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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:FGFR3-AMBRA1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FGFR3-AMBRA1
FusionPDB ID: 30300
FusionGDB2.0 ID: 30300
HgeneTgene
Gene symbol

FGFR3

AMBRA1

Gene ID

2261

55626

Gene namefibroblast growth factor receptor 3autophagy and beclin 1 regulator 1
SynonymsACH|CD333|CEK2|HSFGFR3EX|JTK4DCAF3|WDR94
Cytomap

4p16.3

11p11.2

Type of geneprotein-codingprotein-coding
Descriptionfibroblast growth factor receptor 3FGFR-3fibroblast growth factor receptor 3 variant 4fibroblast growth factor receptor 3-Shydroxyaryl-protein kinasetyrosine kinase JTK4activating molecule in BECN1-regulated autophagy protein 1DDB1 and CUL4 associated factor 3WD repeat domain 94activating molecule in beclin-1-regulated autophagyautophagy/beclin-1 regulator 1
Modification date2020031320200313
UniProtAcc

P22607

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 and apoptosis. Plays an essential role in the regulation of chondrocyte differentiation, proliferation and apoptosis, and is required for normal skeleton development. Regulates both osteogenesis and postnatal bone mineralization by osteoblasts. Promotes apoptosis in chondrocytes, but can also promote cancer cell proliferation. Required for normal development of the inner ear. Phosphorylates PLCG1, CBL and FRS2. 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. Plays a role in the regulation of vitamin D metabolism. Mutations that lead to constitutive kinase activation or impair normal FGFR3 maturation, internalization and degradation lead to aberrant signaling. Over-expressed or constitutively activated FGFR3 promotes activation of PTPN11/SHP2, STAT1, STAT5A and STAT5B. Secreted isoform 3 retains its capacity to bind FGF1 and FGF2 and hence may interfere with FGF signaling. {ECO:0000269|PubMed:10611230, ECO:0000269|PubMed:11294897, ECO:0000269|PubMed:11703096, ECO:0000269|PubMed:14534538, ECO:0000269|PubMed:16410555, ECO:0000269|PubMed:16597617, ECO:0000269|PubMed:17145761, ECO:0000269|PubMed:17311277, ECO:0000269|PubMed:17509076, ECO:0000269|PubMed:17561467, ECO:0000269|PubMed:19088846, ECO:0000269|PubMed:19286672, ECO:0000269|PubMed:8663044}.

Q9C0C7

Main function of 5'-partner protein: FUNCTION: Regulates autophagy and development of the nervous system. Involved in autophagy in controlling protein turnover during neuronal development, and in regulating normal cell survival and proliferation (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000260795, ENST00000340107, 
ENST00000352904, ENST00000412135, 
ENST00000440486, ENST00000481110, 
ENST00000474521, 		ENST00000529963, 
ENST00000298834, ENST00000314845, 
ENST00000426438, ENST00000458649, 
ENST00000528950, ENST00000533727, 
ENST00000534300, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 22 X 14=308017 X 12 X 8=1632
# samples 3319
** MAII scorelog2(33/3080*10)=-3.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1632*10)=-3.10256973364055
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: FGFR3 [Title/Abstract] AND AMBRA1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FGFR3 [Title/Abstract] AND AMBRA1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FGFR3(1808661)-AMBRA1(46439602), # samples:1
Anticipated loss of major functional domain due to fusion event.FGFR3-AMBRA1 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.
FGFR3-AMBRA1 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.
FGFR3-AMBRA1 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.
FGFR3-AMBRA1 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.
FGFR3-AMBRA1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
FGFR3-AMBRA1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
FGFR3-AMBRA1 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
FGFR3-AMBRA1 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
HgeneFGFR3

