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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:WIPF2-ERBB2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: WIPF2-ERBB2
FusionPDB ID: 99267
FusionGDB2.0 ID: 99267
HgeneTgene
Gene symbol

WIPF2

ERBB2

Gene ID

147179

2064

Gene nameWAS/WASL interacting protein family member 2erb-b2 receptor tyrosine kinase 2
SynonymsWICH|WIRECD340|HER-2|HER-2/neu|HER2|MLN 19|NEU|NGL|TKR1
Cytomap

17q21.2

17q12

Type of geneprotein-codingprotein-coding
DescriptionWAS/WASL-interacting protein family member 2WASP-binding proteinWASP-interacting protein-related proteinWIP- and CR16-homologous proteinWIP-related proteinreceptor tyrosine-protein kinase erbB-2c-erb B2/neu proteinherstatinhuman epidermal growth factor receptor 2metastatic lymph node gene 19 proteinneuro/glioblastoma derived oncogene homologneuroblastoma/glioblastoma derived oncogene homologp185erbB2
Modification date2020032720200329
UniProtAcc.

P04626

Main function of 5'-partner protein: FUNCTION: Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. Essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. GP30 is a potential ligand for this receptor. Regulates outgrowth and stabilization of peripheral microtubules (MTs). Upon ERBB2 activation, the MEMO1-RHOA-DIAPH1 signaling pathway elicits the phosphorylation and thus the inhibition of GSK3B at cell membrane. This prevents the phosphorylation of APC and CLASP2, allowing its association with the cell membrane. In turn, membrane-bound APC allows the localization of MACF1 to the cell membrane, which is required for microtubule capture and stabilization. {ECO:0000305}.; FUNCTION: In the nucleus is involved in transcriptional regulation. Associates with the 5'-TCAAATTC-3' sequence in the PTGS2/COX-2 promoter and activates its transcription. Implicated in transcriptional activation of CDKN1A; the function involves STAT3 and SRC. Involved in the transcription of rRNA genes by RNA Pol I and enhances protein synthesis and cell growth. {ECO:0000269|PubMed:10358079, ECO:0000269|PubMed:15380516, ECO:0000269|PubMed:21555369}.
Ensembl transtripts involved in fusion geneENST idsENST00000494757, ENST00000323571, 
ENST00000583130, ENST00000585043, 
ENST00000394103, ENST00000536600, 
ENST00000269571, ENST00000406381, 
ENST00000445658, ENST00000540042, 
ENST00000540147, ENST00000541774, 
ENST00000578199, ENST00000584450, 
ENST00000584601, ENST00000584888, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score40 X 12 X 16=768034 X 40 X 10=13600
# samples 5043
** MAII scorelog2(50/7680*10)=-3.94110631094643
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(43/13600*10)=-4.9831261814356
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: WIPF2 [Title/Abstract] AND ERBB2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: WIPF2 [Title/Abstract] AND ERBB2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ERBB2(37873733)-WIPF2(38412643), # samples:2
WIPF2(38421398)-ERBB2(37872554), # samples:2
Anticipated loss of major functional domain due to fusion event.WIPF2-ERBB2 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.
WIPF2-ERBB2 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.
WIPF2-ERBB2 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.
WIPF2-ERBB2 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
TgeneERBB2

