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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:FGFR2-CCDC6

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FGFR2-CCDC6
FusionPDB ID: 30282
FusionGDB2.0 ID: 30282
HgeneTgene
Gene symbol

FGFR2

CCDC6

Gene ID

2263

8030

Gene namefibroblast growth factor receptor 2coiled-coil domain containing 6
SynonymsBBDS|BEK|BFR-1|CD332|CEK3|CFD1|ECT1|JWS|K-SAM|KGFR|TK14|TK25D10S170|H4|PTC|TPC|TST1
Cytomap

10q26.13

10q21.2

Type of geneprotein-codingprotein-coding
Descriptionfibroblast growth factor receptor 2BEK fibroblast growth factor receptorbacteria-expressed kinasekeratinocyte growth factor receptorprotein tyrosine kinase, receptor like 14coiled-coil domain-containing protein 6papillary thyroid carcinoma-encoded protein
Modification date2020032220200327
UniProtAcc

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}.

A6NI79

Main function of 5'-partner protein: FUNCTION: May act as a scaffold to regulate the recruitment and assembly of spindle midzone components. Required for the localization of AURKB and PLK1 to the spindle midzone. {ECO:0000305|PubMed:20962590}.
Ensembl transtripts involved in fusion geneENST idsENST00000351936, ENST00000356226, 
ENST00000357555, ENST00000358487, 
ENST00000360144, ENST00000369059, 
ENST00000369060, ENST00000457416, 
ENST00000478859, ENST00000346997, 
ENST00000369056, ENST00000369061, 
ENST00000359354, ENST00000490349, 
ENST00000263102, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 20 X 12=576012 X 8 X 6=576
# samples 3814
** MAII scorelog2(38/5760*10)=-3.92199748799873
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/576*10)=-2.04064198449735
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: FGFR2 [Title/Abstract] AND CCDC6 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FGFR2 [Title/Abstract] AND CCDC6 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FGFR2(123243212)-CCDC6(61612460), # samples:3
Anticipated loss of major functional domain due to fusion event.FGFR2-CCDC6 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-CCDC6 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-CCDC6 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-CCDC6 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-CCDC6 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
FGFR2-CCDC6 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
FGFR2-CCDC6 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
FGFR2-CCDC6 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
FGFR2-CCDC6 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
HgeneFGFR2

GO:0008284

positive regulation of cell proliferation

8663044

HgeneFGFR2

GO:0008543

fibroblast growth factor receptor signaling pathway

8663044|15629145

HgeneFGFR2

GO:0018108

peptidyl-tyrosine phosphorylation

15629145|16844695

HgeneFGFR2

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/chr10:61612460)
- 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 FGFR2 (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 CCDC6 (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)
ENST00000369061FGFR2chr10123243212-ENST00000263102CCDC6chr1061612460-739121154832361062
ENST00000346997FGFR2chr10123243212-ENST00000263102CCDC6chr1061612460-758323071234281138
ENST00000369056FGFR2chr10123243212-ENST00000263102CCDC6chr1061612460-760423282434491141

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
ENST00000369061ENST00000263102FGFR2chr10123243212-CCDC6chr1061612460-0.0001854930.99981457
ENST00000346997ENST00000263102FGFR2chr10123243212-CCDC6chr1061612460-0.0002147710.99978524
ENST00000369056ENST00000263102FGFR2chr10123243212-CCDC6chr1061612460-0.0001763850.99982363

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 FGFR2-CCDC6

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FGFR2chr10123243212CCDC6chr10616124602115689EDLDRILTLTTNEQARAEQEEEFISN
FGFR2chr10123243212CCDC6chr10616124602307765EDLDRILTLTTNEQARAEQEEEFISN
FGFR2chr10123243212CCDC6chr10616124602328768EDLDRILTLTTNEQARAEQEEEFISN

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Potential FusionNeoAntigen Information of FGFR2-CCDC6 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.

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)