GO:0008543

fibroblast growth factor receptor signaling pathway

8663044

HgeneFGFR3

GO:0018108

peptidyl-tyrosine phosphorylation

11294897

HgeneFGFR3

GO:0046777

protein autophosphorylation

11294897

TgeneAMBRA1

GO:0000423

mitophagy

21753002

TgeneAMBRA1

GO:0043552

positive regulation of phosphatidylinositol 3-kinase activity

21753002

TgeneAMBRA1

GO:0098780

response to mitochondrial depolarisation

21753002



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/chr4:1808661/chr11:46439602)
- 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 FGFR3 (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 AMBRA1 (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)
ENST00000440486FGFR3chr41808661+ENST00000298834AMBRA1chr1146439602-4487253022334501075
ENST00000440486FGFR3chr41808661+ENST00000426438AMBRA1chr1146439602-4487253022334501075
ENST00000440486FGFR3chr41808661+ENST00000314845AMBRA1chr1146439602-4487253022334501075
ENST00000440486FGFR3chr41808661+ENST00000533727AMBRA1chr1146439602-4487253022334501075
ENST00000440486FGFR3chr41808661+ENST00000534300AMBRA1chr1146439602-4487253022334501075
ENST00000440486FGFR3chr41808661+ENST00000458649AMBRA1chr1146439602-4486253022334501075
ENST00000440486FGFR3chr41808661+ENST00000528950AMBRA1chr1146439602-3451253022334501076
ENST00000412135FGFR3chr41808661+ENST00000298834AMBRA1chr1146439602-415121942233114963
ENST00000412135FGFR3chr41808661+ENST00000426438AMBRA1chr1146439602-415121942233114963
ENST00000412135FGFR3chr41808661+ENST00000314845AMBRA1chr1146439602-415121942233114963
ENST00000412135FGFR3chr41808661+ENST00000533727AMBRA1chr1146439602-415121942233114963
ENST00000412135FGFR3chr41808661+ENST00000534300AMBRA1chr1146439602-415121942233114963
ENST00000412135FGFR3chr41808661+ENST00000458649AMBRA1chr1146439602-415021942233114963
ENST00000412135FGFR3chr41808661+ENST00000528950AMBRA1chr1146439602-311521942233114964
ENST00000340107FGFR3chr41808661+ENST00000298834AMBRA1chr1146439602-4493253622334561077
ENST00000340107FGFR3chr41808661+ENST00000426438AMBRA1chr1146439602-4493253622334561077
ENST00000340107FGFR3chr41808661+ENST00000314845AMBRA1chr1146439602-4493253622334561077
ENST00000340107FGFR3chr41808661+ENST00000533727AMBRA1chr1146439602-4493253622334561077
ENST00000340107FGFR3chr41808661+ENST00000534300AMBRA1chr1146439602-4493253622334561077
ENST00000340107FGFR3chr41808661+ENST00000458649AMBRA1chr1146439602-4492253622334561077
ENST00000340107FGFR3chr41808661+ENST00000528950AMBRA1chr1146439602-3457253622334561078
ENST00000260795FGFR3chr41808661+ENST00000298834AMBRA1chr1146439602-433323766932961075
ENST00000260795FGFR3chr41808661+ENST00000426438AMBRA1chr1146439602-433323766932961075
ENST00000260795FGFR3chr41808661+ENST00000314845AMBRA1chr1146439602-433323766932961075
ENST00000260795FGFR3chr41808661+ENST00000533727AMBRA1chr1146439602-433323766932961075
ENST00000260795FGFR3chr41808661+ENST00000534300AMBRA1chr1146439602-433323766932961075
ENST00000260795FGFR3chr41808661+ENST00000458649AMBRA1chr1146439602-433223766932961075
ENST00000260795FGFR3chr41808661+ENST00000528950AMBRA1chr1146439602-329723766932961075
ENST00000352904FGFR3chr41808661+ENST00000298834AMBRA1chr1146439602-3934197762897963
ENST00000352904FGFR3chr41808661+ENST00000426438AMBRA1chr1146439602-3934197762897963
ENST00000352904FGFR3chr41808661+ENST00000314845AMBRA1chr1146439602-3934197762897963
ENST00000352904FGFR3chr41808661+ENST00000533727AMBRA1chr1146439602-3934197762897963
ENST00000352904FGFR3chr41808661+ENST00000534300AMBRA1chr1146439602-3934197762897963
ENST00000352904FGFR3chr41808661+ENST00000458649AMBRA1chr1146439602-3933197762897963
ENST00000352904FGFR3chr41808661+ENST00000528950AMBRA1chr1146439602-2898197762897963

