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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:CTNND1-WDR5

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CTNND1-WDR5
FusionPDB ID: 20385
FusionGDB2.0 ID: 20385
HgeneTgene
Gene symbol

CTNND1

WDR5

Gene ID

100528016

11091

Gene nameTMX2-CTNND1 readthrough (NMD candidate)WD repeat domain 5
SynonymsCAS|CTNND1|p120(cas)|p120(ctn)BIG-3|CFAP89|SWD3
Cytomap

11q12.1

9q34.2

Type of genencRNAprotein-coding
DescriptionCadherin-associated Src substrateCatenin delta-1TMX2-CTNND1 readthrough (non-protein coding)p120 cateninWD repeat-containing protein 5BMP2-induced 3-kb gene proteinSWD3, Set1c WD40 repeat protein, homologcilia and flagella associated protein 89
Modification date2020031320200327
UniProtAcc

O60716

Main function of 5'-partner protein: FUNCTION: Key regulator of cell-cell adhesion that associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability (PubMed:14610055, PubMed:20371349). Beside cell-cell adhesion, regulates gene transcription through several transcription factors including ZBTB33/Kaiso2 and GLIS2, and the activity of Rho family GTPases and downstream cytoskeletal dynamics (PubMed:10207085, PubMed:20371349). Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors (PubMed:17344476). {ECO:0000269|PubMed:10207085, ECO:0000269|PubMed:14610055, ECO:0000269|PubMed:17344476, ECO:0000269|PubMed:20371349}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000358694, ENST00000360682, 
ENST00000361332, ENST00000361391, 
ENST00000361796, ENST00000399039, 
ENST00000399050, ENST00000415361, 
ENST00000426142, ENST00000428599, 
ENST00000524630, ENST00000525902, 
ENST00000526357, ENST00000526772, 
ENST00000526938, ENST00000527467, 
ENST00000528232, ENST00000528621, 
ENST00000529526, ENST00000529873, 
ENST00000529919, ENST00000529986, 
ENST00000530094, ENST00000530748, 
ENST00000531014, ENST00000532245, 
ENST00000532463, ENST00000532649, 
ENST00000532787, ENST00000532844, 
ENST00000533667, ENST00000534579, 
ENST00000358625, ENST00000425041, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score29 X 18 X 15=78304 X 5 X 3=60
# samples 355
** MAII scorelog2(35/7830*10)=-4.48358548034607
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/60*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CTNND1 [Title/Abstract] AND WDR5 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CTNND1 [Title/Abstract] AND WDR5 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CTNND1(57582972)-WDR5(137005824), # samples:1
Anticipated loss of major functional domain due to fusion event.CTNND1-WDR5 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.
CTNND1-WDR5 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
TgeneWDR5