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Potential FusionNeoAntigen Information of FGFR2-CCDC6 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.
FGFR2-CCDC6_123243212_61612460.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)
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0401LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0401DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0401DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0403LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0403DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0403DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0403EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0407LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0407DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0407DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0411LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0411DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0411DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0413LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0413DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0413DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0413EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0415LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0415DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0415DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0415EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0419LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0419DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0419DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0422DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0422LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0422DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0424LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0427LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0427DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0427DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0427EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0431LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0431DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0431DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0433LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0433DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0433DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0434LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0435LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0435DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0435DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0436LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0436DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0436DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0436EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0437LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0437DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0437DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0438LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0438DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0438DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0439LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0439DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0439DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0439EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0440LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0440DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0440DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0440EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0441LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0441DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0441DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0441EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0442LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0442DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0442DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0442EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0443LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0443DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0443DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0444LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0444DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0444DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0444EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0446LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0446DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0446DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0446EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0447LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0447DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0447DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0449LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0449DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0449DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0449EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0450LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0450DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0450DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0450EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0451LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0451DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0451DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0451EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0452LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0452DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0452DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0452EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0453LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0453DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0453DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0453EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0454LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0454DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0454DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0455LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0455DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0455DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0455EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0456LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0456DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0456DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0456EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0458LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0458DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0458DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0458EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0459LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0459DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0459DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0459EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0460LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0460DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0460DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0460EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0461LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0461DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0461DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0462LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0463LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0463DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0463DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0464LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0465LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0465DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0465DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0467LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0467DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0467DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0468LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0468DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0468DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0468EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0469DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0470LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0470DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0470DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0470EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0471LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0471DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0471DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0471EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0472LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0472DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0473LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0473DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0473DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0474DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0474LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0475LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0475DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0475DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0476LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0476DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0476DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0478LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0478DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0478DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0478EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0478RILTLTTNEQARAEQ419
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0479LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0479DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0479DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0479EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0480LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0482LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0482DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0482DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0485LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0485DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0485DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0485EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0486LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0487LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0488LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0488DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0488DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0488EDLDRILTLTTNEQA015
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0491LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0491DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0491DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-0831LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1002LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1002DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1002DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1204LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1209LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1410LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1410DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1410DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1452LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1452DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1457LDRILTLTTNEQARA217
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1457DRILTLTTNEQARAE318
FGFR2-CCDC6chr10123243212chr10616124602307DRB1-1457DLDRILTLTTNEQAR116
FGFR2-CCDC6chr10123243212chr10616124602307DRB3-0201ILTLTTNEQARAEQE520
FGFR2-CCDC6chr10123243212chr10616124602307DRB3-0204ILTLTTNEQARAEQE520
FGFR2-CCDC6chr10123243212chr10616124602307DRB3-0204RILTLTTNEQARAEQ419
FGFR2-CCDC6chr10123243212chr10616124602307DRB3-0224ILTLTTNEQARAEQE520

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Fusion breakpoint peptide structures of FGFR2-CCDC6

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FGFR2-CCDC6

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

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Vaccine Design for the FusionNeoAntigens of FGFR2-CCDC6

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

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
FGFR2-CCDC6chr10123243212chr1061612460015EDLDRILTLTTNEQAGAAGACTTGGATCGAATTCTCACTCTCACAACCAATGAGCAAGCC
FGFR2-CCDC6chr10123243212chr1061612460116DLDRILTLTTNEQARGACTTGGATCGAATTCTCACTCTCACAACCAATGAGCAAGCCAGG
FGFR2-CCDC6chr10123243212chr1061612460217LDRILTLTTNEQARATTGGATCGAATTCTCACTCTCACAACCAATGAGCAAGCCAGGGCT
FGFR2-CCDC6chr10123243212chr1061612460318DRILTLTTNEQARAEGATCGAATTCTCACTCTCACAACCAATGAGCAAGCCAGGGCTGAG
FGFR2-CCDC6chr10123243212chr1061612460419RILTLTTNEQARAEQCGAATTCTCACTCTCACAACCAATGAGCAAGCCAGGGCTGAGCAG
FGFR2-CCDC6chr10123243212chr1061612460520ILTLTTNEQARAEQEATTCTCACTCTCACAACCAATGAGCAAGCCAGGGCTGAGCAGGAA

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Information of the samples that have these potential fusion neoantigens of FGFR2-CCDC6

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

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Potential target of CAR-T therapy development for FGFR2-CCDC6

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
HgeneFGFR2chr10:123243212chr10:61612460ENST00000346997-1617378_398765820.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000351936-1718378_398765786.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000356226-1516378_398650705.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000357555-1617378_398678708.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000358487-1718378_398767822.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000360144-1617378_398679681.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000369056-1617378_398768770.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000369060-1516378_398651706.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000369061-1415378_398655710.0TransmembraneHelical
HgeneFGFR2chr10:123243212chr10:61612460ENST00000457416-1718378_398768823.0TransmembraneHelical

