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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:FGFR1-CSMD1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FGFR1-CSMD1
FusionPDB ID: 30241
FusionGDB2.0 ID: 30241
HgeneTgene
Gene symbol

FGFR1

CSMD1

Gene ID

2260

64478

Gene namefibroblast growth factor receptor 1CUB and Sushi multiple domains 1
SynonymsBFGFR|CD331|CEK|ECCL|FGFBR|FGFR-1|FLG|FLT-2|FLT2|HBGFR|HH2|HRTFDS|KAL2|N-SAM|OGD|bFGF-R-1PPP1R24
Cytomap

8p11.23

8p23.2

Type of geneprotein-codingprotein-coding
Descriptionfibroblast growth factor receptor 1FGFR1/PLAG1 fusionFMS-like tyrosine kinase 2basic fibroblast growth factor receptor 1fms-related tyrosine kinase 2heparin-binding growth factor receptorhydroxyaryl-protein kinaseproto-oncogene c-FgrCUB and sushi domain-containing protein 1protein phosphatase 1, regulatory subunit 24
Modification date2020032920200313
UniProtAcc

Q9NVK5

Main function of 5'-partner protein: FUNCTION: May be involved in wound healing pathway. {ECO:0000250}.

Q96PZ7

Main function of 5'-partner protein: FUNCTION: Potential suppressor of squamous cell carcinomas.
Ensembl transtripts involved in fusion geneENST idsENST00000326324, ENST00000341462, 
ENST00000356207, ENST00000397091, 
ENST00000397103, ENST00000397108, 
ENST00000397113, ENST00000425967, 
ENST00000447712, ENST00000532791, 
ENST00000335922, ENST00000496629, 
ENST00000523387, ENST00000400186, 
ENST00000520002, ENST00000537824, 
ENST00000539096, ENST00000542608, 
ENST00000602557, ENST00000602723, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 24 X 9=367222 X 20 X 8=3520
# samples 2023
** MAII scorelog2(20/3672*10)=-4.19849415363908
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(23/3520*10)=-3.93586966258028
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: FGFR1 [Title/Abstract] AND CSMD1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FGFR1 [Title/Abstract] AND CSMD1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FGFR1(38314874)-CSMD1(3889621), # samples:2
Anticipated loss of major functional domain due to fusion event.FGFR1-CSMD1 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.
FGFR1-CSMD1 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.
FGFR1-CSMD1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
FGFR1-CSMD1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
FGFR1-CSMD1 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
FGFR1-CSMD1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgeneFGFR1