GO:0043966

histone H3 acetylation

18838386

TgeneWDR5

GO:0043981

histone H4-K5 acetylation

20018852

TgeneWDR5

GO:0043982

histone H4-K8 acetylation

20018852

TgeneWDR5

GO:0043984

histone H4-K16 acetylation

20018852

TgeneWDR5

GO:0051568

histone H3-K4 methylation

17355966|19556245

TgeneWDR5

GO:0051571

positive regulation of histone H3-K4 methylation

26324722

TgeneWDR5

GO:0051572

negative regulation of histone H3-K4 methylation

26324722



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/chr11:57582972/chr9:137005824)
- 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 CTNND1 (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 WDR5 (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)
ENST00000524630CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6202330351342261237
ENST00000524630CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6205330351342261237
ENST00000529919CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6038313933140621243
ENST00000529919CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6041313933140621243
ENST00000399039CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6038313933140621243
ENST00000399039CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6041313933140621243
ENST00000360682CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6215331657142391222
ENST00000360682CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6218331657142391222
ENST00000361796CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6260336157142841237
ENST00000361796CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6263336157142841237
ENST00000361391CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6162326353641861216
ENST00000361391CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6165326353641861216
ENST00000530094CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5744284530137681155
ENST00000530094CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5747284530137681155
ENST00000428599CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6033313434440571237
ENST00000428599CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6036313434440571237
ENST00000361332CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6225332653642491237
ENST00000361332CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6228332653642491237
ENST00000527467CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+50012102683025985
ENST00000527467CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+50042102683025985
ENST00000415361CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5762286330137861161
ENST00000415361CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5765286330137861161
ENST00000532245CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5672277328636961136
ENST00000532245CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5675277328636961136
ENST00000532463CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+576628676837901240
ENST00000532463CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+576928676837901240
ENST00000528232CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5762286330137861161
ENST00000528232CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5765286330137861161
ENST00000529986CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5744284530137681155
ENST00000529986CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5747284530137681155
ENST00000531014CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+49832084683007979
ENST00000531014CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+49862084683007979
ENST00000358694CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6152325346341761237
ENST00000358694CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6155325346341761237
ENST00000526772CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+49832084683007979
ENST00000526772CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+49862084683007979
ENST00000532787CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5681278230137051134
ENST00000532787CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5684278230137051134
ENST00000533667CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+49202021682944958
ENST00000533667CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+49232021682944958
ENST00000529873CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5861296227138851204
ENST00000529873CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5864296227138851204
ENST00000525902CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+50012102683025985
ENST00000525902CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+50042102683025985
ENST00000529526CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6116321746341401225
ENST00000529526CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6119321746341401225
ENST00000532649CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6043314439040671225
ENST00000532649CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6046314439040671225
ENST00000426142CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+581729186838411257
ENST00000426142CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+582029186838411257
ENST00000532844CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5942304327139661231
ENST00000532844CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5945304327139661231
ENST00000528621CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5924302527139481225
ENST00000528621CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5927302527139481225
ENST00000399050CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+6243334453642671243
ENST00000399050CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+6246334453642671243
ENST00000526357CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5924302527139481225
ENST00000526357CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5927302527139481225
ENST00000530748CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5942304327139661231
ENST00000530748CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5945304327139661231
ENST00000534579CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+604131426440651333
ENST00000534579CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+604431426440651333
ENST00000526938CTNND1chr1157582972+ENST00000358625WDR5chr9137005824+5967306832339911222
ENST00000526938CTNND1chr1157582972+ENST00000425041WDR5chr9137005824+5970306832339911222

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
ENST00000524630ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0011820230.998818
ENST00000524630ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0011797910.99882025
ENST00000529919ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008094690.9991905
ENST00000529919ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008078970.99919206
ENST00000399039ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008094690.9991905
ENST00000399039ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008078970.99919206
ENST00000360682ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0006500210.99935
ENST00000360682ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0006486410.9993513
ENST00000361796ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0010186360.9989813
ENST00000361796ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0010165130.99898344
ENST00000361391ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0007378980.99926203
ENST00000361391ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0007363290.9992637
ENST00000530094ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008394390.9991605
ENST00000530094ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008375920.99916244
ENST00000428599ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0009144220.99908555
ENST00000428599ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0009119970.99908805
ENST00000361332ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0009724180.9990276
ENST00000361332ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0009701730.9990299
ENST00000527467ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0006470350.999353
ENST00000527467ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.000645160.9993549
ENST00000415361ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0007194480.9992805
ENST00000415361ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0007176340.9992824
ENST00000532245ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.000768420.9992316
ENST00000532245ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0007666990.99923337
ENST00000532463ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008040080.999196
ENST00000532463ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008023440.99919766
ENST00000528232ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0007194480.9992805
ENST00000528232ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0007176340.9992824
ENST00000529986ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008394390.9991605
ENST00000529986ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008375920.99916244
ENST00000531014ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0006974740.9993025
ENST00000531014ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0006954360.99930453
ENST00000358694ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0009940040.999006
ENST00000358694ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0009918210.99900824
ENST00000526772ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0006974740.9993025
ENST00000526772ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0006954360.99930453
ENST00000532787ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0006361890.99936384
ENST00000532787ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0006345160.9993655
ENST00000533667ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0007591910.9992409
ENST00000533667ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0007569560.999243
ENST00000529873ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0007592830.99924076
ENST00000529873ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0007576950.9992423
ENST00000525902ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0006470350.999353
ENST00000525902ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.000645160.9993549
ENST00000529526ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.001044020.99895597
ENST00000529526ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0010416350.99895835
ENST00000532649ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0010728690.99892706
ENST00000532649ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0010703870.99892956
ENST00000426142ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008137550.9991862
ENST00000426142ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008121030.9991879
ENST00000532844ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008593420.9991406
ENST00000532844ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.000856930.999143
ENST00000528621ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0009872040.9990128
ENST00000528621ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0009845490.99901545
ENST00000399050ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008339420.99916613
ENST00000399050ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0008321840.9991678
ENST00000526357ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0009872040.9990128
ENST00000526357ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0009845490.99901545
ENST00000530748ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0008593420.9991406
ENST00000530748ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.000856930.999143
ENST00000534579ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0010530560.99894696
ENST00000534579ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0010506130.99894947
ENST00000526938ENST00000358625CTNND1chr1157582972+WDR5chr9137005824+0.0005816370.9994184
ENST00000526938ENST00000425041CTNND1chr1157582972+WDR5chr9137005824+0.0005804830.99941957