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 FGFR2-CCDC6

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 FGFR2-CCDC6

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
HgeneFGFR2C2931196Craniofacial dysostosis type 123CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR2C0220658Pfeiffer Syndrome21CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR2C0001193Apert syndrome19CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C0795998JACKSON-WEISS SYNDROME10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C0175699Saethre-Chotzen Syndrome8CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneFGFR2C1852406Cutis Gyrata Syndrome of Beare And Stevenson8CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C2936791Antley-Bixler Syndrome, Autosomal Dominant7CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C1510455Acrocephalosyndactylia6CTD_human;ORPHANET
HgeneFGFR2C0265269Lacrimoauriculodentodigital syndrome5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C0010278Craniosynostosis4CTD_human;GENOMICS_ENGLAND
HgeneFGFR2C1863389Apert-Crouzon Disease4CTD_human
HgeneFGFR2C1865070SCAPHOCEPHALY, MAXILLARY RETRUSION, AND MENTAL RETARDATION4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C0006142Malignant neoplasm of breast3CTD_human;UNIPROT
HgeneFGFR2C0030044Acrocephaly3CTD_human
HgeneFGFR2C0036341Schizophrenia3PSYGENET
HgeneFGFR2C0221356Brachycephaly3CTD_human
HgeneFGFR2C0265534Scaphycephaly3CTD_human
HgeneFGFR2C0265535Trigonocephaly3CTD_human
HgeneFGFR2C0376634Craniofacial Abnormalities3CTD_human
HgeneFGFR2C0678222Breast Carcinoma3CTD_human
HgeneFGFR2C1257931Mammary Neoplasms, Human3CTD_human
HgeneFGFR2C1458155Mammary Neoplasms3CTD_human
HgeneFGFR2C1833340Synostotic Posterior Plagiocephaly3CTD_human
HgeneFGFR2C1860819Metopic synostosis3CTD_human
HgeneFGFR2C2931150Synostotic Anterior Plagiocephaly3CTD_human
HgeneFGFR2C3281247BENT BONE DYSPLASIA SYNDROME3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR2C4551902Craniosynostosis, Type 13CTD_human
HgeneFGFR2C4704874Mammary Carcinoma, Human3CTD_human
HgeneFGFR2C0008925Cleft Palate2CTD_human
HgeneFGFR2C0011570Mental Depression2PSYGENET
HgeneFGFR2C0011581Depressive disorder2PSYGENET
HgeneFGFR2C0024623Malignant neoplasm of stomach2CGI;CTD_human
HgeneFGFR2C0038356Stomach Neoplasms2CGI;CTD_human
HgeneFGFR2C1708349Hereditary Diffuse Gastric Cancer2CTD_human
HgeneFGFR2C1837218Cleft palate, isolated2CTD_human
HgeneFGFR2C0000772Multiple congenital anomalies1CTD_human
HgeneFGFR2C0003090Ankylosis1CTD_human
HgeneFGFR2C0005586Bipolar Disorder1PSYGENET
HgeneFGFR2C0008924Cleft upper lip1CTD_human
HgeneFGFR2C0010273Craniofacial Dysostosis1CTD_human
HgeneFGFR2C0011757Developmental Coordination Disorder1CTD_human
HgeneFGFR2C0014170Endometrial Neoplasms1CTD_human
HgeneFGFR2C0018553Hamartoma Syndrome, Multiple1CTD_human
HgeneFGFR2C0020796Profound Mental Retardation1CTD_human
HgeneFGFR2C0023890Liver Cirrhosis1CTD_human
HgeneFGFR2C0024121Lung Neoplasms1CTD_human
HgeneFGFR2C0025363Mental Retardation, Psychosocial1CTD_human
HgeneFGFR2C0026613Motor Skills Disorders1CTD_human
HgeneFGFR2C0033975Psychotic Disorders1PSYGENET
HgeneFGFR2C0037268Skin Abnormalities1CTD_human
HgeneFGFR2C0037274Dermatologic disorders1CTD_human
HgeneFGFR2C0038219Status Dysraphicus1CTD_human
HgeneFGFR2C0040427Tooth Abnormalities1CTD_human
HgeneFGFR2C0080178Spina Bifida1CTD_human
HgeneFGFR2C0152423Congenital small ears1GENOMICS_ENGLAND
HgeneFGFR2C0206698Cholangiocarcinoma1CTD_human
HgeneFGFR2C0206762Limb Deformities, Congenital1CTD_human
HgeneFGFR2C0239946Fibrosis, Liver1CTD_human
HgeneFGFR2C0242379Malignant neoplasm of lung1CTD_human
HgeneFGFR2C0265326Bannayan-Riley-Ruvalcaba Syndrome1CTD_human
HgeneFGFR2C0266508Rachischisis1CTD_human
HgeneFGFR2C0345905Intrahepatic Cholangiocarcinoma1CTD_human
HgeneFGFR2C0349204Nonorganic psychosis1PSYGENET
HgeneFGFR2C0391826Lhermitte-Duclos disease1CTD_human
HgeneFGFR2C0476089Endometrial Carcinoma1CGI;CTD_human
HgeneFGFR2C0524730Odontome1CTD_human
HgeneFGFR2C0699791Stomach Carcinoma1CGI;GENOMICS_ENGLAND
HgeneFGFR2C0917816Mental deficiency1CTD_human
HgeneFGFR2C1450010Plagiocephaly, Nonsynostotic1CTD_human
HgeneFGFR2C1860042Antley-Bixler Syndrome with Disordered Steroidogenesis1CTD_human
HgeneFGFR2C1867564SCAPHOCEPHALY AND AXENFELD-RIEGER ANOMALY1GENOMICS_ENGLAND
HgeneFGFR2C1959582PTEN Hamartoma Tumor Syndrome1CTD_human
HgeneFGFR2C2350233Antley-Bixler Syndrome Phenotype1CTD_human
HgeneFGFR2C3267076Familial scaphocephaly syndrome1GENOMICS_ENGLAND
HgeneFGFR2C3714756Intellectual Disability1CTD_human
HgeneFGFR2C3805278Extrahepatic Cholangiocarcinoma1CTD_human
TgeneCCDC6C0238463Papillary thyroid carcinoma2CTD_human;ORPHANET
TgeneCCDC6C3501843Nonmedullary Thyroid Carcinoma1CTD_human
TgeneCCDC6C3501844Familial Nonmedullary Thyroid Cancer1CTD_human