GO:0008284

positive regulation of cell proliferation

8663044

HgeneFGFR1

GO:0008543

fibroblast growth factor receptor signaling pathway

8663044

HgeneFGFR1

GO:0010863

positive regulation of phospholipase C activity

18480409

HgeneFGFR1

GO:0018108

peptidyl-tyrosine phosphorylation

8622701|18480409

HgeneFGFR1

GO:0043406

positive regulation of MAP kinase activity

8622701|18480409

HgeneFGFR1

GO:0046777

protein autophosphorylation

8622701

HgeneFGFR1

GO:2000546

positive regulation of endothelial cell chemotaxis to fibroblast growth factor

21885851



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/chr8:38314874/chr8:3889621)
- 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 FGFR1 (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 CSMD1 (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)
ENST00000397091FGFR1chr838314874-ENST00000602723CSMD1chr83889621-11078840368105913407
ENST00000397091FGFR1chr838314874-ENST00000400186CSMD1chr83889621-11078840368105913407
ENST00000397091FGFR1chr838314874-ENST00000520002CSMD1chr83889621-11609840368111223584
ENST00000397091FGFR1chr838314874-ENST00000602557CSMD1chr83889621-11609840368111223584
ENST00000397091FGFR1chr838314874-ENST00000537824CSMD1chr83889621-11120840368111193584
ENST00000397091FGFR1chr838314874-ENST00000542608CSMD1chr83889621-10589840368105883407
ENST00000397091FGFR1chr838314874-ENST00000539096CSMD1chr83889621-675584036867542129
ENST00000447712FGFR1chr838314874-ENST00000602723CSMD1chr83889621-112711033561107843407
ENST00000447712FGFR1chr838314874-ENST00000400186CSMD1chr83889621-112711033561107843407
ENST00000447712FGFR1chr838314874-ENST00000520002CSMD1chr83889621-118021033561113153584
ENST00000447712FGFR1chr838314874-ENST00000602557CSMD1chr83889621-118021033561113153584
ENST00000447712FGFR1chr838314874-ENST00000537824CSMD1chr83889621-113131033561113123583
ENST00000447712FGFR1chr838314874-ENST00000542608CSMD1chr83889621-107821033561107813406
ENST00000447712FGFR1chr838314874-ENST00000539096CSMD1chr83889621-6948103356169472128
ENST00000341462FGFR1chr838314874-ENST00000602723CSMD1chr83889621-112711033561107843407
ENST00000341462FGFR1chr838314874-ENST00000400186CSMD1chr83889621-112711033561107843407
ENST00000341462FGFR1chr838314874-ENST00000520002CSMD1chr83889621-118021033561113153584
ENST00000341462FGFR1chr838314874-ENST00000602557CSMD1chr83889621-118021033561113153584
ENST00000341462FGFR1chr838314874-ENST00000537824CSMD1chr83889621-113131033561113123583
ENST00000341462FGFR1chr838314874-ENST00000542608CSMD1chr83889621-107821033561107813406
ENST00000341462FGFR1chr838314874-ENST00000539096CSMD1chr83889621-6948103356169472128
ENST00000532791FGFR1chr838314874-ENST00000602723CSMD1chr83889621-11059821349105723407
ENST00000532791FGFR1chr838314874-ENST00000400186CSMD1chr83889621-11059821349105723407
ENST00000532791FGFR1chr838314874-ENST00000520002CSMD1chr83889621-11590821349111033584
ENST00000532791FGFR1chr838314874-ENST00000602557CSMD1chr83889621-11590821349111033584
ENST00000532791FGFR1chr838314874-ENST00000537824CSMD1chr83889621-11101821349111003584
ENST00000532791FGFR1chr838314874-ENST00000542608CSMD1chr83889621-10570821349105693407
ENST00000532791FGFR1chr838314874-ENST00000539096CSMD1chr83889621-673682134967352129
ENST00000397113FGFR1chr838314874-ENST00000602723CSMD1chr83889621-10646408131101593342
ENST00000397113FGFR1chr838314874-ENST00000400186CSMD1chr83889621-10646408131101593342
ENST00000397113FGFR1chr838314874-ENST00000520002CSMD1chr83889621-11177408131106903519
ENST00000397113FGFR1chr838314874-ENST00000602557CSMD1chr83889621-11177408131106903519
ENST00000397113FGFR1chr838314874-ENST00000537824CSMD1chr83889621-10688408131106873519
ENST00000397113FGFR1chr838314874-ENST00000542608CSMD1chr83889621-10157408131101563342
ENST00000397113FGFR1chr838314874-ENST00000539096CSMD1chr83889621-632340813163222064
ENST00000356207FGFR1chr838314874-ENST00000602723CSMD1chr83889621-11053815343105663407
ENST00000356207FGFR1chr838314874-ENST00000400186CSMD1chr83889621-11053815343105663407
ENST00000356207FGFR1chr838314874-ENST00000520002CSMD1chr83889621-11584815343110973584
ENST00000356207FGFR1chr838314874-ENST00000602557CSMD1chr83889621-11584815343110973584
ENST00000356207FGFR1chr838314874-ENST00000537824CSMD1chr83889621-11095815343110943584
ENST00000356207FGFR1chr838314874-ENST00000542608CSMD1chr83889621-10564815343105633407
ENST00000356207FGFR1chr838314874-ENST00000539096CSMD1chr83889621-673081534367292129
ENST00000326324FGFR1chr838314874-ENST00000602723CSMD1chr83889621-11053815343105663407
ENST00000326324FGFR1chr838314874-ENST00000400186CSMD1chr83889621-11053815343105663407
ENST00000326324FGFR1chr838314874-ENST00000520002CSMD1chr83889621-11584815343110973584
ENST00000326324FGFR1chr838314874-ENST00000602557CSMD1chr83889621-11584815343110973584
ENST00000326324FGFR1chr838314874-ENST00000537824CSMD1chr83889621-11095815343110943584
ENST00000326324FGFR1chr838314874-ENST00000542608CSMD1chr83889621-10564815343105633407
ENST00000326324FGFR1chr838314874-ENST00000539096CSMD1chr83889621-673081534367292129

