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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:BICC1-FGFR2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BICC1-FGFR2
FusionPDB ID: 9672
FusionGDB2.0 ID: 9672
HgeneTgene
Gene symbol

BICC1

FGFR2

Gene ID

80114

2263

Gene nameBicC family RNA binding protein 1fibroblast growth factor receptor 2
SynonymsBICC|CYSRDBBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25
Cytomap

10q21.1

10q26.13

Type of geneprotein-codingprotein-coding
Descriptionprotein bicaudal C homolog 1FGFR2-BICC1 fusion kinase proteinbicaudal C homolog 1fibroblast growth factor receptor 2BEK fibroblast growth factor receptorbacteria-expressed kinasekeratinocyte growth factor receptorprotein tyrosine kinase, receptor like 14
Modification date2020031320200322
UniProtAcc

Q9H694

Main function of 5'-partner protein: FUNCTION: Putative RNA-binding protein. Acts as a negative regulator of Wnt signaling. May be involved in regulating gene expression during embryonic development. {ECO:0000269|PubMed:21922595}.

P21802

Main function of 5'-partner protein: FUNCTION: Tyrosine-protein kinase that acts as cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of cell proliferation, differentiation, migration and apoptosis, and in the regulation of embryonic development. Required for normal embryonic patterning, trophoblast function, limb bud development, lung morphogenesis, osteogenesis and skin development. Plays an essential role in the regulation of osteoblast differentiation, proliferation and apoptosis, and is required for normal skeleton development. Promotes cell proliferation in keratinocytes and immature osteoblasts, but promotes apoptosis in differentiated osteoblasts. Phosphorylates PLCG1, FRS2 and PAK4. Ligand binding leads to the activation of several signaling cascades. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate. Phosphorylation of FRS2 triggers recruitment of GRB2, GAB1, PIK3R1 and SOS1, and mediates activation of RAS, MAPK1/ERK2, MAPK3/ERK1 and the MAP kinase signaling pathway, as well as of the AKT1 signaling pathway. FGFR2 signaling is down-regulated by ubiquitination, internalization and degradation. Mutations that lead to constitutive kinase activation or impair normal FGFR2 maturation, internalization and degradation lead to aberrant signaling. Over-expressed FGFR2 promotes activation of STAT1. {ECO:0000269|PubMed:12529371, ECO:0000269|PubMed:15190072, ECO:0000269|PubMed:15629145, ECO:0000269|PubMed:16384934, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17623664, ECO:0000269|PubMed:18374639, ECO:0000269|PubMed:19103595, ECO:0000269|PubMed:19387476, ECO:0000269|PubMed:19410646, ECO:0000269|PubMed:21596750, ECO:0000269|PubMed:8663044}.
Ensembl transtripts involved in fusion geneENST idsENST00000263103, ENST00000373886, 
ENST00000476684, 		ENST00000346997, 
ENST00000351936, ENST00000356226, 
ENST00000357555, ENST00000358487, 
ENST00000359354, ENST00000360144, 
ENST00000369056, ENST00000369059, 
ENST00000369060, ENST00000457416, 
ENST00000478859, ENST00000490349, 
ENST00000369061, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 9 X 6=54011 X 11 X 8=968
# samples 916
** MAII scorelog2(9/540*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/968*10)=-2.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: BICC1 [Title/Abstract] AND FGFR2 [Title/Abstract] AND fusion [Title/Abstract]

Identification of Targetable FGFR Gene Fusions in Diverse Cancers (pmid: 23558953)
Fusion neoantigen context

PubMed: BICC1 [Title/Abstract] AND FGFR2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FGFR2(123243212)-BICC1(60461834), # samples:6
BICC1(60563002)-FGFR2(123239535), # samples:2
Anticipated loss of major functional domain due to fusion event.BICC1-FGFR2 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.
BICC1-FGFR2 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.
BICC1-FGFR2 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.
BICC1-FGFR2 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.
FGFR2-BICC1 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.
FGFR2-BICC1 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.
FGFR2-BICC1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
FGFR2-BICC1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
FGFR2-BICC1 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
FGFR2-BICC1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneBICC1