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
ENST00000440486ENST00000298834FGFR3chr41808661+AMBRA1chr1146439602-0.0027240150.997276
ENST00000440486ENST00000426438FGFR3chr41808661+AMBRA1chr1146439602-0.0027240150.997276
ENST00000440486ENST00000314845FGFR3chr41808661+AMBRA1chr1146439602-0.0027240150.997276
ENST00000440486ENST00000533727FGFR3chr41808661+AMBRA1chr1146439602-0.0027240150.997276
ENST00000440486ENST00000534300FGFR3chr41808661+AMBRA1chr1146439602-0.0027240150.997276
ENST00000440486ENST00000458649FGFR3chr41808661+AMBRA1chr1146439602-0.0027158710.9972842
ENST00000440486ENST00000528950FGFR3chr41808661+AMBRA1chr1146439602-0.0047061090.9952939
ENST00000412135ENST00000298834FGFR3chr41808661+AMBRA1chr1146439602-0.0021454760.99785453
ENST00000412135ENST00000426438FGFR3chr41808661+AMBRA1chr1146439602-0.0021454760.99785453
ENST00000412135ENST00000314845FGFR3chr41808661+AMBRA1chr1146439602-0.0021454760.99785453
ENST00000412135ENST00000533727FGFR3chr41808661+AMBRA1chr1146439602-0.0021454760.99785453
ENST00000412135ENST00000534300FGFR3chr41808661+AMBRA1chr1146439602-0.0021454760.99785453
ENST00000412135ENST00000458649FGFR3chr41808661+AMBRA1chr1146439602-0.0021385370.99786144
ENST00000412135ENST00000528950FGFR3chr41808661+AMBRA1chr1146439602-0.0039314210.9960686
ENST00000340107ENST00000298834FGFR3chr41808661+AMBRA1chr1146439602-0.0032089120.99679106
ENST00000340107ENST00000426438FGFR3chr41808661+AMBRA1chr1146439602-0.0032089120.99679106
ENST00000340107ENST00000314845FGFR3chr41808661+AMBRA1chr1146439602-0.0032089120.99679106
ENST00000340107ENST00000533727FGFR3chr41808661+AMBRA1chr1146439602-0.0032089120.99679106
ENST00000340107ENST00000534300FGFR3chr41808661+AMBRA1chr1146439602-0.0032089120.99679106
ENST00000340107ENST00000458649FGFR3chr41808661+AMBRA1chr1146439602-0.0032010710.9967989
ENST00000340107ENST00000528950FGFR3chr41808661+AMBRA1chr1146439602-0.005454790.9945452
ENST00000260795ENST00000298834FGFR3chr41808661+AMBRA1chr1146439602-0.0023156550.99768436
ENST00000260795ENST00000426438FGFR3chr41808661+AMBRA1chr1146439602-0.0023156550.99768436
ENST00000260795ENST00000314845FGFR3chr41808661+AMBRA1chr1146439602-0.0023156550.99768436
ENST00000260795ENST00000533727FGFR3chr41808661+AMBRA1chr1146439602-0.0023156550.99768436
ENST00000260795ENST00000534300FGFR3chr41808661+AMBRA1chr1146439602-0.0023156550.99768436
ENST00000260795ENST00000458649FGFR3chr41808661+AMBRA1chr1146439602-0.0023078820.9976921
ENST00000260795ENST00000528950FGFR3chr41808661+AMBRA1chr1146439602-0.0041746690.9958254
ENST00000352904ENST00000298834FGFR3chr41808661+AMBRA1chr1146439602-0.0020517180.99794835
ENST00000352904ENST00000426438FGFR3chr41808661+AMBRA1chr1146439602-0.0020517180.99794835
ENST00000352904ENST00000314845FGFR3chr41808661+AMBRA1chr1146439602-0.0020517180.99794835
ENST00000352904ENST00000533727FGFR3chr41808661+AMBRA1chr1146439602-0.0020517180.99794835
ENST00000352904ENST00000534300FGFR3chr41808661+AMBRA1chr1146439602-0.0020517180.99794835
ENST00000352904ENST00000458649FGFR3chr41808661+AMBRA1chr1146439602-0.0020441730.9979558
ENST00000352904ENST00000528950FGFR3chr41808661+AMBRA1chr1146439602-0.0039673020.99603266

