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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:ABHD12-PPP2R2A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ABHD12-PPP2R2A
FusionPDB ID: 379
FusionGDB2.0 ID: 379
HgeneTgene
Gene symbol

ABHD12

PPP2R2A

Gene ID

26090

5520

Gene nameabhydrolase domain containing 12, lysophospholipaseprotein phosphatase 2 regulatory subunit Balpha
SynonymsABHD12A|BEM46L2|C20orf22|PHARC|dJ965G21.2|hABHD12B55A|B55ALPHA|PR52A|PR55A|PR55alpha
Cytomap

20p11.21

8p21.2

Type of geneprotein-codingprotein-coding
Descriptionlysophosphatidylserine lipase ABHD122-arachidonoylglycerol hydrolase2-arachidonoylglycerol hydrolase ABHD12abhydrolase domain containing 12abhydrolase domain-containing protein 12monoacylglycerol lipase ABHD12oxidized phosphatidylserine lipase ABHD1serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoformprotein phosphatase 2, regulatory subunit B, alpha
Modification date2020031320200327
UniProtAcc

Q7Z5M8

Main function of 5'-partner protein:
.
Ensembl transtripts involved in fusion geneENST idsENST00000339157, ENST00000376542, 
ENST00000481556, 
ENST00000523473, 
ENST00000315985, ENST00000380737, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 8 X 6=5288 X 13 X 5=520
# samples 1313
** MAII scorelog2(13/528*10)=-2.02202630633
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/520*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ABHD12 [Title/Abstract] AND PPP2R2A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ABHD12 [Title/Abstract] AND PPP2R2A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ABHD12(25295561)-PPP2R2A(26196406), # samples:2
Anticipated loss of major functional domain due to fusion event.ABHD12-PPP2R2A 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.
ABHD12-PPP2R2A 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
HgeneABHD12

GO:0006660

phosphatidylserine catabolic process

30643283

HgeneABHD12

GO:0009395

phospholipid catabolic process

30237167

HgeneABHD12

GO:0046464

acylglycerol catabolic process

22969151

HgeneABHD12

GO:0046475

glycerophospholipid catabolic process

25290914

HgeneABHD12

GO:0052651

monoacylglycerol catabolic process

25290914|30237167

TgenePPP2R2A

GO:0006470

protein dephosphorylation

1849734



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/chr20:25295561/chr8:26196406)
- 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 ABHD12 (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 PPP2R2A (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)
ENST00000376542ABHD12chr2025295561-ENST00000380737PPP2R2Achr826196406+44288991992160653
ENST00000376542ABHD12chr2025295561-ENST00000315985PPP2R2Achr826196406+26348991992160653
ENST00000339157ABHD12chr2025295561-ENST00000380737PPP2R2Achr826196406+44218921922153653
ENST00000339157ABHD12chr2025295561-ENST00000315985PPP2R2Achr826196406+26278921922153653
ENST00000376542ABHD12chr2025295560-ENST00000380737PPP2R2Achr826196405+44288991992160653
ENST00000376542ABHD12chr2025295560-ENST00000315985PPP2R2Achr826196405+26348991992160653
ENST00000339157ABHD12chr2025295560-ENST00000380737PPP2R2Achr826196405+44218921922153653
ENST00000339157ABHD12chr2025295560-ENST00000315985PPP2R2Achr826196405+26278921922153653

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
ENST00000376542ENST00000380737ABHD12chr2025295561-PPP2R2Achr826196406+0.0005447760.9994553
ENST00000376542ENST00000315985ABHD12chr2025295561-PPP2R2Achr826196406+0.0012810470.998719
ENST00000339157ENST00000380737ABHD12chr2025295561-PPP2R2Achr826196406+0.0005446470.9994554
ENST00000339157ENST00000315985ABHD12chr2025295561-PPP2R2Achr826196406+0.0012694130.9987306
ENST00000376542ENST00000380737ABHD12chr2025295560-PPP2R2Achr826196405+0.0005447760.9994553
ENST00000376542ENST00000315985ABHD12chr2025295560-PPP2R2Achr826196405+0.0012810470.998719
ENST00000339157ENST00000380737ABHD12chr2025295560-PPP2R2Achr826196405+0.0005446470.9994554
ENST00000339157ENST00000315985ABHD12chr2025295560-PPP2R2Achr826196405+0.0012694130.9987306

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 ABHD12-PPP2R2A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ABHD12chr2025295560PPP2R2Achr826196405892231VLSSLGYHVVTFDYRADIISTVEFNH
ABHD12chr2025295560PPP2R2Achr826196405899231VLSSLGYHVVTFDYRADIISTVEFNH
ABHD12chr2025295561PPP2R2Achr826196406892231VLSSLGYHVVTFDYRADIISTVEFNH
ABHD12chr2025295561PPP2R2Achr826196406899231VLSSLGYHVVTFDYRADIISTVEFNH