GO:0090090

negative regulation of canonical Wnt signaling pathway

21922595

TgeneFGFR2

GO:0008284

positive regulation of cell proliferation

8663044

TgeneFGFR2

GO:0008543

fibroblast growth factor receptor signaling pathway

8663044|15629145

TgeneFGFR2

GO:0018108

peptidyl-tyrosine phosphorylation

15629145|16844695

TgeneFGFR2

GO:0046777

protein autophosphorylation

15629145



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/chr10:123243212/chr10:60461834)
- 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 BICC1 (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 FGFR2 (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)
ENST00000373886BICC1chr1060563002+ENST00000369061FGFR2chr10123239535-3873218542349781
ENST00000263103BICC1chr1060563002+ENST00000369061FGFR2chr10123239535-27711083211247408

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
ENST00000373886ENST00000369061BICC1chr1060563002+FGFR2chr10123239535-0.0006246660.9993754
ENST00000263103ENST00000369061BICC1chr1060563002+FGFR2chr10123239535-0.0015882560.9984118

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 BICC1-FGFR2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
BICC1chr1060563002FGFR2chr101232395351083353RAHLAPRSSYVNMQEYLDLSQPLEQY
BICC1chr1060563002FGFR2chr101232395352185726RAHLAPRSSYVNMQEYLDLSQPLEQY