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 FGFR3-AMBRA1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FGFR3chr41808661AMBRA1chr11464396021977654QLVEDLDRVLTVTSTDRVFNVLYPMP
FGFR3chr41808661AMBRA1chr11464396022194654QLVEDLDRVLTVTSTDRVFNVLYPMP
FGFR3chr41808661AMBRA1chr11464396022376766QLVEDLDRVLTVTSTDRVFNVLYPMP
FGFR3chr41808661AMBRA1chr11464396022530766QLVEDLDRVLTVTSTDRVFNVLYPMP
FGFR3chr41808661AMBRA1chr11464396022536768QLVEDLDRVLTVTSTDRVFNVLYPMP

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Potential FusionNeoAntigen Information of FGFR3-AMBRA1 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.
FGFR3-AMBRA1_1808661_46439602.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)
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A74:09RVLTVTSTDR0.98610.5933717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A74:03RVLTVTSTDR0.98610.5933717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A74:11RVLTVTSTDR0.98610.5933717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A31:06RVLTVTSTDR0.98170.5297717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A03:12RVLTVTSTDR0.97360.5456717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A31:02RVLTVTSTDR0.96030.603717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C15:06TSTDRVFNV0.99920.85661221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C12:04TSTDRVFNV0.92750.98951221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C06:03TSTDRVFNV0.90540.98141221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C02:06TSTDRVFNV0.60680.94641221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A31:01RVLTVTSTDR0.98810.5666717
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C15:02TSTDRVFNV0.99950.82391221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C15:05TSTDRVFNV0.99950.85681221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A69:01TSTDRVFNV0.99240.74241221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C16:02TSTDRVFNV0.98240.99041221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C16:04TSTDRVFNV0.93790.94271221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C03:02TVTSTDRVF0.93120.9581019
FGFR3-AMBRA1chr41808661chr11464396022376HLA-C12:03TSTDRVFNV0.7130.94761221
FGFR3-AMBRA1chr41808661chr11464396022376HLA-A74:01RVLTVTSTDR0.98610.5933717

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Potential FusionNeoAntigen Information of FGFR3-AMBRA1 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.
FGFR3-AMBRA1_1808661_46439602.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)
FGFR3-AMBRA1chr41808661chr11464396022376DRB1-1410DRVLTVTSTDRVFNV621
FGFR3-AMBRA1chr41808661chr11464396022376DRB1-1410LDRVLTVTSTDRVFN520
FGFR3-AMBRA1chr41808661chr11464396022376DRB4-0101DRVLTVTSTDRVFNV621
FGFR3-AMBRA1chr41808661chr11464396022376DRB4-0103DRVLTVTSTDRVFNV621
FGFR3-AMBRA1chr41808661chr11464396022376DRB4-0104DRVLTVTSTDRVFNV621
FGFR3-AMBRA1chr41808661chr11464396022376DRB4-0106DRVLTVTSTDRVFNV621
FGFR3-AMBRA1chr41808661chr11464396022376DRB4-0107DRVLTVTSTDRVFNV621
FGFR3-AMBRA1chr41808661chr11464396022376DRB4-0108DRVLTVTSTDRVFNV621

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Fusion breakpoint peptide structures of FGFR3-AMBRA1

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
1391DRVLTVTSTDRVFNFGFR3AMBRA1chr41808661chr11464396022376

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FGFR3-AMBRA1

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-B14:023BVN1391DRVLTVTSTDRVFN-7.15543-7.26883
HLA-B14:023BVN1391DRVLTVTSTDRVFN-4.77435-5.80965
HLA-B52:013W391391DRVLTVTSTDRVFN-6.80875-6.92215
HLA-B52:013W391391DRVLTVTSTDRVFN-4.20386-5.23916
HLA-A11:014UQ21391DRVLTVTSTDRVFN-7.5194-8.5547
HLA-A11:014UQ21391DRVLTVTSTDRVFN-6.9601-7.0735
HLA-A24:025HGA1391DRVLTVTSTDRVFN-7.52403-7.63743
HLA-A24:025HGA1391DRVLTVTSTDRVFN-5.82433-6.85963
HLA-B27:056PYJ1391DRVLTVTSTDRVFN-3.28285-4.31815
HLA-B44:053DX81391DRVLTVTSTDRVFN-5.91172-6.94702
HLA-B44:053DX81391DRVLTVTSTDRVFN-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of FGFR3-AMBRA1

