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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:PPP6R3-YAP1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PPP6R3-YAP1
FusionPDB ID: 68322
FusionGDB2.0 ID: 68322
HgeneTgene
Gene symbol

PPP6R3

YAP1

Gene ID

55291

10413

Gene nameprotein phosphatase 6 regulatory subunit 3Yes1 associated transcriptional regulator
SynonymsC11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3COB1|YAP|YAP2|YAP65|YKI
Cytomap

11q13.2

11q22.1

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 6 regulatory subunit 3SAPS domain family, member 3sporulation-induced transcript 4-associated protein SAPLtranscriptional coactivator YAP165 kDa Yes-associated proteinYes associated protein 1protein yorkie homologyes-associated protein 1yes-associated protein 2yes-associated protein YAP65 homologyorkie homolog
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000265636, ENST00000265637, 
ENST00000393799, ENST00000393800, 
ENST00000393801, ENST00000524845, 
ENST00000524904, ENST00000527403, 
ENST00000529710, ENST00000530427, 
ENST00000534534, 		ENST00000528834, 
ENST00000282441, ENST00000345877, 
ENST00000524575, ENST00000526343, 
ENST00000531439, ENST00000537274, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score34 X 21 X 15=1071020 X 10 X 13=2600
# samples 4321
** MAII scorelog2(43/10710*10)=-4.63847801004816
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/2600*10)=-3.63005039024969
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PPP6R3 [Title/Abstract] AND YAP1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PPP6R3 [Title/Abstract] AND YAP1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PPP6R3(68326147)-YAP1(102098200), # samples:3
Anticipated loss of major functional domain due to fusion event.PPP6R3-YAP1 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.
PPP6R3-YAP1 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.
PPP6R3-YAP1 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.
PPP6R3-YAP1 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
HgenePPP6R3