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
ENST00000397091ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0017007740.9982993
ENST00000397091ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0017007740.9982993
ENST00000397091ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0016230590.99837697
ENST00000397091ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0016230590.99837697
ENST00000397091ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0016819550.9983181
ENST00000397091ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.0017605130.9982395
ENST00000397091ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0015556470.9984444
ENST00000447712ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0021924630.99780756
ENST00000447712ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0021924630.99780756
ENST00000447712ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0020742390.99792576
ENST00000447712ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0020742390.99792576
ENST00000447712ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0021455140.9978544
ENST00000447712ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.0022709820.997729
ENST00000447712ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0020593360.9979406
ENST00000341462ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0021924630.99780756
ENST00000341462ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0021924630.99780756
ENST00000341462ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0020742390.99792576
ENST00000341462ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0020742390.99792576
ENST00000341462ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0021455140.9978544
ENST00000341462ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.0022709820.997729
ENST00000341462ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0020593360.9979406
ENST00000532791ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0016597650.99834025
ENST00000532791ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0016597650.99834025
ENST00000532791ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0015847630.99841523
ENST00000532791ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0015847630.99841523
ENST00000532791ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0016412210.9983588
ENST00000532791ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.001716370.9982836
ENST00000532791ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0015074060.9984926
ENST00000397113ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0010507490.9989492
ENST00000397113ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0010507490.9989492
ENST00000397113ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0010068440.9989931
ENST00000397113ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0010068440.9989931
ENST00000397113ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0010354880.99896455
ENST00000397113ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.0010781860.9989219
ENST00000397113ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0008995740.99910045
ENST00000356207ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0016514570.9983486
ENST00000356207ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0016514570.9983486
ENST00000356207ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0015767860.9984232
ENST00000356207ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0015767860.9984232
ENST00000356207ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0016330840.9983669
ENST00000356207ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.0017076540.9982924
ENST00000356207ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0015043560.9984957
ENST00000326324ENST00000602723FGFR1chr838314874-CSMD1chr83889621-0.0016514570.9983486
ENST00000326324ENST00000400186FGFR1chr838314874-CSMD1chr83889621-0.0016514570.9983486
ENST00000326324ENST00000520002FGFR1chr838314874-CSMD1chr83889621-0.0015767860.9984232
ENST00000326324ENST00000602557FGFR1chr838314874-CSMD1chr83889621-0.0015767860.9984232
ENST00000326324ENST00000537824FGFR1chr838314874-CSMD1chr83889621-0.0016330840.9983669
ENST00000326324ENST00000542608FGFR1chr838314874-CSMD1chr83889621-0.0017076540.9982924
ENST00000326324ENST00000539096FGFR1chr838314874-CSMD1chr83889621-0.0015043560.9984957

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 FGFR1-CSMD1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FGFR1chr838314874CSMD1chr838896211033157LCTARPSPTLPEQVLPSHTCGNPGEI
FGFR1chr838314874CSMD1chr8388962140892LCTARPSPTLPEQVLPSHTCGNPGEI
FGFR1chr838314874CSMD1chr83889621815157LCTARPSPTLPEQVLPSHTCGNPGEI
FGFR1chr838314874CSMD1chr83889621821157LCTARPSPTLPEQVLPSHTCGNPGEI
FGFR1chr838314874CSMD1chr83889621840157LCTARPSPTLPEQVLPSHTCGNPGEI