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 CTNND1-WDR5

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CTNND1chr1157582972WDR5chr91370058242021649DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242084670DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242102676DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242773827DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242782825DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242845846DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242863852DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242867931DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242918948DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058242962895DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243025916DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243043922DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243068913DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243134928DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243139934DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr913700582431421024DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243144916DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243217916DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243253928DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243263907DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243303928DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243316913DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243326928DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243344934DLGDMEPLKGTTPLMPTPVKPNYALK
CTNND1chr1157582972WDR5chr91370058243361928DLGDMEPLKGTTPLMPTPVKPNYALK

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Potential FusionNeoAntigen Information of CTNND1-WDR5 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.
CTNND1-WDR5_57582972_137005824.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)
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:01TPLMPTPV0.99790.84151119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:02TPLMPTPV0.99790.83041119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B08:01EPLKGTTPL0.98660.5378514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B08:09EPLKGTTPL0.97510.5113514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:08EPLKGTTPL0.97220.5133514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:03EPLKGTTPL0.9720.666514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:01EPLKGTTPL0.97150.6908514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B39:01EPLKGTTPL0.89310.8533514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:02EPLKGTTPL0.87920.7381514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:04EPLKGTTPL0.87920.7381514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B56:01TPLMPTPVKP0.9290.51121121
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:03MEPLKGTTPL0.82950.806414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:03EPLKGTTPLM0.80350.6362515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:02MEPLKGTTPL0.74680.8664414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:04MEPLKGTTPL0.74680.8664414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:04EPLKGTTPLM0.55730.7309515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:02EPLKGTTPLM0.55730.7309515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B78:01TPLMPTPV0.99780.91961119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:08TPLMPTPV0.99060.76771119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B42:02EPLKGTTPL0.99350.5563514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B42:01EPLKGTTPL0.99080.5462514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B39:09EPLKGTTPL0.91160.5995514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B39:10EPLKGTTPL0.9090.8392514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B14:03EPLKGTTPL0.90330.7399514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:12EPLKGTTPL0.87920.7381514
CTNND1-WDR5chr1157582972chr91370058243253HLA-C01:17TTPLMPTPV0.59380.97371019
CTNND1-WDR5chr1157582972chr91370058243253HLA-C01:30TTPLMPTPV0.47210.97741019
CTNND1-WDR5chr1157582972chr91370058243253HLA-B42:02MEPLKGTTPL0.98020.9154414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B42:01MEPLKGTTPL0.97570.9103414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B54:01TPLMPTPVKP0.97380.64941121
CTNND1-WDR5chr1157582972chr91370058243253HLA-B39:10MEPLKGTTPL0.93390.957414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B42:02EPLKGTTPLM0.87580.6147515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:12MEPLKGTTPL0.74680.8664414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:12EPLKGTTPLM0.55730.7309515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B39:10EPLKGTTPLM0.51730.839515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B78:02TPLMPTPV0.99830.93541119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:13TPLMPTPV0.99770.82011119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:14TPLMPTPV0.99770.72291119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:21TPLMPTPV0.99640.79571119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B56:05TPLMPTPV0.99560.76811119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:29TPLMPTPV0.9950.68191119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B51:09TPLMPTPV0.99490.85241119
CTNND1-WDR5chr1157582972chr91370058243253HLA-B59:01TPLMPTPV0.96250.92281119
CTNND1-WDR5chr1157582972chr91370058243253HLA-A68:02TTPLMPTPV0.99260.75791019
CTNND1-WDR5chr1157582972chr91370058243253HLA-B08:18EPLKGTTPL0.98660.5378514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:77EPLKGTTPL0.97150.6908514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:23EPLKGTTPL0.97080.6865514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:13EPLKGTTPL0.96850.6633514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:11EPLKGTTPL0.89870.818514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B67:01EPLKGTTPL0.89860.6731514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:09EPLKGTTPL0.87920.7381514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:24EPLKGTTPL0.87650.7733514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:30EPLKGTTPL0.87070.5944514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:17EPLKGTTPL0.87070.5944514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B08:12EPLKGTTPL0.78760.6355514
CTNND1-WDR5chr1157582972chr91370058243253HLA-C01:02TTPLMPTPV0.60760.97351019
CTNND1-WDR5chr1157582972chr91370058243253HLA-C01:03TTPLMPTPV0.54850.97911019
CTNND1-WDR5chr1157582972chr91370058243253HLA-B18:07EPLKGTTPL0.10090.6891514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:43EPLKGTTPL0.05350.6485514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B15:08EPLKGTTPL0.03350.6374514
CTNND1-WDR5chr1157582972chr91370058243253HLA-B67:01MEPLKGTTPL0.94440.7908414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B55:02TPLMPTPVKP0.92260.53821121
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:09MEPLKGTTPL0.74680.8664414
CTNND1-WDR5chr1157582972chr91370058243253HLA-B35:09EPLKGTTPLM0.55730.7309515
CTNND1-WDR5chr1157582972chr91370058243253HLA-B67:01EPLKGTTPLM0.50310.6592515