GO:0043666

regulation of phosphoprotein phosphatase activity

16716191

TgeneYAP1

GO:0006974

cellular response to DNA damage stimulus

18280240

TgeneYAP1

GO:0008283

cell proliferation

17974916

TgeneYAP1

GO:0032570

response to progesterone

16772533

TgeneYAP1

GO:0033148

positive regulation of intracellular estrogen receptor signaling pathway

16772533

TgeneYAP1

GO:0045893

positive regulation of transcription, DNA-templated

20368466

TgeneYAP1

GO:0045944

positive regulation of transcription by RNA polymerase II

25796446

TgeneYAP1

GO:0050767

regulation of neurogenesis

25433207

TgeneYAP1

GO:0050847

progesterone receptor signaling pathway

16772533

TgeneYAP1

GO:0060242

contact inhibition

17974916

TgeneYAP1

GO:0065003

protein-containing complex assembly

20368466

TgeneYAP1

GO:0071480

cellular response to gamma radiation

18280240

TgeneYAP1

GO:0072091

regulation of stem cell proliferation

25433207



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/chr11:68326147/chr11:102098200)
- 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 PPP6R3 (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 YAP1 (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)
ENST00000393799PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+211611122671463398
ENST00000393799PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+494711122671463398
ENST00000393799PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+494711122671463398
ENST00000393799PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+494711122671463398
ENST00000393799PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+148711122671463398
ENST00000393799PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+167611122671463398
ENST00000393800PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+210310992541450398
ENST00000393800PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+493410992541450398
ENST00000393800PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+493410992541450398
ENST00000393800PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+493410992541450398
ENST00000393800PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+147410992541450398
ENST00000393800PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+166310992541450398
ENST00000524845PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+208510812361432398
ENST00000524845PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+491610812361432398
ENST00000524845PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+491610812361432398
ENST00000524845PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+491610812361432398
ENST00000524845PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+145610812361432398
ENST00000524845PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+164510812361432398
ENST00000265637PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+1931927821278398
ENST00000265637PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+4762927821278398
ENST00000265637PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+4762927821278398
ENST00000265637PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+4762927821278398
ENST00000265637PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+1302927821278398
ENST00000265637PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+1491927821278398
ENST00000524904PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+207910752301426398
ENST00000524904PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+491010752301426398
ENST00000524904PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+491010752301426398
ENST00000524904PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+491010752301426398
ENST00000524904PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+145010752301426398
ENST00000524904PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+163910752301426398
ENST00000393801PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+206410602151411398
ENST00000393801PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+489510602151411398
ENST00000393801PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+489510602151411398
ENST00000393801PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+489510602151411398
ENST00000393801PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+143510602151411398
ENST00000393801PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+162410602151411398
ENST00000265636PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+212611222771473398
ENST00000265636PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+495711222771473398
ENST00000265636PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+495711222771473398
ENST00000265636PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+495711222771473398
ENST00000265636PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+149711222771473398
ENST00000265636PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+168611222771473398
ENST00000529710PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+212611222771473398
ENST00000529710PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+495711222771473398
ENST00000529710PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+495711222771473398
ENST00000529710PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+495711222771473398
ENST00000529710PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+149711222771473398
ENST00000529710PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+168611222771473398
ENST00000527403PPP6R3chr1168326147+ENST00000526343YAP1chr11102098200+20019971521348398
ENST00000527403PPP6R3chr1168326147+ENST00000282441YAP1chr11102098200+48329971521348398
ENST00000527403PPP6R3chr1168326147+ENST00000537274YAP1chr11102098200+48329971521348398
ENST00000527403PPP6R3chr1168326147+ENST00000345877YAP1chr11102098200+48329971521348398
ENST00000527403PPP6R3chr1168326147+ENST00000531439YAP1chr11102098200+13729971521348398
ENST00000527403PPP6R3chr1168326147+ENST00000524575YAP1chr11102098200+15619971521348398

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
ENST00000393799ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.0018795870.99812037
ENST00000393799ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002854320.99971455
ENST00000393799ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002854320.99971455
ENST00000393799ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002854320.99971455
ENST00000393799ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0053528060.9946472
ENST00000393799ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.004301330.9956987
ENST00000393800ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.0018133670.99818665
ENST00000393800ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002804820.99971944
ENST00000393800ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002804820.99971944
ENST00000393800ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002804820.99971944
ENST00000393800ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0052135040.9947865
ENST00000393800ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0042181390.9957819
ENST00000524845ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.0018972380.99810284
ENST00000524845ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002794920.9997205
ENST00000524845ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002794920.9997205
ENST00000524845ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002794920.9997205
ENST00000524845ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0057969370.99420303
ENST00000524845ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0046446510.99535537
ENST00000265637ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.0022320570.9977679
ENST00000265637ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002806890.9997193
ENST00000265637ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002806890.9997193
ENST00000265637ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002806890.9997193
ENST00000265637ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0088005290.99119943
ENST00000265637ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0066445490.9933555
ENST00000524904ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.0019124550.99808747
ENST00000524904ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002811320.99971884
ENST00000524904ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002811320.99971884
ENST00000524904ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002811320.99971884
ENST00000524904ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0058994350.9941005
ENST00000524904ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0047221710.9952779
ENST00000393801ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.0020337190.9979663
ENST00000393801ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002853670.99971455
ENST00000393801ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002853670.99971455
ENST00000393801ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002853670.99971455
ENST00000393801ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.006421570.99357843
ENST00000393801ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.005038590.9949614
ENST00000265636ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.001853580.9981464
ENST00000265636ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002886930.99971133
ENST00000265636ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002886930.99971133
ENST00000265636ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002886930.99971133
ENST00000265636ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0053744260.9946255
ENST00000265636ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0044361930.99556386
ENST00000529710ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.001853580.9981464
ENST00000529710ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002886930.99971133
ENST00000529710ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002886930.99971133
ENST00000529710ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002886930.99971133
ENST00000529710ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0053744260.9946255
ENST00000529710ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0044361930.99556386
ENST00000527403ENST00000526343PPP6R3chr1168326147+YAP1chr11102098200+0.001959690.9980404
ENST00000527403ENST00000282441PPP6R3chr1168326147+YAP1chr11102098200+0.0002822990.99971765
ENST00000527403ENST00000537274PPP6R3chr1168326147+YAP1chr11102098200+0.0002822990.99971765
ENST00000527403ENST00000345877PPP6R3chr1168326147+YAP1chr11102098200+0.0002822990.99971765
ENST00000527403ENST00000531439PPP6R3chr1168326147+YAP1chr11102098200+0.0063444020.99365556
ENST00000527403ENST00000524575PPP6R3chr1168326147+YAP1chr11102098200+0.0048847450.9951153