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Potential FusionNeoAntigen Information of FGFR1-CSMD1 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.
FGFR1-CSMD1_38314874_3889621.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)
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:01SPTLPEQV0.9910.5617614
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:02SPTLPEQV0.9910.562614
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:01LPEQVLPSH0.97710.9512918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:08LPEQVLPSH0.97420.8884918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:03SPTLPEQVL0.95230.8678615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:05LPEQVLPSH0.94970.8157918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:01SPTLPEQVL0.940.8811615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:08SPTLPEQVL0.92890.7749615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:05SPTLPEQVL0.83320.6545615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:04SPTLPEQVL0.80870.952615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:02SPTLPEQVL0.80870.952615
FGFR1-CSMD1chr838314874chr83889621815HLA-B15:10SPTLPEQVL0.75530.6292615
FGFR1-CSMD1chr838314874chr83889621815HLA-B39:01SPTLPEQVL0.59490.8957615
FGFR1-CSMD1chr838314874chr83889621815HLA-B39:06EQVLPSHTC0.49230.90151120
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:02RPSPTLPEQV0.9810.5775414
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:05RPSPTLPEQV0.9810.5683414
FGFR1-CSMD1chr838314874chr83889621815HLA-B82:01RPSPTLPEQV0.5110.7056414
FGFR1-CSMD1chr838314874chr83889621815HLA-B81:01RPSPTLPEQV0.50290.5626414
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:10RPSPTLPEQVL0.99960.566415
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:02RPSPTLPEQVL0.99950.5272415
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:03RPSPTLPEQVL0.92060.7429415
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:02RPSPTLPEQVL0.87530.8815415
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:04RPSPTLPEQVL0.87530.8815415
FGFR1-CSMD1chr838314874chr83889621815HLA-B82:01RPSPTLPEQVL0.77730.5134415
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:08SPTLPEQV0.96070.6196614
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:12SPTLPEQVL0.80870.952615
FGFR1-CSMD1chr838314874chr83889621815HLA-B14:03SPTLPEQVL0.71910.8651615
FGFR1-CSMD1chr838314874chr83889621815HLA-B39:10SPTLPEQVL0.6260.9086615
FGFR1-CSMD1chr838314874chr83889621815HLA-B39:09SPTLPEQVL0.62270.7233615
FGFR1-CSMD1chr838314874chr83889621815HLA-B78:01SPTLPEQVL0.52830.5044615
FGFR1-CSMD1chr838314874chr83889621815HLA-B42:02SPTLPEQVL0.35220.6187615
FGFR1-CSMD1chr838314874chr83889621815HLA-B42:01SPTLPEQVL0.28140.6158615
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:12RPSPTLPEQV0.97220.6644414
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:04RPSPTLPEQV0.88650.5774414
FGFR1-CSMD1chr838314874chr83889621815HLA-B56:04RPSPTLPEQV0.68570.5086414
FGFR1-CSMD1chr838314874chr83889621815HLA-B42:01RPSPTLPEQV0.49880.6099414
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:12RPSPTLPEQVL0.99910.6332415
FGFR1-CSMD1chr838314874chr83889621815HLA-B39:10RPSPTLPEQVL0.94520.8759415
FGFR1-CSMD1chr838314874chr83889621815HLA-B42:02RPSPTLPEQVL0.94340.6046415
FGFR1-CSMD1chr838314874chr83889621815HLA-B42:01RPSPTLPEQVL0.91090.5961415
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:12RPSPTLPEQVL0.87530.8815415
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:13SPTLPEQV0.99020.6154614
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:14SPTLPEQV0.98780.5925614
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:09SPTLPEQV0.97990.7089614
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:21SPTLPEQV0.96970.5821614
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:29SPTLPEQV0.92870.5795614
FGFR1-CSMD1chr838314874chr83889621815HLA-B51:05SPTLPEQV0.92670.5124614
FGFR1-CSMD1chr838314874chr83889621815HLA-B59:01SPTLPEQV0.75780.6454614
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:77LPEQVLPSH0.97710.9512918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:23LPEQVLPSH0.97220.9581918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:30LPEQVLPSH0.96440.9089918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:17LPEQVLPSH0.96440.9089918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:77SPTLPEQVL0.940.8811615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:23SPTLPEQVL0.93540.8706615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:13SPTLPEQVL0.93490.8717615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:24LPEQVLPSH0.93070.9421918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:11LPEQVLPSH0.92560.9613918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:17SPTLPEQVL0.84460.7855615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:30SPTLPEQVL0.84460.7855615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:09SPTLPEQVL0.80870.952615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:11SPTLPEQVL0.78360.9053615
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:24SPTLPEQVL0.69610.9083615
FGFR1-CSMD1chr838314874chr83889621815HLA-B67:01SPTLPEQVL0.64760.8786615
FGFR1-CSMD1chr838314874chr83889621815HLA-B78:02SPTLPEQVL0.58230.6451615
FGFR1-CSMD1chr838314874chr83889621815HLA-B39:11SPTLPEQVL0.56040.7762615
FGFR1-CSMD1chr838314874chr83889621815HLA-B15:09SPTLPEQVL0.46160.7117615
FGFR1-CSMD1chr838314874chr83889621815HLA-B08:12SPTLPEQVL0.34230.7579615
FGFR1-CSMD1chr838314874chr83889621815HLA-B18:07LPEQVLPSH0.32030.9059918
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:43SPTLPEQVL0.02070.8705615
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:22RPSPTLPEQV0.9810.5775414
FGFR1-CSMD1chr838314874chr83889621815HLA-B55:02RPSPTLPEQV0.87550.5562414
FGFR1-CSMD1chr838314874chr83889621815HLA-B56:02RPSPTLPEQV0.68570.5086414
FGFR1-CSMD1chr838314874chr83889621815HLA-B67:01RPSPTLPEQV0.52520.7842414
FGFR1-CSMD1chr838314874chr83889621815HLA-B82:02RPSPTLPEQV0.5110.7056414
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:09RPSPTLPEQVL0.99950.5189415
FGFR1-CSMD1chr838314874chr83889621815HLA-B07:22RPSPTLPEQVL0.99950.5272415
FGFR1-CSMD1chr838314874chr83889621815HLA-B67:01RPSPTLPEQVL0.93360.7781415
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:13RPSPTLPEQVL0.90920.7531415
FGFR1-CSMD1chr838314874chr83889621815HLA-B35:09RPSPTLPEQVL0.87530.8815415
FGFR1-CSMD1chr838314874chr83889621815HLA-B82:02RPSPTLPEQVL0.77730.5134415