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
FGFR3-AMBRA1chr41808661chr11464396021019TVTSTDRVFTCCACCGACAGAGTTTTCAACGTCCTT
FGFR3-AMBRA1chr41808661chr11464396021221TSTDRVFNVGACAGAGTTTTCAACGTCCTTTATCCC
FGFR3-AMBRA1chr41808661chr1146439602717RVLTVTSTDRACCGTGACGTCCACCGACAGAGTTTTCAAC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
FGFR3-AMBRA1chr41808661chr1146439602520LDRVLTVTSTDRVFNGTCCTTACCGTGACGTCCACCGACAGAGTTTTCAACGTCCTTTAT
FGFR3-AMBRA1chr41808661chr1146439602621DRVLTVTSTDRVFNVCTTACCGTGACGTCCACCGACAGAGTTTTCAACGTCCTTTATCCC

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Information of the samples that have these potential fusion neoantigens of FGFR3-AMBRA1

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
GBMFGFR3-AMBRA1chr41808661ENST00000260795chr1146439602ENST00000298834TCGA-19-A6J4-01A

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Potential target of CAR-T therapy development for FGFR3-AMBRA1

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
HgeneFGFR3chr4:1808661chr11:46439602ENST00000260795+1617376_396758807.0TransmembraneHelical
HgeneFGFR3chr4:1808661chr11:46439602ENST00000340107+1718376_396760809.0TransmembraneHelical
HgeneFGFR3chr4:1808661chr11:46439602ENST00000352904+1415376_396646695.0TransmembraneHelical
HgeneFGFR3chr4:1808661chr11:46439602ENST00000412135+1516376_396646695.0TransmembraneHelical
HgeneFGFR3chr4:1808661chr11:46439602ENST00000440486+1718376_396758807.0TransmembraneHelical

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 FGFR3-AMBRA1

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 FGFR3-AMBRA1

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
HgeneFGFR3C0001080Achondroplasia13CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR3C0410529Hypochondroplasia (disorder)10CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR3C1864436Muenke Syndrome9CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR3C1868678THANATOPHORIC DYSPLASIA, TYPE I (disorder)9CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR3C2677099CROUZON SYNDROME WITH ACANTHOSIS NIGRICANS (disorder)7CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR3C0005684Malignant neoplasm of urinary bladder6CGI;CTD_human;UNIPROT
HgeneFGFR3C0005695Bladder Neoplasm4CGI;CTD_human
HgeneFGFR3C1300257Thanatophoric dysplasia, type 24CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneFGFR3C1864852CATSHL syndrome4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR3C2674173Achondroplasia, Severe, With Developmental Delay And Acanthosis Nigricans3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR3C0265269Lacrimoauriculodentodigital syndrome2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneFGFR3C0007138Carcinoma, Transitional Cell1CTD_human
HgeneFGFR3C0008924Cleft upper lip1CTD_human
HgeneFGFR3C0008925Cleft Palate1CTD_human
HgeneFGFR3C0014544Epilepsy1GENOMICS_ENGLAND
HgeneFGFR3C0014547Epilepsies, Partial1GENOMICS_ENGLAND
HgeneFGFR3C0022603Seborrheic keratosis1UNIPROT
HgeneFGFR3C0026764Multiple Myeloma1CGI;CTD_human
HgeneFGFR3C0036631Seminoma1CTD_human
HgeneFGFR3C0039743Thanatophoric Dysplasia1CTD_human
HgeneFGFR3C0152423Congenital small ears1GENOMICS_ENGLAND
HgeneFGFR3C0206726gliosarcoma1ORPHANET
HgeneFGFR3C0221356Brachycephaly1ORPHANET
HgeneFGFR3C0265529Plagiocephaly1ORPHANET
HgeneFGFR3C0334082NEVUS, EPIDERMAL (disorder)1CTD_human;UNIPROT
HgeneFGFR3C0334588Giant Cell Glioblastoma1ORPHANET
HgeneFGFR3C0406803Syringocystadenoma Papilliferum1GENOMICS_ENGLAND
HgeneFGFR3C1336708Testicular Germ Cell Tumor1CTD_human;UNIPROT
HgeneFGFR3C1837218Cleft palate, isolated1CTD_human
HgeneFGFR3C4048328cervical cancer1CTD_human;UNIPROT