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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:FDFT1-CASK

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FDFT1-CASK
FusionPDB ID: 30039
FusionGDB2.0 ID: 30039
HgeneTgene
Gene symbol

FDFT1

CASK

Gene ID

2222

8573

Gene namefarnesyl-diphosphate farnesyltransferase 1calcium/calmodulin dependent serine protein kinase
SynonymsDGPT|ERG9|SQS|SQSD|SSCAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK
Cytomap

8p23.1

Xp11.4

Type of geneprotein-codingprotein-coding
Descriptionsqualene synthaseFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthetaseperipheral plasma membrane protein CASKcalcium/calmodulin-dependent serin protein kinasecalcium/calmodulin-dependent serine protein kinase (MAGUK family)calcium/calmodulin-dependent serine protein kinase membrane-associated guanylate kinaseprotein lin
Modification date2020032020200327
UniProtAcc

P37268

Main function of 5'-partner protein: FUNCTION: Catalyzes the condensation of 2 farnesyl pyrophosphate (FPP) moieties to form squalene. Proceeds in two distinct steps. In the first half-reaction, two molecules of FPP react to form the stable presqualene diphosphate intermediate (PSQPP), with concomitant release of a proton and a molecule of inorganic diphosphate. In the second half-reaction, PSQPP undergoes heterolysis, isomerization, and reduction with NADPH or NADH to form squalene. It is the first committed enzyme of the sterol biosynthesis pathway. {ECO:0000269|PubMed:10896663, ECO:0000269|PubMed:24531458}.

Q8WXE0

Main function of 5'-partner protein:
Ensembl transtripts involved in fusion geneENST idsENST00000220584, ENST00000525777, 
ENST00000525900, ENST00000528643, 
ENST00000528812, ENST00000530664, 
ENST00000538689, ENST00000443614, 
ENST00000446331, 		ENST00000378154, 
ENST00000472704, ENST00000318588, 
ENST00000361962, ENST00000378158, 
ENST00000378163, ENST00000378166, 
ENST00000421587, ENST00000442742, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 12 X 9=172815 X 14 X 9=1890
# samples 2017
** MAII scorelog2(20/1728*10)=-3.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1890*10)=-3.47477958297073
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: FDFT1 [Title/Abstract] AND CASK [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FDFT1 [Title/Abstract] AND CASK [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FDFT1(11679387)-CASK(41530783), # samples:1
Anticipated loss of major functional domain due to fusion event.FDFT1-CASK 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.
FDFT1-CASK 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.
FDFT1-CASK 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.
FDFT1-CASK seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