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 PPP6R3-YAP1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PPP6R3chr1168326147YAP1chr111020982001060282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr111020982001075282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr111020982001081282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr111020982001099282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr111020982001112282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr111020982001122282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr11102098200927282QILLTLLETRRPTGTYHSRDESTDSG
PPP6R3chr1168326147YAP1chr11102098200997282QILLTLLETRRPTGTYHSRDESTDSG

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Potential FusionNeoAntigen Information of PPP6R3-YAP1 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.
PPP6R3-YAP1_68326147_102098200.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)
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:18TRRPTGTY0.92640.6775816
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:02ETRRPTGTY0.87760.7853716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-C07:46TRRPTGTY0.95590.8801816
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:68TRRPTGTY0.89240.577816
PPP6R3-YAP1chr1168326147chr111020982001122HLA-A25:01ETRRPTGTY0.98890.6821716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B35:11ETRRPTGTY0.86610.7394716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:11ETRRPTGTY0.83190.6457716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:08ETRRPTGTY0.82650.6386716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B35:43ETRRPTGTY0.78190.6392716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:12ETRRPTGTY0.44750.7467716
PPP6R3-YAP1chr1168326147chr111020982001122HLA-B15:53LETRRPTGTY0.97230.6817616

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Potential FusionNeoAntigen Information of PPP6R3-YAP1 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 PPP6R3-YAP1

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
4939LETRRPTGTYHSRDPPP6R3YAP1chr1168326147chr111020982001122

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PPP6R3-YAP1

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-B14:023BVN4939LETRRPTGTYHSRD-4.69119-4.80579
HLA-B14:023BVN4939LETRRPTGTYHSRD-4.49255-5.52905
HLA-B52:013W394939LETRRPTGTYHSRD-5.18361-5.29821
HLA-B52:013W394939LETRRPTGTYHSRD-2.61311-3.64961
HLA-A11:014UQ24939LETRRPTGTYHSRD-8.7194-8.834
HLA-A11:014UQ24939LETRRPTGTYHSRD-6.92879-7.96529
HLA-A24:025HGA4939LETRRPTGTYHSRD-6.17828-6.29288
HLA-A24:025HGA4939LETRRPTGTYHSRD-4.95642-5.99292
HLA-B27:056PYJ4939LETRRPTGTYHSRD-6.04314-7.07964
HLA-B27:056PYJ4939LETRRPTGTYHSRD-5.74939-5.86399
HLA-B27:036PZ54939LETRRPTGTYHSRD-4.11233-5.14883
HLA-B44:053DX84939LETRRPTGTYHSRD-6.50138-7.53788
HLA-B44:053DX84939LETRRPTGTYHSRD-4.47086-4.58546
HLA-A02:016TDR4939LETRRPTGTYHSRD-4.72103-4.83563

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Vaccine Design for the FusionNeoAntigens of PPP6R3-YAP1

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
PPP6R3-YAP1chr1168326147chr11102098200616LETRRPTGTYACTTGAGACACGACGACCAACTGGCACCTA
PPP6R3-YAP1chr1168326147chr11102098200716ETRRPTGTYTGAGACACGACGACCAACTGGCACCTA
PPP6R3-YAP1chr1168326147chr11102098200816TRRPTGTYGACACGACGACCAACTGGCACCTA

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 PPP6R3-YAP1

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
BLCAPPP6R3-YAP1chr1168326147ENST00000265636chr11102098200ENST00000282441TCGA-BT-A20N-01A

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Potential target of CAR-T therapy development for PPP6R3-YAP1

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 PPP6R3-YAP1

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 PPP6R3-YAP1

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