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Potential FusionNeoAntigen Information of BICC1-FGFR2 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.
BICC1-FGFR2_60563002_123239535.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)
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:25SSYVNMQEY0.99960.8949716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:01SSYVNMQEY0.99890.9291716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:02SSYVNMQEY0.99820.8994716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:08SSYVNMQEY0.99810.7671716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:17SSYVNMQEY0.99740.8362716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:01SSYVNMQEY0.99190.8348716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:16SSYVNMQEY0.98080.5186716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B58:01SSYVNMQEY0.97710.7563716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:03SSYVNMQEY0.95420.6962716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B58:02SSYVNMQEY0.95150.8336716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:17RSSYVNMQEY0.99680.9408616
BICC1-FGFR2chr1060563002chr101232395351083HLA-B58:02RSSYVNMQEY0.99350.9618616
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:16RSSYVNMQEY0.95390.7025616
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:80SYVNMQEY0.93360.9058816
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:67SYVNMQEY0.93360.9058816
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:21SSYVNMQEY0.9980.8572716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:05SSYVNMQEY0.99750.7938716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:07SSYVNMQEY0.99410.6849716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:31SSYVNMQEY0.99060.8076716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C12:16SSYVNMQEY0.94690.9401716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:10SSYVNMQEY0.94670.9382716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:19SSYVNMQEY0.93950.6691716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:95SSYVNMQEY0.93190.7295716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C15:04SSYVNMQEY0.92130.8404716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:27SSYVNMQEY0.91840.9486716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:04SSYVNMQEY0.88010.9336716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:46SSYVNMQEY0.85660.8343716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C03:14SSYVNMQEY0.73750.9554716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C12:12SSYVNMQEY0.62440.865716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C12:04SSYVNMQEY0.52250.9926716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C06:03SSYVNMQEY0.52150.9901716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:29SYVNMQEYL0.48370.9448817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:13SYVNMQEYL0.47710.9475817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:05SYVNMQEYL0.47080.9595817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:10SYVNMQEYL0.44070.9578817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:67SYVNMQEYL0.43740.9344817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:80SYVNMQEYL0.43740.9344817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:27SYVNMQEYL0.39210.9482817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:19SYVNMQEYL0.37790.7524817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:46SYVNMQEYL0.34910.8672817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C04:14SYVNMQEYL0.21810.824817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:17SYVNMQEY0.96390.9404816
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:02SYVNMQEY0.93360.9058816
BICC1-FGFR2chr1060563002chr101232395351083HLA-C14:03SYVNMQEY0.66930.9294816
BICC1-FGFR2chr1060563002chr101232395351083HLA-C14:02SYVNMQEY0.66930.9294816
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:39SSYVNMQEY0.99960.7711716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:33SSYVNMQEY0.99890.9291716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:27SSYVNMQEY0.99890.9279716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:125SSYVNMQEY0.99890.9291716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:34SSYVNMQEY0.99890.9291716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:135SSYVNMQEY0.99860.9331716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:11SSYVNMQEY0.99820.8398716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:11SSYVNMQEY0.9980.8748716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:53SSYVNMQEY0.99790.8946716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:08SSYVNMQEY0.99770.8692716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:20SSYVNMQEY0.99760.8668716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:50SSYVNMQEY0.99760.8923716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:43SSYVNMQEY0.99710.8653716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B57:04SSYVNMQEY0.99610.5619716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:28SSYVNMQEY0.99610.8615716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:24SSYVNMQEY0.99530.9205716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:12SSYVNMQEY0.99280.8933716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:23SSYVNMQEY0.9920.7935716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:77SSYVNMQEY0.99190.8348716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:20SSYVNMQEY0.98950.8688716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:35SSYVNMQEY0.98910.9181716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B58:06SSYVNMQEY0.98330.6214716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:30SSYVNMQEY0.9750.6323716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:17SSYVNMQEY0.9750.6323716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C03:02SSYVNMQEY0.9720.9585716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:22SSYVNMQEY0.96920.67716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:17SSYVNMQEY0.9620.9434716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:01SSYVNMQEY0.93160.6798716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C15:09SSYVNMQEY0.92130.8404716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B35:24SSYVNMQEY0.90680.8498716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:54SSYVNMQEY0.85270.8806716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C12:02SSYVNMQEY0.84290.9515716
BICC1-FGFR2chr1060563002chr101232395351083HLA-A25:01SSYVNMQEY0.78470.6201716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B48:02SSYVNMQEY0.78090.8413716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C16:04SSYVNMQEY0.77160.9662716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C12:03SSYVNMQEY0.69440.9683716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C16:01SSYVNMQEY0.56080.9605716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B15:68SSYVNMQEY0.53340.5896716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B18:04SSYVNMQEY0.47660.9423716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C03:67SYVNMQEYL0.46850.9846817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:02SYVNMQEYL0.43740.9344817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C07:17SYVNMQEYL0.42870.9552817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C16:02SSYVNMQEY0.35450.9892716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B18:07SSYVNMQEY0.3010.9101716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C04:04SYVNMQEYL0.27880.8975817
BICC1-FGFR2chr1060563002chr101232395351083HLA-B18:08SSYVNMQEY0.24750.9116716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C06:06SYVNMQEYL0.09120.988817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C14:02SYVNMQEYL0.0750.9485817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C14:03SYVNMQEYL0.0750.9485817
BICC1-FGFR2chr1060563002chr101232395351083HLA-C06:08SSYVNMQEY0.05470.9812716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C02:10SSYVNMQEY0.02050.9588716
BICC1-FGFR2chr1060563002chr101232395351083HLA-C02:02SSYVNMQEY0.02050.9588716
BICC1-FGFR2chr1060563002chr101232395351083HLA-B57:04RSSYVNMQEY0.99840.7242616
BICC1-FGFR2chr1060563002chr101232395351083HLA-B58:06RSSYVNMQEY0.99340.8843616

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Potential FusionNeoAntigen Information of BICC1-FGFR2 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.
BICC1-FGFR2_60563002_123239535.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)
BICC1-FGFR2chr1060563002chr101232395351083DRB1-0832RSSYVNMQEYLDLSQ621

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Fusion breakpoint peptide structures of BICC1-FGFR2

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
8253RSSYVNMQEYLDLSBICC1FGFR2chr1060563002chr101232395351083

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BICC1-FGFR2

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-B14:023BVN8253RSSYVNMQEYLDLS-7.63365-7.82815
HLA-B14:023BVN8253RSSYVNMQEYLDLS-3.60138-4.35588
HLA-B52:013W398253RSSYVNMQEYLDLS-5.8895-6.084
HLA-B52:013W398253RSSYVNMQEYLDLS-4.25087-5.00537
HLA-A11:014UQ28253RSSYVNMQEYLDLS-10.5357-10.7302
HLA-A24:025HGA8253RSSYVNMQEYLDLS-9.72019-10.4747
HLA-A24:025HGA8253RSSYVNMQEYLDLS-7.29887-7.49337
HLA-B27:056PYJ8253RSSYVNMQEYLDLS-6.8902-7.0847
HLA-B44:053DX88253RSSYVNMQEYLDLS-6.63235-6.82685
HLA-B44:053DX88253RSSYVNMQEYLDLS-3.412-4.1665
HLA-A02:016TDR8253RSSYVNMQEYLDLS-5.60289-5.79739
HLA-A02:016TDR8253RSSYVNMQEYLDLS-4.63947-5.39397