GO:0007165

signal transduction

10572067

TgeneERBB2

GO:0007166

cell surface receptor signaling pathway

9685399

TgeneERBB2

GO:0007169

transmembrane receptor protein tyrosine kinase signaling pathway

7514177

TgeneERBB2

GO:0014065

phosphatidylinositol 3-kinase signaling

7556068

TgeneERBB2

GO:0018108

peptidyl-tyrosine phosphorylation

12000754

TgeneERBB2

GO:0032886

regulation of microtubule-based process

20937854

TgeneERBB2

GO:0035556

intracellular signal transduction

19372587

TgeneERBB2

GO:0042060

wound healing

12646923

TgeneERBB2

GO:0043406

positive regulation of MAP kinase activity

10572067

TgeneERBB2

GO:0045785

positive regulation of cell adhesion

7556068

TgeneERBB2

GO:0046777

protein autophosphorylation

7556068

TgeneERBB2

GO:0050679

positive regulation of epithelial cell proliferation

10572067

TgeneERBB2

GO:0071363

cellular response to growth factor stimulus

20010870

TgeneERBB2

GO:0090314

positive regulation of protein targeting to membrane

20010870



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/chr17:37873733/chr17:38412643)
- 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 WIPF2 (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 ERBB2 (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)
ENST00000323571WIPF2chr1738421398+ENST00000584601ERBB2chr1737872554+3782121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000406381ERBB2chr1737872554+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000541774ERBB2chr1737872554+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000445658ERBB2chr1737872554+3500121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000540147ERBB2chr1737872554+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000584450ERBB2chr1737872554+321212102402864874
ENST00000323571WIPF2chr1738421398+ENST00000269571ERBB2chr1737872554+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000578199ERBB2chr1737872554+177212102401598452
ENST00000323571WIPF2chr1738421398+ENST00000540042ERBB2chr1737872554+176812102401598452
ENST00000585043WIPF2chr1738421398+ENST00000584601ERBB2chr1737872554+3780120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000406381ERBB2chr1737872554+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000541774ERBB2chr1737872554+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000445658ERBB2chr1737872554+3498120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000540147ERBB2chr1737872554+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000584450ERBB2chr1737872554+321012082382862874
ENST00000585043WIPF2chr1738421398+ENST00000269571ERBB2chr1737872554+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000578199ERBB2chr1737872554+177012082381596452
ENST00000585043WIPF2chr1738421398+ENST00000540042ERBB2chr1737872554+176612082381596452
ENST00000583130WIPF2chr1738421398+ENST00000584601ERBB2chr1737872554+3742117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000406381ERBB2chr1737872554+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000541774ERBB2chr1737872554+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000445658ERBB2chr1737872554+3460117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000540147ERBB2chr1737872554+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000584450ERBB2chr1737872554+317211702002824874
ENST00000583130WIPF2chr1738421398+ENST00000269571ERBB2chr1737872554+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000578199ERBB2chr1737872554+173211702001558452
ENST00000583130WIPF2chr1738421398+ENST00000540042ERBB2chr1737872554+172811702001558452
ENST00000323571WIPF2chr1738421398+ENST00000584601ERBB2chr1737872553+3782121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000406381ERBB2chr1737872553+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000541774ERBB2chr1737872553+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000445658ERBB2chr1737872553+3500121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000540147ERBB2chr1737872553+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000584450ERBB2chr1737872553+321212102402864874
ENST00000323571WIPF2chr1738421398+ENST00000269571ERBB2chr1737872553+4083121024034641074
ENST00000323571WIPF2chr1738421398+ENST00000578199ERBB2chr1737872553+177212102401598452
ENST00000323571WIPF2chr1738421398+ENST00000540042ERBB2chr1737872553+176812102401598452
ENST00000585043WIPF2chr1738421398+ENST00000584601ERBB2chr1737872553+3780120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000406381ERBB2chr1737872553+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000541774ERBB2chr1737872553+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000445658ERBB2chr1737872553+3498120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000540147ERBB2chr1737872553+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000584450ERBB2chr1737872553+321012082382862874
ENST00000585043WIPF2chr1738421398+ENST00000269571ERBB2chr1737872553+4081120823834621074
ENST00000585043WIPF2chr1738421398+ENST00000578199ERBB2chr1737872553+177012082381596452
ENST00000585043WIPF2chr1738421398+ENST00000540042ERBB2chr1737872553+176612082381596452
ENST00000583130WIPF2chr1738421398+ENST00000584601ERBB2chr1737872553+3742117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000406381ERBB2chr1737872553+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000541774ERBB2chr1737872553+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000445658ERBB2chr1737872553+3460117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000540147ERBB2chr1737872553+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000584450ERBB2chr1737872553+317211702002824874
ENST00000583130WIPF2chr1738421398+ENST00000269571ERBB2chr1737872553+4043117020034241074
ENST00000583130WIPF2chr1738421398+ENST00000578199ERBB2chr1737872553+173211702001558452
ENST00000583130WIPF2chr1738421398+ENST00000540042ERBB2chr1737872553+172811702001558452