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

GO:0010839

negative regulation of keratinocyte proliferation

18664494



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/chr8:11679387/chrX:41530783)
- 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 FDFT1 (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 CASK (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)
ENST00000538689FDFT1chr811679387+ENST00000421587CASKchrX41530783-86018503763114912
ENST00000538689FDFT1chr811679387+ENST00000318588CASKchrX41530783-86738503763186936
ENST00000538689FDFT1chr811679387+ENST00000361962CASKchrX41530783-86378503763150924
ENST00000538689FDFT1chr811679387+ENST00000378163CASKchrX41530783-43578503763201941
ENST00000538689FDFT1chr811679387+ENST00000378158CASKchrX41530783-39188503763150924
ENST00000538689FDFT1chr811679387+ENST00000378166CASKchrX41530783-35178503763186936
ENST00000538689FDFT1chr811679387+ENST00000442742CASKchrX41530783-32028503763117913
ENST00000220584FDFT1chr811679387+ENST00000421587CASKchrX41530783-84837322222996924
ENST00000220584FDFT1chr811679387+ENST00000318588CASKchrX41530783-85557322223068948
ENST00000220584FDFT1chr811679387+ENST00000361962CASKchrX41530783-85197322223032936
ENST00000220584FDFT1chr811679387+ENST00000378163CASKchrX41530783-42397322223083953
ENST00000220584FDFT1chr811679387+ENST00000378158CASKchrX41530783-38007322223032936
ENST00000220584FDFT1chr811679387+ENST00000378166CASKchrX41530783-33997322223068948
ENST00000220584FDFT1chr811679387+ENST00000442742CASKchrX41530783-30847322222999925
ENST00000525900FDFT1chr811679387+ENST00000421587CASKchrX41530783-8307556672820917
ENST00000525900FDFT1chr811679387+ENST00000318588CASKchrX41530783-8379556672892941
ENST00000525900FDFT1chr811679387+ENST00000361962CASKchrX41530783-8343556672856929
ENST00000525900FDFT1chr811679387+ENST00000378163CASKchrX41530783-4063556672907946
ENST00000525900FDFT1chr811679387+ENST00000378158CASKchrX41530783-3624556672856929
ENST00000525900FDFT1chr811679387+ENST00000378166CASKchrX41530783-3223556672892941
ENST00000525900FDFT1chr811679387+ENST00000442742CASKchrX41530783-2908556672823918
ENST00000528812FDFT1chr811679387+ENST00000421587CASKchrX41530783-86699185253182885
ENST00000528812FDFT1chr811679387+ENST00000318588CASKchrX41530783-87419185253254909
ENST00000528812FDFT1chr811679387+ENST00000361962CASKchrX41530783-87059185253218897
ENST00000528812FDFT1chr811679387+ENST00000378163CASKchrX41530783-44259185253269914
ENST00000528812FDFT1chr811679387+ENST00000378158CASKchrX41530783-39869185253218897
ENST00000528812FDFT1chr811679387+ENST00000378166CASKchrX41530783-35859185253254909
ENST00000528812FDFT1chr811679387+ENST00000442742CASKchrX41530783-32709185253185886
ENST00000530664FDFT1chr811679387+ENST00000421587CASKchrX41530783-85377863453050901
ENST00000530664FDFT1chr811679387+ENST00000318588CASKchrX41530783-86097863453122925
ENST00000530664FDFT1chr811679387+ENST00000361962CASKchrX41530783-85737863453086913
ENST00000530664FDFT1chr811679387+ENST00000378163CASKchrX41530783-42937863453137930
ENST00000530664FDFT1chr811679387+ENST00000378158CASKchrX41530783-38547863453086913
ENST00000530664FDFT1chr811679387+ENST00000378166CASKchrX41530783-34537863453122925
ENST00000530664FDFT1chr811679387+ENST00000442742CASKchrX41530783-31387863453053902
ENST00000528643FDFT1chr811679387+ENST00000421587CASKchrX41530783-84116603692924851
ENST00000528643FDFT1chr811679387+ENST00000318588CASKchrX41530783-84836603692996875
ENST00000528643FDFT1chr811679387+ENST00000361962CASKchrX41530783-84476603692960863
ENST00000528643FDFT1chr811679387+ENST00000378163CASKchrX41530783-41676603693011880
ENST00000528643FDFT1chr811679387+ENST00000378158CASKchrX41530783-37286603692960863
ENST00000528643FDFT1chr811679387+ENST00000378166CASKchrX41530783-33276603692996875
ENST00000528643FDFT1chr811679387+ENST00000442742CASKchrX41530783-30126603692927852
ENST00000525777FDFT1chr811679387+ENST00000421587CASKchrX41530783-84757244332988851
ENST00000525777FDFT1chr811679387+ENST00000318588CASKchrX41530783-85477244333060875
ENST00000525777FDFT1chr811679387+ENST00000361962CASKchrX41530783-85117244333024863
ENST00000525777FDFT1chr811679387+ENST00000378163CASKchrX41530783-42317244333075880
ENST00000525777FDFT1chr811679387+ENST00000378158CASKchrX41530783-37927244333024863
ENST00000525777FDFT1chr811679387+ENST00000378166CASKchrX41530783-33917244333060875
ENST00000525777FDFT1chr811679387+ENST00000442742CASKchrX41530783-30767244332991852