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Vaccine Design for the FusionNeoAntigens of BICC1-FGFR2

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
BICC1-FGFR2chr1060563002chr10123239535616RSSYVNMQEYTCATCATATGTCAACATGCAGGAATACTTG
BICC1-FGFR2chr1060563002chr10123239535716SSYVNMQEYTCATATGTCAACATGCAGGAATACTTG
BICC1-FGFR2chr1060563002chr10123239535816SYVNMQEYTATGTCAACATGCAGGAATACTTG
BICC1-FGFR2chr1060563002chr10123239535817SYVNMQEYLTATGTCAACATGCAGGAATACTTGGAC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
BICC1-FGFR2chr1060563002chr10123239535621RSSYVNMQEYLDLSQTCATCATATGTCAACATGCAGGAATACTTGGACCTCAGCCAACCT

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Information of the samples that have these potential fusion neoantigens of BICC1-FGFR2

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
CHOLBICC1-FGFR2chr1060563002ENST00000263103chr10123239535ENST00000369061TCGA-W5-AA2W-01A

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Potential target of CAR-T therapy development for BICC1-FGFR2

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
TgeneFGFR2chr10:60563002chr10:123239535ENST00000351936018378_3980786.0TransmembraneHelical
TgeneFGFR2chr10:60563002chr10:123239535ENST00000357555017378_3980708.0TransmembraneHelical
TgeneFGFR2chr10:60563002chr10:123239535ENST0000035935407378_3980255.0TransmembraneHelical
TgeneFGFR2chr10:60563002chr10:123239535ENST00000360144017378_3980681.0TransmembraneHelical
TgeneFGFR2chr10:60563002chr10:123239535ENST00000369056017378_3980770.0TransmembraneHelical