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
ENST00000323571ENST00000584601WIPF2chr1738421398+ERBB2chr1737872554+0.0019324560.99806756
ENST00000323571ENST00000406381WIPF2chr1738421398+ERBB2chr1737872554+0.0014105660.99858946
ENST00000323571ENST00000541774WIPF2chr1738421398+ERBB2chr1737872554+0.0014105660.99858946
ENST00000323571ENST00000445658WIPF2chr1738421398+ERBB2chr1737872554+0.002025010.99797505
ENST00000323571ENST00000540147WIPF2chr1738421398+ERBB2chr1737872554+0.0014105660.99858946
ENST00000323571ENST00000584450WIPF2chr1738421398+ERBB2chr1737872554+0.0045777220.9954223
ENST00000323571ENST00000269571WIPF2chr1738421398+ERBB2chr1737872554+0.0014105660.99858946
ENST00000323571ENST00000578199WIPF2chr1738421398+ERBB2chr1737872554+0.266915950.733084
ENST00000323571ENST00000540042WIPF2chr1738421398+ERBB2chr1737872554+0.266724770.73327523
ENST00000585043ENST00000584601WIPF2chr1738421398+ERBB2chr1737872554+0.0019149450.998085
ENST00000585043ENST00000406381WIPF2chr1738421398+ERBB2chr1737872554+0.0013969880.99860305
ENST00000585043ENST00000541774WIPF2chr1738421398+ERBB2chr1737872554+0.0013969880.99860305
ENST00000585043ENST00000445658WIPF2chr1738421398+ERBB2chr1737872554+0.001994050.9980059
ENST00000585043ENST00000540147WIPF2chr1738421398+ERBB2chr1737872554+0.0013969880.99860305
ENST00000585043ENST00000584450WIPF2chr1738421398+ERBB2chr1737872554+0.0045082470.9954918
ENST00000585043ENST00000269571WIPF2chr1738421398+ERBB2chr1737872554+0.0013969880.99860305
ENST00000585043ENST00000578199WIPF2chr1738421398+ERBB2chr1737872554+0.266248760.73375124
ENST00000585043ENST00000540042WIPF2chr1738421398+ERBB2chr1737872554+0.26601920.73398083
ENST00000583130ENST00000584601WIPF2chr1738421398+ERBB2chr1737872554+0.001548950.998451
ENST00000583130ENST00000406381WIPF2chr1738421398+ERBB2chr1737872554+0.0012169150.99878305
ENST00000583130ENST00000541774WIPF2chr1738421398+ERBB2chr1737872554+0.0012169150.99878305
ENST00000583130ENST00000445658WIPF2chr1738421398+ERBB2chr1737872554+0.0016038510.9983961
ENST00000583130ENST00000540147WIPF2chr1738421398+ERBB2chr1737872554+0.0012169150.99878305
ENST00000583130ENST00000584450WIPF2chr1738421398+ERBB2chr1737872554+0.003859890.99614006
ENST00000583130ENST00000269571WIPF2chr1738421398+ERBB2chr1737872554+0.0012169150.99878305
ENST00000583130ENST00000578199WIPF2chr1738421398+ERBB2chr1737872554+0.24716590.7528341
ENST00000583130ENST00000540042WIPF2chr1738421398+ERBB2chr1737872554+0.246322590.75367737
ENST00000323571ENST00000584601WIPF2chr1738421398+ERBB2chr1737872553+0.0019324560.99806756
ENST00000323571ENST00000406381WIPF2chr1738421398+ERBB2chr1737872553+0.0014105660.99858946
ENST00000323571ENST00000541774WIPF2chr1738421398+ERBB2chr1737872553+0.0014105660.99858946
ENST00000323571ENST00000445658WIPF2chr1738421398+ERBB2chr1737872553+0.002025010.99797505
ENST00000323571ENST00000540147WIPF2chr1738421398+ERBB2chr1737872553+0.0014105660.99858946
ENST00000323571ENST00000584450WIPF2chr1738421398+ERBB2chr1737872553+0.0045777220.9954223
ENST00000323571ENST00000269571WIPF2chr1738421398+ERBB2chr1737872553+0.0014105660.99858946
ENST00000323571ENST00000578199WIPF2chr1738421398+ERBB2chr1737872553+0.266915950.733084
ENST00000323571ENST00000540042WIPF2chr1738421398+ERBB2chr1737872553+0.266724770.73327523
ENST00000585043ENST00000584601WIPF2chr1738421398+ERBB2chr1737872553+0.0019149450.998085
ENST00000585043ENST00000406381WIPF2chr1738421398+ERBB2chr1737872553+0.0013969880.99860305
ENST00000585043ENST00000541774WIPF2chr1738421398+ERBB2chr1737872553+0.0013969880.99860305
ENST00000585043ENST00000445658WIPF2chr1738421398+ERBB2chr1737872553+0.001994050.9980059
ENST00000585043ENST00000540147WIPF2chr1738421398+ERBB2chr1737872553+0.0013969880.99860305
ENST00000585043ENST00000584450WIPF2chr1738421398+ERBB2chr1737872553+0.0045082470.9954918
ENST00000585043ENST00000269571WIPF2chr1738421398+ERBB2chr1737872553+0.0013969880.99860305
ENST00000585043ENST00000578199WIPF2chr1738421398+ERBB2chr1737872553+0.266248760.73375124
ENST00000585043ENST00000540042WIPF2chr1738421398+ERBB2chr1737872553+0.26601920.73398083
ENST00000583130ENST00000584601WIPF2chr1738421398+ERBB2chr1737872553+0.001548950.998451
ENST00000583130ENST00000406381WIPF2chr1738421398+ERBB2chr1737872553+0.0012169150.99878305
ENST00000583130ENST00000541774WIPF2chr1738421398+ERBB2chr1737872553+0.0012169150.99878305
ENST00000583130ENST00000445658WIPF2chr1738421398+ERBB2chr1737872553+0.0016038510.9983961
ENST00000583130ENST00000540147WIPF2chr1738421398+ERBB2chr1737872553+0.0012169150.99878305
ENST00000583130ENST00000584450WIPF2chr1738421398+ERBB2chr1737872553+0.003859890.99614006
ENST00000583130ENST00000269571WIPF2chr1738421398+ERBB2chr1737872553+0.0012169150.99878305
ENST00000583130ENST00000578199WIPF2chr1738421398+ERBB2chr1737872553+0.24716590.7528341
ENST00000583130ENST00000540042WIPF2chr1738421398+ERBB2chr1737872553+0.246322590.75367737

