST00000376285PCCAchr13100861717+ENST00000376673MBNL2chr1397986529+4257638381585515
ENST00000376285PCCAchr13100861717+ENST00000445661MBNL2chr1397986529+1249638381084348

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
ENST00000376279ENST00000343600PCCAchr13100809594+MBNL2chr1398043576+0.0014469960.998553
ENST00000376279ENST00000345429PCCAchr13100809594+MBNL2chr1398043576+0.0014087930.99859124
ENST00000376286ENST00000343600PCCAchr13100809594+MBNL2chr1398043576+0.0025890030.99741095
ENST00000376286ENST00000345429PCCAchr13100809594+MBNL2chr1398043576+0.0025006620.9974993
ENST00000376285ENST00000343600PCCAchr13100809594+MBNL2chr1398043576+0.0014872440.9985128
ENST00000376285ENST00000345429PCCAchr13100809594+MBNL2chr1398043576+0.0014476490.9985524
ENST00000376279ENST00000397601PCCAchr13100861717+MBNL2chr1397986530+0.0003158380.9996842
ENST00000376279ENST00000343600PCCAchr13100861717+MBNL2chr1397986530+0.0003152510.9996848
ENST00000376279ENST00000345429PCCAchr13100861717+MBNL2chr1397986530+0.0004047350.9995952
ENST00000376279ENST00000376673PCCAchr13100861717+MBNL2chr1397986530+0.0003201690.9996798
ENST00000376279ENST00000445661PCCAchr13100861717+MBNL2chr1397986530+0.0019833360.9980167
ENST00000376286ENST00000397601PCCAchr13100861717+MBNL2chr1397986530+0.0002318940.9997681
ENST00000376286ENST00000343600PCCAchr13100861717+MBNL2chr1397986530+0.0002314880.99976856
ENST00000376286ENST00000345429PCCAchr13100861717+MBNL2chr1397986530+0.0003650550.999635
ENST00000376286ENST00000376673PCCAchr13100861717+MBNL2chr1397986530+0.0002632190.9997367
ENST00000376286ENST00000445661PCCAchr13100861717+MBNL2chr1397986530+0.00274450.9972555
ENST00000376285ENST00000397601PCCAchr13100861717+MBNL2chr1397986530+0.0003141820.9996859
ENST00000376285ENST00000343600PCCAchr13100861717+MBNL2chr1397986530+0.0003143160.99968565
ENST00000376285ENST00000345429PCCAchr13100861717+MBNL2chr1397986530+0.0004053880.9995946
ENST00000376285ENST00000376673PCCAchr13100861717+MBNL2chr1397986530+0.0003170780.9996829
ENST00000376285ENST00000445661PCCAchr13100861717+MBNL2chr1397986530+0.001963810.9980362
ENST00000376279ENST00000397601PCCAchr13100861717+MBNL2chr1397986529+0.0003158380.9996842
ENST00000376279ENST00000343600PCCAchr13100861717+MBNL2chr1397986529+0.0003152510.9996848
ENST00000376279ENST00000345429PCCAchr13100861717+MBNL2chr1397986529+0.0004047350.9995952
ENST00000376279ENST00000376673PCCAchr13100861717+MBNL2chr1397986529+0.0003201690.9996798
ENST00000376279ENST00000445661PCCAchr13100861717+MBNL2chr1397986529+0.0019833360.9980167
ENST00000376286ENST00000397601PCCAchr13100861717+MBNL2chr1397986529+0.0002318940.9997681
ENST00000376286ENST00000343600PCCAchr13100861717+MBNL2chr1397986529+0.0002314880.99976856
ENST00000376286ENST00000345429PCCAchr13100861717+MBNL2chr1397986529+0.0003650550.999635
ENST00000376286ENST00000376673PCCAchr13100861717+MBNL2chr1397986529+0.0002632190.9997367
ENST00000376286ENST00000445661PCCAchr13100861717+MBNL2chr1397986529+0.00274450.9972555
ENST00000376285ENST00000397601PCCAchr13100861717+MBNL2chr1397986529+0.0003141820.9996859
ENST00000376285ENST00000343600PCCAchr13100861717+MBNL2chr1397986529+0.0003143160.99968565
ENST00000376285ENST00000345429PCCAchr13100861717+MBNL2chr1397986529+0.0004053880.9995946
ENST00000376285ENST00000376673PCCAchr13100861717+MBNL2chr1397986529+0.0003170780.9996829
ENST00000376285ENST00000445661PCCAchr13100861717+MBNL2chr1397986529+0.001963810.9980362

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 PCCA-MBNL2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PCCAchr13100861717MBNL2chr1397986529628188EVNTIPGFDGVVKGRCSRENCKYLHP
PCCAchr13100861717MBNL2chr1397986529638200EVNTIPGFDGVVKGRCSRENCKYLHP
PCCAchr13100861717MBNL2chr1397986529706214EVNTIPGFDGVVKGRCSRENCKYLHP
PCCAchr13100861717MBNL2chr1397986530628188EVNTIPGFDGVVKGRCSRENCKYLHP
PCCAchr13100861717MBNL2chr1397986530638200EVNTIPGFDGVVKGRCSRENCKYLHP
PCCAchr13100861717MBNL2chr1397986530706214EVNTIPGFDGVVKGRCSRENCKYLHP

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Potential FusionNeoAntigen Information of PCCA-MBNL2 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.
PCCA-MBNL2_100861717_97986529.msa

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)
PCCA-MBNL2chr13100861717chr1397986529706HLA-A31:02GVVKGRCSR0.77260.5123918

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Potential FusionNeoAntigen Information of PCCA-MBNL2 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 PCCA-MBNL2

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.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
2767GFDGVVKGRCSRENPCCAMBNL2chr13100861717chr1397986529706

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PCCA-MBNL2

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
HLA-B14:023BVN2767GFDGVVKGRCSREN-7.9962-8.1096
HLA-B14:023BVN2767GFDGVVKGRCSREN-5.70842-6.74372
HLA-B52:013W392767GFDGVVKGRCSREN-6.83737-6.95077
HLA-B52:013W392767GFDGVVKGRCSREN-4.4836-5.5189
HLA-A11:014UQ22767GFDGVVKGRCSREN-10.0067-10.1201
HLA-A11:014UQ22767GFDGVVKGRCSREN-9.03915-10.0745
HLA-A24:025HGA2767GFDGVVKGRCSREN-6.56204-6.67544
HLA-A24:025HGA2767GFDGVVKGRCSREN-5.42271-6.45801
HLA-B44:053DX82767GFDGVVKGRCSREN-7.85648-8.89178
HLA-B44:053DX82767GFDGVVKGRCSREN-5.3978-5.5112
HLA-A02:016TDR2767GFDGVVKGRCSREN-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PCCA-MBNL2

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
PCCA-MBNL2chr13100861717chr1397986529918GVVKGRCSRGGAGTAGTCAAGGGCCGTTGTTCGAGA

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 PCCA-MBNL2

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
OVPCCA-MBNL2chr13100861717ENST00000376279chr1397986529ENST00000343600TCGA-09-1673

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Potential target of CAR-T therapy development for PCCA-MBNL2

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 PCCA-MBNL2

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 PCCA-MBNL2

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