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Potential FusionNeoAntigen Information of FGFR1-CSMD1 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 FGFR1-CSMD1

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
8902SPTLPEQVLPSHTCFGFR1CSMD1chr838314874chr83889621815

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FGFR1-CSMD1

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-B14:023BVN8902SPTLPEQVLPSHTC-7.9962-8.1096
HLA-B14:023BVN8902SPTLPEQVLPSHTC-5.70842-6.74372
HLA-B52:013W398902SPTLPEQVLPSHTC-6.83737-6.95077
HLA-B52:013W398902SPTLPEQVLPSHTC-4.4836-5.5189
HLA-A11:014UQ28902SPTLPEQVLPSHTC-10.0067-10.1201
HLA-A11:014UQ28902SPTLPEQVLPSHTC-9.03915-10.0745
HLA-A24:025HGA8902SPTLPEQVLPSHTC-6.56204-6.67544
HLA-A24:025HGA8902SPTLPEQVLPSHTC-5.42271-6.45801
HLA-B44:053DX88902SPTLPEQVLPSHTC-7.85648-8.89178
HLA-B44:053DX88902SPTLPEQVLPSHTC-5.3978-5.5112
HLA-A02:016TDR8902SPTLPEQVLPSHTC-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of FGFR1-CSMD1

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
FGFR1-CSMD1chr838314874chr838896211120EQVLPSHTCAACAAGTTTTACCTAGCCACACTTGTG
FGFR1-CSMD1chr838314874chr83889621414RPSPTLPEQVGGCCGTCCCCGACCTTGCCTGAACAAGTTT
FGFR1-CSMD1chr838314874chr83889621415RPSPTLPEQVLGGCCGTCCCCGACCTTGCCTGAACAAGTTTTAC
FGFR1-CSMD1chr838314874chr83889621614SPTLPEQVCCCCGACCTTGCCTGAACAAGTTT
FGFR1-CSMD1chr838314874chr83889621615SPTLPEQVLCCCCGACCTTGCCTGAACAAGTTTTAC
FGFR1-CSMD1chr838314874chr83889621918LPEQVLPSHTGCCTGAACAAGTTTTACCTAGCCACA

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 FGFR1-CSMD1

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
BRCAFGFR1-CSMD1chr838314874ENST00000326324chr83889621ENST00000400186TCGA-BH-A1ES-01A

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Potential target of CAR-T therapy development for FGFR1-CSMD1