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
ENST00000538689ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.0002659180.9997341
ENST00000538689ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0001803120.9998197
ENST00000538689ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0002001090.9997999
ENST00000538689ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.0002769320.999723
ENST00000538689ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.0004697870.9995302
ENST00000538689ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.0011271560.9988728
ENST00000538689ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.0024730550.99752694
ENST00000220584ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.0004096520.99959034
ENST00000220584ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0003982950.9996018
ENST00000220584ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0004108560.99958915
ENST00000220584ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.000491620.9995084
ENST00000220584ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.0008057470.9991942
ENST00000220584ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.0020226590.9979773
ENST00000220584ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.0044738770.99552613
ENST00000525900ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.0002030690.9997969
ENST00000525900ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0001872350.9998128
ENST00000525900ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0001907590.9998092
ENST00000525900ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.0002003320.99979967
ENST00000525900ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.000394570.9996055
ENST00000525900ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.001072480.99892753
ENST00000525900ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.0022602150.9977398
ENST00000528812ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.000256560.9997434
ENST00000528812ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0001738760.99982613
ENST00000528812ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0001928830.9998072
ENST00000528812ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.0002279990.999772
ENST00000528812ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.0003925520.9996075
ENST00000528812ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.0008579850.99914205
ENST00000528812ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.0015557820.99844426
ENST00000530664ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.0002600980.99973994
ENST00000530664ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0001768410.99982315
ENST00000530664ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0001957460.9998043
ENST00000530664ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.0002510720.9997489
ENST00000530664ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.0004572080.99954283
ENST00000530664ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.0010662030.99893373
ENST00000530664ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.002456720.99754333
ENST00000528643ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.0005773960.99942267
ENST00000528643ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0004863320.9995136
ENST00000528643ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0005183840.9994816
ENST00000528643ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.0005358340.9994642
ENST00000528643ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.0008626770.9991373
ENST00000528643ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.0019231730.9980768
ENST00000528643ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.0033347140.9966653
ENST00000525777ENST00000421587FDFT1chr811679387+CASKchrX41530783-0.0004946460.9995054
ENST00000525777ENST00000318588FDFT1chr811679387+CASKchrX41530783-0.0004159790.999584
ENST00000525777ENST00000361962FDFT1chr811679387+CASKchrX41530783-0.0004427540.9995572
ENST00000525777ENST00000378163FDFT1chr811679387+CASKchrX41530783-0.0003873350.99961275
ENST00000525777ENST00000378158FDFT1chr811679387+CASKchrX41530783-0.0005768340.99942315
ENST00000525777ENST00000378166FDFT1chr811679387+CASKchrX41530783-0.0010518730.99894816
ENST00000525777ENST00000442742FDFT1chr811679387+CASKchrX41530783-0.0019159260.99808407

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 FDFT1-CASK

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FDFT1chr811679387CASKchrX41530783556163LDKHVTSEQEWDKPHCVLLASKENSA
FDFT1chr811679387CASKchrX4153078366097LDKHVTSEQEWDKPHCVLLASKENSA
FDFT1chr811679387CASKchrX4153078372497LDKHVTSEQEWDKPHCVLLASKENSA
FDFT1chr811679387CASKchrX41530783732170LDKHVTSEQEWDKPHCVLLASKENSA
FDFT1chr811679387CASKchrX41530783786147LDKHVTSEQEWDKPHCVLLASKENSA
FDFT1chr811679387CASKchrX41530783850158LDKHVTSEQEWDKPHCVLLASKENSA
FDFT1chr811679387CASKchrX41530783918131LDKHVTSEQEWDKPHCVLLASKENSA