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 BICC1-FGFR2

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 BICC1-FGFR2

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
TgeneFGFR2C2931196Craniofacial dysostosis type 123CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneFGFR2C0220658Pfeiffer Syndrome21CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneFGFR2C0001193Apert syndrome19CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C0795998JACKSON-WEISS SYNDROME10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C0175699Saethre-Chotzen Syndrome8CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneFGFR2C1852406Cutis Gyrata Syndrome of Beare And Stevenson8CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C2936791Antley-Bixler Syndrome, Autosomal Dominant7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C1510455Acrocephalosyndactylia6CTD_human;ORPHANET
TgeneFGFR2C0265269Lacrimoauriculodentodigital syndrome5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C0010278Craniosynostosis4CTD_human;GENOMICS_ENGLAND
TgeneFGFR2C1863389Apert-Crouzon Disease4CTD_human
TgeneFGFR2C1865070SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C0006142Malignant neoplasm of breast3CTD_human;UNIPROT
TgeneFGFR2C0030044Acrocephaly3CTD_human
TgeneFGFR2C0036341Schizophrenia3PSYGENET
TgeneFGFR2C0221356Brachycephaly3CTD_human
TgeneFGFR2C0265534Scaphycephaly3CTD_human
TgeneFGFR2C0265535Trigonocephaly3CTD_human
TgeneFGFR2C0376634Craniofacial Abnormalities3CTD_human
TgeneFGFR2C0678222Breast Carcinoma3CTD_human
TgeneFGFR2C1257931Mammary Neoplasms, Human3CTD_human
TgeneFGFR2C1458155Mammary Neoplasms3CTD_human
TgeneFGFR2C1833340Synostotic Posterior Plagiocephaly3CTD_human
TgeneFGFR2C1860819Metopic synostosis3CTD_human
TgeneFGFR2C2931150Synostotic Anterior Plagiocephaly3CTD_human
TgeneFGFR2C3281247BENT BONE DYSPLASIA SYNDROME3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneFGFR2C4551902Craniosynostosis, Type 13CTD_human
TgeneFGFR2C4704874Mammary Carcinoma, Human3CTD_human
TgeneFGFR2C0008925Cleft Palate2CTD_human
TgeneFGFR2C0011570Mental Depression2PSYGENET
TgeneFGFR2C0011581Depressive disorder2PSYGENET
TgeneFGFR2C0024623Malignant neoplasm of stomach2CGI;CTD_human
TgeneFGFR2C0038356Stomach Neoplasms2CGI;CTD_human
TgeneFGFR2C1708349Hereditary Diffuse Gastric Cancer2CTD_human
TgeneFGFR2C1837218Cleft palate, isolated2CTD_human
TgeneFGFR2C0000772Multiple congenital anomalies1CTD_human
TgeneFGFR2C0003090Ankylosis1CTD_human
TgeneFGFR2C0005586Bipolar Disorder1PSYGENET
TgeneFGFR2C0008924Cleft upper lip1CTD_human
TgeneFGFR2C0010273Craniofacial Dysostosis1CTD_human
TgeneFGFR2C0011757Developmental Coordination Disorder1CTD_human
TgeneFGFR2C0014170Endometrial Neoplasms1CTD_human
TgeneFGFR2C0018553Hamartoma Syndrome, Multiple1CTD_human
TgeneFGFR2C0020796Profound Mental Retardation1CTD_human
TgeneFGFR2C0023890Liver Cirrhosis1CTD_human
TgeneFGFR2C0024121Lung Neoplasms1CTD_human
TgeneFGFR2C0025363Mental Retardation, Psychosocial1CTD_human
TgeneFGFR2C0026613Motor Skills Disorders1CTD_human
TgeneFGFR2C0033975Psychotic Disorders1PSYGENET
TgeneFGFR2C0037268Skin Abnormalities1CTD_human
TgeneFGFR2C0037274Dermatologic disorders1CTD_human
TgeneFGFR2C0038219Status Dysraphicus1CTD_human
TgeneFGFR2C0040427Tooth Abnormalities1CTD_human
TgeneFGFR2C0080178Spina Bifida1CTD_human
TgeneFGFR2C0152423Congenital small ears1GENOMICS_ENGLAND
TgeneFGFR2C0206698Cholangiocarcinoma1CTD_human
TgeneFGFR2C0206762Limb Deformities, Congenital1CTD_human
TgeneFGFR2C0239946Fibrosis, Liver1CTD_human
TgeneFGFR2C0242379Malignant neoplasm of lung1CTD_human
TgeneFGFR2C0265326Bannayan-Riley-Ruvalcaba Syndrome1CTD_human
TgeneFGFR2C0266508Rachischisis1CTD_human
TgeneFGFR2C0345905Intrahepatic Cholangiocarcinoma1CTD_human
TgeneFGFR2C0349204Nonorganic psychosis1PSYGENET
TgeneFGFR2C0391826Lhermitte-Duclos disease1CTD_human
TgeneFGFR2C0476089Endometrial Carcinoma1CGI;CTD_human
TgeneFGFR2C0524730Odontome1CTD_human
TgeneFGFR2C0699791Stomach Carcinoma1CGI;GENOMICS_ENGLAND
TgeneFGFR2C0917816Mental deficiency1CTD_human
TgeneFGFR2C1450010Plagiocephaly, Nonsynostotic1CTD_human
TgeneFGFR2C1860042Antley-Bixler Syndrome with Disordered Steroidogenesis1CTD_human
TgeneFGFR2C1867564SCAPHOCEPHALY AND AXENFELD-RIEGER ANOMALY1GENOMICS_ENGLAND
TgeneFGFR2C1959582PTEN Hamartoma Tumor Syndrome1CTD_human
TgeneFGFR2C2350233Antley-Bixler Syndrome Phenotype1CTD_human
TgeneFGFR2C3267076Familial scaphocephaly syndrome1GENOMICS_ENGLAND
TgeneFGFR2C3714756Intellectual Disability1CTD_human
TgeneFGFR2C3805278Extrahepatic Cholangiocarcinoma1CTD_human