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Potential FusionNeoAntigen Information of ABHD12-PPP2R2A 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.
ABHD12-PPP2R2A_25295560_26196405.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)
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-B15:18YHVVTFDY0.94220.6782614
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C04:10TFDYRADII0.99330.58471019
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C04:07TFDYRADII0.9920.61071019
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C04:14TFDYRADII0.56720.64931019
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-B73:01DYRADIISTV0.90210.75421222
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C04:01TFDYRADII0.9920.61071019
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C18:01TFDYRADII0.99110.63551019
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C06:08FDYRADIISTV0.99290.9961122
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C06:02FDYRADIISTV0.98480.99691122
ABHD12-PPP2R2Achr2025295560chr826196405892HLA-C06:17FDYRADIISTV0.98480.99691122

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Potential FusionNeoAntigen Information of ABHD12-PPP2R2A 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.
ABHD12-PPP2R2A_25295560_26196405.msa

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)
ABHD12-PPP2R2Achr2025295560chr826196405892DRB1-0338TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0101TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0101VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0104TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0104VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0105TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0105VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0108TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0108VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0109TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0109VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0109VVTFDYRADIISTVE823
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0111TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0111VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0112TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0112VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0113TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0113VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0114TFDYRADIISTVEFN1025
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0114VTFDYRADIISTVEF924
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0114VVTFDYRADIISTVE823
ABHD12-PPP2R2Achr2025295560chr826196405892DRB3-0303TFDYRADIISTVEFN1025

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Fusion breakpoint peptide structures of ABHD12-PPP2R2A

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
10666YHVVTFDYRADIISABHD12PPP2R2Achr2025295560chr826196405892

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ABHD12-PPP2R2A

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-B14:023BVN10666YHVVTFDYRADIIS-5.8104-6.0039
HLA-B14:023BVN10666YHVVTFDYRADIIS-2.46474-3.22184
HLA-B52:013W3910666YHVVTFDYRADIIS-4.96909-5.16259
HLA-B52:013W3910666YHVVTFDYRADIIS-2.83438-3.59148
HLA-A24:025HGA10666YHVVTFDYRADIIS-4.92647-5.11997
HLA-A24:025HGA10666YHVVTFDYRADIIS-1.97102-2.72812
HLA-B44:053DX810666YHVVTFDYRADIIS-4.85277-5.04627
HLA-B44:053DX810666YHVVTFDYRADIIS-2.80218-3.55928

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Vaccine Design for the FusionNeoAntigens of ABHD12-PPP2R2A

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
ABHD12-PPP2R2Achr2025295560chr8261964051019TFDYRADIIACTACAGAGCAGATATAATTTCTACAG
ABHD12-PPP2R2Achr2025295560chr8261964051122FDYRADIISTVACAGAGCAGATATAATTTCTACAGTAGAATTTA
ABHD12-PPP2R2Achr2025295560chr8261964051222DYRADIISTVGAGCAGATATAATTTCTACAGTAGAATTTA
ABHD12-PPP2R2Achr2025295560chr826196405614YHVVTFDYTGGTCACCTTTGACTACAGAGCAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ABHD12-PPP2R2Achr2025295560chr8261964051025TFDYRADIISTVEFNACTACAGAGCAGATATAATTTCTACAGTAGAATTTAATCATTCTG
ABHD12-PPP2R2Achr2025295560chr826196405823VVTFDYRADIISTVECCTTTGACTACAGAGCAGATATAATTTCTACAGTAGAATTTAATC
ABHD12-PPP2R2Achr2025295560chr826196405924VTFDYRADIISTVEFTTGACTACAGAGCAGATATAATTTCTACAGTAGAATTTAATCATT

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Information of the samples that have these potential fusion neoantigens of ABHD12-PPP2R2A

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
COADABHD12-PPP2R2Achr2025295560ENST00000339157chr826196405ENST00000315985TCGA-CM-5860

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Potential target of CAR-T therapy development for ABHD12-PPP2R2A

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
HgeneABHD12chr20:25295560chr8:26196405ENST00000339157-61375_95206399.0TransmembraneHelical
HgeneABHD12chr20:25295560chr8:26196405ENST00000376542-61375_95206405.0TransmembraneHelical
HgeneABHD12chr20:25295561chr8:26196406ENST00000339157-61375_95206399.0TransmembraneHelical
HgeneABHD12chr20:25295561chr8:26196406ENST00000376542-61375_95206405.0TransmembraneHelical

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 ABHD12-PPP2R2A

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 ABHD12-PPP2R2A

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