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Potential FusionNeoAntigen Information of FDFT1-CASK 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.
FDFT1-CASK_11679387_41530783.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)
FDFT1-CASKchr811679387chrX41530783732HLA-B40:02QEWDKPHCV0.99950.5438817
FDFT1-CASKchr811679387chrX41530783732HLA-B45:01QEWDKPHCV0.99870.9939817
FDFT1-CASKchr811679387chrX41530783732HLA-B50:02QEWDKPHCV0.99860.9521817
FDFT1-CASKchr811679387chrX41530783732HLA-B13:02QEWDKPHCV0.9960.9921817
FDFT1-CASKchr811679387chrX41530783732HLA-B40:01QEWDKPHCV0.98650.8995817
FDFT1-CASKchr811679387chrX41530783732HLA-B13:01QEWDKPHCV0.98290.9956817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:05QEWDKPHCV0.9550.9306817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:02QEWDKPHCV0.94890.7649817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:03QEWDKPHCV0.94520.9808817
FDFT1-CASKchr811679387chrX41530783732HLA-B47:01QEWDKPHCV0.91510.7995817
FDFT1-CASKchr811679387chrX41530783732HLA-B18:01QEWDKPHCV0.82470.9625817
FDFT1-CASKchr811679387chrX41530783732HLA-B41:01QEWDKPHCV0.81290.9779817
FDFT1-CASKchr811679387chrX41530783732HLA-B41:02QEWDKPHCV0.79510.6196817
FDFT1-CASKchr811679387chrX41530783732HLA-B40:05QEWDKPHCV0.73850.5225817
FDFT1-CASKchr811679387chrX41530783732HLA-B39:13QEWDKPHCV0.71830.984817
FDFT1-CASKchr811679387chrX41530783732HLA-B50:01QEWDKPHCV0.53840.9753817
FDFT1-CASKchr811679387chrX41530783732HLA-B08:01EWDKPHCVL0.13980.6831918
FDFT1-CASKchr811679387chrX41530783732HLA-B07:10EWDKPHCVL0.01960.5359918
FDFT1-CASKchr811679387chrX41530783732HLA-B48:01QEWDKPHCVL0.99660.7369818
FDFT1-CASKchr811679387chrX41530783732HLA-B40:01QEWDKPHCVL0.99160.5927818
FDFT1-CASKchr811679387chrX41530783732HLA-B13:01QEWDKPHCVL0.98280.9867818
FDFT1-CASKchr811679387chrX41530783732HLA-B47:01QEWDKPHCVL0.97850.7702818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:03QEWDKPHCVL0.97690.9551818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:05QEWDKPHCVL0.97130.6474818
FDFT1-CASKchr811679387chrX41530783732HLA-B39:13QEWDKPHCVL0.90780.9772818
FDFT1-CASKchr811679387chrX41530783732HLA-B41:02QEWDKPHCVL0.89110.5034818
FDFT1-CASKchr811679387chrX41530783732HLA-B41:01QEWDKPHCVL0.65230.9737818
FDFT1-CASKchr811679387chrX41530783732HLA-B48:01QEWDKPHCVLL0.99920.7291819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:03QEWDKPHCVLL0.99880.9535819
FDFT1-CASKchr811679387chrX41530783732HLA-B40:01QEWDKPHCVLL0.99850.5227819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:05QEWDKPHCVLL0.99810.6209819
FDFT1-CASKchr811679387chrX41530783732HLA-B13:01QEWDKPHCVLL0.99810.9778819
FDFT1-CASKchr811679387chrX41530783732HLA-B47:01QEWDKPHCVLL0.99730.7327819
FDFT1-CASKchr811679387chrX41530783732HLA-B39:13QEWDKPHCVLL0.99450.9741819
FDFT1-CASKchr811679387chrX41530783732HLA-C04:07EWDKPHCV0.99970.9829917
FDFT1-CASKchr811679387chrX41530783732HLA-C04:10WDKPHCVL0.99880.96821018
FDFT1-CASKchr811679387chrX41530783732HLA-C04:07WDKPHCVL0.99860.96761018
FDFT1-CASKchr811679387chrX41530783732HLA-B40:06QEWDKPHCV0.99950.9777817