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 WIPF2-ERBB2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
WIPF2chr1738421398ERBB2chr17378725531170322RPPPPARDPPSRGAVGEGLACHQLCA
WIPF2chr1738421398ERBB2chr17378725531208322RPPPPARDPPSRGAVGEGLACHQLCA
WIPF2chr1738421398ERBB2chr17378725531210322RPPPPARDPPSRGAVGEGLACHQLCA
WIPF2chr1738421398ERBB2chr17378725541170322RPPPPARDPPSRGAVGEGLACHQLCA
WIPF2chr1738421398ERBB2chr17378725541208322RPPPPARDPPSRGAVGEGLACHQLCA
WIPF2chr1738421398ERBB2chr17378725541210322RPPPPARDPPSRGAVGEGLACHQLCA

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Potential FusionNeoAntigen Information of WIPF2-ERBB2 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.
WIPF2-ERBB2_38421398_37872553.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)
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B27:07SRGAVGEGL0.98850.78531019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B27:04SRGAVGEGL0.98850.76921019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B39:06ARDPPSRGA0.97710.9398514
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B39:01SRGAVGEGL0.9590.93131019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B38:02SRGAVGEGL0.9270.97751019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B07:10SRGAVGEGL0.00350.77421019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B07:10ARDPPSRGAV0.9040.7676515
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B27:14ARDPPSRGA0.94770.6035514
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B73:01ARDPPSRGA0.94630.9084514
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B27:06SRGAVGEGL0.99090.81691019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B27:09SRGAVGEGL0.98910.6341019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B27:08SRGAVGEGL0.98530.60411019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-B39:31SRGAVGEGL0.9620.93171019
WIPF2-ERBB2chr1738421398chr17378725531210HLA-C07:04ARDPPSRGAV0.80060.9314515

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Potential FusionNeoAntigen Information of WIPF2-ERBB2 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 WIPF2-ERBB2

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
7744RDPPSRGAVGEGLAWIPF2ERBB2chr1738421398chr17378725531210

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of WIPF2-ERBB2

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-B14:023BVN7744RDPPSRGAVGEGLA-9.38616-9.49956
HLA-B14:023BVN7744RDPPSRGAVGEGLA-2.96308-3.99838
HLA-B52:013W397744RDPPSRGAVGEGLA-6.86378-6.97718
HLA-B52:013W397744RDPPSRGAVGEGLA-2.9876-4.0229
HLA-A11:014UQ27744RDPPSRGAVGEGLA-7.95435-8.06775
HLA-A24:025HGA7744RDPPSRGAVGEGLA-7.59672-7.71012
HLA-A24:025HGA7744RDPPSRGAVGEGLA-6.33737-7.37267
HLA-B44:053DX87744RDPPSRGAVGEGLA-7.16165-7.27505
HLA-B44:053DX87744RDPPSRGAVGEGLA-2.8843-3.9196
HLA-A02:016TDR7744RDPPSRGAVGEGLA-5.10343-5.21683

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Vaccine Design for the FusionNeoAntigens of WIPF2-ERBB2

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
WIPF2-ERBB2chr1738421398chr17378725531019SRGAVGEGLGGGGAGCAGTGGGCGAGGGCCTGGCCT
WIPF2-ERBB2chr1738421398chr1737872553514ARDPPSRGAGAGACCCTCCCAGTCGGGGAGCAGTGG
WIPF2-ERBB2chr1738421398chr1737872553515ARDPPSRGAVGAGACCCTCCCAGTCGGGGAGCAGTGGGCG

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 WIPF2-ERBB2

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
STADWIPF2-ERBB2chr1738421398ENST00000323571chr1737872553ENST00000269571TCGA-R5-A7ZE

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Potential target of CAR-T therapy development for WIPF2-ERBB2

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
TgeneERBB2chr17:38421398chr17:37872553ENST000002695711127653_67501256.0TransmembraneHelical
TgeneERBB2chr17:38421398chr17:37872553ENST000005417741127653_67501241.0TransmembraneHelical
TgeneERBB2chr17:38421398chr17:37872554ENST000002695711127653_67501256.0TransmembraneHelical
TgeneERBB2chr17:38421398chr17:37872554ENST000005417741127653_67501241.0TransmembraneHelical

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 WIPF2-ERBB2

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 WIPF2-ERBB2

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