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to FGFR1-CSMD1

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 FGFR1-CSMD1

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
HgeneFGFR1C1563720Kallmann Syndrome 2 (disorder)18CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR1C1845146Holoprosencephaly, Ectrodactyly, and Bilateral Cleft Lip-Palate6GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR1C0011570Mental Depression5PSYGENET
HgeneFGFR1C0011581Depressive disorder5CTD_human;PSYGENET
HgeneFGFR1C0220658Pfeiffer Syndrome5GENOMICS_ENGLAND;UNIPROT
HgeneFGFR1C0432283Osteoglophonic dwarfism5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR1C0041696Unipolar Depression4CTD_human;PSYGENET
HgeneFGFR1C0406612Encephalocraniocutaneous lipomatosis4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR1C0005586Bipolar Disorder3PSYGENET
HgeneFGFR1C0795998JACKSON-WEISS SYNDROME3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR1C1269683Major Depressive Disorder3PSYGENET
HgeneFGFR1C0006142Malignant neoplasm of breast2CGI;CTD_human
HgeneFGFR1C0007131Non-Small Cell Lung Carcinoma2CTD_human
HgeneFGFR1C0007137Squamous cell carcinoma2CTD_human
HgeneFGFR1C0027022Myeloproliferative disease2CTD_human
HgeneFGFR1C0162809Kallmann Syndrome2CTD_human;ORPHANET
HgeneFGFR1C0432122Interfrontal craniofaciosynostosis2GENOMICS_ENGLAND;UNIPROT
HgeneFGFR1C0678222Breast Carcinoma2CGI;CTD_human
HgeneFGFR1C1257931Mammary Neoplasms, Human2CTD_human
HgeneFGFR1C1458155Mammary Neoplasms2CTD_human
HgeneFGFR1C4704874Mammary Carcinoma, Human2CTD_human
HgeneFGFR1C0004114Astrocytoma1CTD_human
HgeneFGFR1C0008924Cleft upper lip1CTD_human
HgeneFGFR1C0008925Cleft Palate1CTD_human
HgeneFGFR1C0010278Craniosynostosis1CTD_human;GENOMICS_ENGLAND
HgeneFGFR1C0011573Endogenous depression1CTD_human
HgeneFGFR1C0017638Glioma1CTD_human
HgeneFGFR1C0018824Heart valve disease1CTD_human
HgeneFGFR1C0024121Lung Neoplasms1CTD_human
HgeneFGFR1C0025193Melancholia1CTD_human
HgeneFGFR1C0036341Schizophrenia1CTD_human
HgeneFGFR1C0085682Hypophosphatemia1GENOMICS_ENGLAND
HgeneFGFR1C0086133Depressive Syndrome1CTD_human
HgeneFGFR1C0149925Small cell carcinoma of lung1CTD_human
HgeneFGFR1C0205768Subependymal Giant Cell Astrocytoma1CTD_human
HgeneFGFR1C0206726gliosarcoma1ORPHANET
HgeneFGFR1C0242379Malignant neoplasm of lung1CTD_human
HgeneFGFR1C0259783mixed gliomas1CTD_human
HgeneFGFR1C0265535Trigonocephaly1CTD_human;ORPHANET
HgeneFGFR1C0280783Juvenile Pilocytic Astrocytoma1CTD_human
HgeneFGFR1C0280785Diffuse Astrocytoma1CTD_human
HgeneFGFR1C0282126Depression, Neurotic1CTD_human
HgeneFGFR1C0334579Anaplastic astrocytoma1CTD_human
HgeneFGFR1C0334580Protoplasmic astrocytoma1CTD_human
HgeneFGFR1C0334581Gemistocytic astrocytoma1CTD_human
HgeneFGFR1C0334582Fibrillary Astrocytoma1CTD_human
HgeneFGFR1C0334583Pilocytic Astrocytoma1CTD_human
HgeneFGFR1C0334588Giant Cell Glioblastoma1ORPHANET
HgeneFGFR1C0338070Childhood Cerebral Astrocytoma1CTD_human
HgeneFGFR1C0338503Septo-Optic Dysplasia1ORPHANET
HgeneFGFR1C0342384Idiopathic hypogonadotropic hypogonadism1GENOMICS_ENGLAND
HgeneFGFR1C0376634Craniofacial Abnormalities1CTD_human
HgeneFGFR1C0431362Lobar Holoprosencephaly1ORPHANET
HgeneFGFR1C0547065Mixed oligoastrocytoma1CTD_human
HgeneFGFR1C0555198Malignant Glioma1CTD_human
HgeneFGFR1C0750935Cerebral Astrocytoma1CTD_human
HgeneFGFR1C0750936Intracranial Astrocytoma1CTD_human
HgeneFGFR1C0751617Semilobar Holoprosencephaly1ORPHANET
HgeneFGFR1C1519086Pilomyxoid astrocytoma1ORPHANET
HgeneFGFR1C1704230Grade I Astrocytoma1CTD_human
HgeneFGFR1C1837218Cleft palate, isolated1CTD_human
HgeneFGFR1C1852406Cutis Gyrata Syndrome of Beare And Stevenson1GENOMICS_ENGLAND
HgeneFGFR1C2931196Craniofacial dysostosis type 11GENOMICS_ENGLAND
HgeneFGFR1C3150773CHROMOSOME 8p11 MYELOPROLIFERATIVE SYNDROME1ORPHANET