FDFT1-CASKchr811679387chrX41530783732HLA-C04:07EWDKPHCVL0.99440.8683918
FDFT1-CASKchr811679387chrX41530783732HLA-C04:10EWDKPHCVL0.99410.8562918
FDFT1-CASKchr811679387chrX41530783732HLA-B44:10QEWDKPHCV0.99220.9639817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:08QEWDKPHCV0.95550.8388817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:09QEWDKPHCV0.9520.9115817
FDFT1-CASKchr811679387chrX41530783732HLA-B48:03QEWDKPHCV0.94940.9191817
FDFT1-CASKchr811679387chrX41530783732HLA-B40:03QEWDKPHCV0.92830.7474817
FDFT1-CASKchr811679387chrX41530783732HLA-B39:08QEWDKPHCV0.77220.9853817
FDFT1-CASKchr811679387chrX41530783732HLA-B14:03EWDKPHCVL0.55990.8909918
FDFT1-CASKchr811679387chrX41530783732HLA-B39:12EWDKPHCVL0.4730.9668918
FDFT1-CASKchr811679387chrX41530783732HLA-C07:29EWDKPHCVL0.40440.9612918
FDFT1-CASKchr811679387chrX41530783732HLA-C07:13EWDKPHCVL0.39430.9352918
FDFT1-CASKchr811679387chrX41530783732HLA-C04:14EWDKPHCVL0.21450.8429918
FDFT1-CASKchr811679387chrX41530783732HLA-B51:07QEWDKPHCV0.14690.9801817
FDFT1-CASKchr811679387chrX41530783732HLA-C04:10EWDKPHCVLL0.99840.8072919
FDFT1-CASKchr811679387chrX41530783732HLA-C04:07EWDKPHCVLL0.9980.8263919
FDFT1-CASKchr811679387chrX41530783732HLA-B40:06QEWDKPHCVL0.99610.9423818
FDFT1-CASKchr811679387chrX41530783732HLA-B48:03QEWDKPHCVL0.99350.6557818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:10QEWDKPHCVL0.98380.6496818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:09QEWDKPHCVL0.97290.6974818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:08QEWDKPHCVL0.96970.5888818
FDFT1-CASKchr811679387chrX41530783732HLA-B40:03QEWDKPHCVL0.95860.5935818
FDFT1-CASKchr811679387chrX41530783732HLA-B39:08QEWDKPHCVL0.95840.9689818
FDFT1-CASKchr811679387chrX41530783732HLA-C04:14EWDKPHCVLL0.85830.8076919
FDFT1-CASKchr811679387chrX41530783732HLA-B40:03QEWDKPHCVLL0.99870.5393819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:09QEWDKPHCVLL0.99870.6367819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:10QEWDKPHCVLL0.99870.7119819
FDFT1-CASKchr811679387chrX41530783732HLA-B48:03QEWDKPHCVLL0.99810.6285819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:08QEWDKPHCVLL0.9980.5296819
FDFT1-CASKchr811679387chrX41530783732HLA-C04:01EWDKPHCV0.99970.9829917
FDFT1-CASKchr811679387chrX41530783732HLA-C04:01WDKPHCVL0.99860.96761018
FDFT1-CASKchr811679387chrX41530783732HLA-B40:40QEWDKPHCV0.99950.5834817
FDFT1-CASKchr811679387chrX41530783732HLA-B40:04QEWDKPHCV0.99460.9527817
FDFT1-CASKchr811679387chrX41530783732HLA-C04:01EWDKPHCVL0.99440.8683918
FDFT1-CASKchr811679387chrX41530783732HLA-C04:03EWDKPHCVL0.99410.8957918
FDFT1-CASKchr811679387chrX41530783732HLA-C18:01EWDKPHCVL0.99330.8788918
FDFT1-CASKchr811679387chrX41530783732HLA-B40:36QEWDKPHCV0.98640.8861817
FDFT1-CASKchr811679387chrX41530783732HLA-B40:49QEWDKPHCV0.98560.9108817
FDFT1-CASKchr811679387chrX41530783732HLA-B40:12QEWDKPHCV0.94940.9191817