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Potential FusionNeoAntigen Information of CTNND1-WDR5 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 CTNND1-WDR5

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
6767PLKGTTPLMPTPVKCTNND1WDR5chr1157582972chr91370058243253

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CTNND1-WDR5

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-B14:023BVN6767PLKGTTPLMPTPVK-7.9962-8.1096
HLA-B14:023BVN6767PLKGTTPLMPTPVK-5.70842-6.74372
HLA-B52:013W396767PLKGTTPLMPTPVK-6.83737-6.95077
HLA-B52:013W396767PLKGTTPLMPTPVK-4.4836-5.5189
HLA-A11:014UQ26767PLKGTTPLMPTPVK-10.0067-10.1201
HLA-A11:014UQ26767PLKGTTPLMPTPVK-9.03915-10.0745
HLA-A24:025HGA6767PLKGTTPLMPTPVK-6.56204-6.67544
HLA-A24:025HGA6767PLKGTTPLMPTPVK-5.42271-6.45801
HLA-B44:053DX86767PLKGTTPLMPTPVK-7.85648-8.89178
HLA-B44:053DX86767PLKGTTPLMPTPVK-5.3978-5.5112
HLA-A02:016TDR6767PLKGTTPLMPTPVK-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of CTNND1-WDR5

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
CTNND1-WDR5chr1157582972chr91370058241019TTPLMPTPVCCCTTGATGCCTACACCTGTGAAGCCA
CTNND1-WDR5chr1157582972chr91370058241119TPLMPTPVTTGATGCCTACACCTGTGAAGCCA
CTNND1-WDR5chr1157582972chr91370058241121TPLMPTPVKPTTGATGCCTACACCTGTGAAGCCAAACTAT
CTNND1-WDR5chr1157582972chr9137005824414MEPLKGTTPLCCATTGAAGGGAACAACACCCTTGATGCCT
CTNND1-WDR5chr1157582972chr9137005824514EPLKGTTPLTTGAAGGGAACAACACCCTTGATGCCT
CTNND1-WDR5chr1157582972chr9137005824515EPLKGTTPLMTTGAAGGGAACAACACCCTTGATGCCTACA

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 CTNND1-WDR5

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
Non-CancerCTNND1-WDR5chr1157582972ENST00000358694chr9137005824ENST0000035862561N

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Potential target of CAR-T therapy development for CTNND1-WDR5

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 CTNND1-WDR5

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 CTNND1-WDR5

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