FDFT1-CASKchr811679387chrX41530783732HLA-B41:03QEWDKPHCV0.94910.9504817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:22QEWDKPHCV0.94890.7649817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:13QEWDKPHCV0.94520.9808817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:07QEWDKPHCV0.94520.9808817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:26QEWDKPHCV0.94520.9808817
FDFT1-CASKchr811679387chrX41530783732HLA-B18:11QEWDKPHCV0.83440.974817
FDFT1-CASKchr811679387chrX41530783732HLA-B18:11SEQEWDKPH0.82620.8832615
FDFT1-CASKchr811679387chrX41530783732HLA-B18:05QEWDKPHCV0.82470.9625817
FDFT1-CASKchr811679387chrX41530783732HLA-B18:08QEWDKPHCV0.80920.9605817
FDFT1-CASKchr811679387chrX41530783732HLA-B18:06QEWDKPHCV0.80480.9556817
FDFT1-CASKchr811679387chrX41530783732HLA-B44:21QEWDKPHCV0.79470.5377817
FDFT1-CASKchr811679387chrX41530783732HLA-B18:03QEWDKPHCV0.77660.9555817
FDFT1-CASKchr811679387chrX41530783732HLA-C14:02EWDKPHCVL0.70060.9699918
FDFT1-CASKchr811679387chrX41530783732HLA-C14:03EWDKPHCVL0.70060.9699918
FDFT1-CASKchr811679387chrX41530783732HLA-B39:02QEWDKPHCV0.64420.9795817
FDFT1-CASKchr811679387chrX41530783732HLA-C03:67EWDKPHCVL0.57130.9795918
FDFT1-CASKchr811679387chrX41530783732HLA-B50:04QEWDKPHCV0.53840.9753817
FDFT1-CASKchr811679387chrX41530783732HLA-B50:05QEWDKPHCV0.53840.9753817
FDFT1-CASKchr811679387chrX41530783732HLA-C07:04EWDKPHCVL0.3930.9243918
FDFT1-CASKchr811679387chrX41530783732HLA-B08:12EWDKPHCVL0.29130.7719918
FDFT1-CASKchr811679387chrX41530783732HLA-C04:04EWDKPHCVL0.21990.9122918
FDFT1-CASKchr811679387chrX41530783732HLA-B08:18EWDKPHCVL0.13980.6831918
FDFT1-CASKchr811679387chrX41530783732HLA-C04:01EWDKPHCVLL0.9980.8263919
FDFT1-CASKchr811679387chrX41530783732HLA-C18:01EWDKPHCVLL0.99690.8344919
FDFT1-CASKchr811679387chrX41530783732HLA-B40:04QEWDKPHCVL0.99370.8955818
FDFT1-CASKchr811679387chrX41530783732HLA-B40:12QEWDKPHCVL0.99350.6557818
FDFT1-CASKchr811679387chrX41530783732HLA-B40:36QEWDKPHCVL0.99160.5918818
FDFT1-CASKchr811679387chrX41530783732HLA-B40:49QEWDKPHCVL0.99130.6192818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:07QEWDKPHCVL0.97690.9551818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:13QEWDKPHCVL0.97690.9551818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:26QEWDKPHCVL0.97690.9551818
FDFT1-CASKchr811679387chrX41530783732HLA-B39:02QEWDKPHCVL0.94180.9746818
FDFT1-CASKchr811679387chrX41530783732HLA-B18:11QEWDKPHCVL0.86830.9489818
FDFT1-CASKchr811679387chrX41530783732HLA-B41:03QEWDKPHCVL0.75590.9399818
FDFT1-CASKchr811679387chrX41530783732HLA-B18:03QEWDKPHCVL0.6320.9277818
FDFT1-CASKchr811679387chrX41530783732HLA-B44:07QEWDKPHCVLL0.99880.9535819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:26QEWDKPHCVLL0.99880.9535819
FDFT1-CASKchr811679387chrX41530783732HLA-B44:13QEWDKPHCVLL0.99880.9535819
FDFT1-CASKchr811679387chrX41530783732HLA-B40:49QEWDKPHCVLL0.99870.5554819
FDFT1-CASKchr811679387chrX41530783732HLA-B40:04QEWDKPHCVLL0.99860.8608819
FDFT1-CASKchr811679387chrX41530783732HLA-B40:36QEWDKPHCVLL0.99860.5357819
FDFT1-CASKchr811679387chrX41530783732HLA-B40:12QEWDKPHCVLL0.99810.6285819
FDFT1-CASKchr811679387chrX41530783732HLA-B39:02QEWDKPHCVLL0.9960.9711819
FDFT1-CASKchr811679387chrX41530783732HLA-B41:03QEWDKPHCVLL0.97130.8444819

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Potential FusionNeoAntigen Information of FDFT1-CASK 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 FDFT1-CASK

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
8528SEQEWDKPHCVLLAFDFT1CASKchr811679387chrX41530783732

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FDFT1-CASK

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-B14:023BVN8528SEQEWDKPHCVLLA-7.15543-7.26883
HLA-B14:023BVN8528SEQEWDKPHCVLLA-4.77435-5.80965
HLA-B52:013W398528SEQEWDKPHCVLLA-6.80875-6.92215
HLA-B52:013W398528SEQEWDKPHCVLLA-4.20386-5.23916
HLA-A11:014UQ28528SEQEWDKPHCVLLA-7.5194-8.5547
HLA-A11:014UQ28528SEQEWDKPHCVLLA-6.9601-7.0735
HLA-A24:025HGA8528SEQEWDKPHCVLLA-7.52403-7.63743
HLA-A24:025HGA8528SEQEWDKPHCVLLA-5.82433-6.85963
HLA-B27:056PYJ8528SEQEWDKPHCVLLA-3.28285-4.31815
HLA-B44:053DX88528SEQEWDKPHCVLLA-5.91172-6.94702
HLA-B44:053DX88528SEQEWDKPHCVLLA-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of FDFT1-CASK

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
FDFT1-CASKchr811679387chrX415307831018WDKPHCVLTGGGACAAGCCCCACTGTGTTCTC
FDFT1-CASKchr811679387chrX41530783615SEQEWDKPHTCTGAACAGGAGTGGGACAAGCCCCAC
FDFT1-CASKchr811679387chrX41530783817QEWDKPHCVCAGGAGTGGGACAAGCCCCACTGTGTT
FDFT1-CASKchr811679387chrX41530783818QEWDKPHCVLCAGGAGTGGGACAAGCCCCACTGTGTTCTC
FDFT1-CASKchr811679387chrX41530783819QEWDKPHCVLLCAGGAGTGGGACAAGCCCCACTGTGTTCTCCTT
FDFT1-CASKchr811679387chrX41530783917EWDKPHCVGAGTGGGACAAGCCCCACTGTGTT
FDFT1-CASKchr811679387chrX41530783918EWDKPHCVLGAGTGGGACAAGCCCCACTGTGTTCTC
FDFT1-CASKchr811679387chrX41530783919EWDKPHCVLLGAGTGGGACAAGCCCCACTGTGTTCTCCTT

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 FDFT1-CASK

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
STADFDFT1-CASKchr811679387ENST00000220584chrX41530783ENST00000318588TCGA-HU-A4H2

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Potential target of CAR-T therapy development for FDFT1-CASK

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 FDFT1-CASK

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 FDFT1-CASK

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