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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:KANSL1-PHF20

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KANSL1-PHF20
FusionPDB ID: 41149
FusionGDB2.0 ID: 41149
HgeneTgene
Gene symbol

KANSL1

PHF20

Gene ID

284058

51230

Gene nameKAT8 regulatory NSL complex subunit 1PHD finger protein 20
SynonymsCENP-36|KDVS|KIAA1267|MSL1v1|NSL1|hMSL1v1C20orf104|GLEA2|HCA58|NZF|TDRD20A|TZP
Cytomap

17q21.31

20q11.22-q11.23

Type of geneprotein-codingprotein-coding
DescriptionKAT8 regulatory NSL complex subunit 1MLL1/MLL complex subunit KANSL1MSL1 homolog 1NSL complex protein NSL1centromere protein 36male-specific lethal 1 homolognon-specific lethal 1 homologPHD finger protein 20glioma-expressed antigen 2hepatocellular carcinoma-associated antigen 58novel zinc finger proteintranscription factor TZPtudor domain containing 20A
Modification date2020032720200313
UniProtAcc

A0AUZ9

Main function of 5'-partner protein:
.
Ensembl transtripts involved in fusion geneENST idsENST00000262419, ENST00000432791, 
ENST00000572904, ENST00000574590, 
ENST00000575318, ENST00000393476, 
ENST00000576248, 
ENST00000439301, 
ENST00000481202, ENST00000374012, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score34 X 33 X 14=1570826 X 25 X 15=9750
# samples 4732
** MAII scorelog2(47/15708*10)=-5.0626949361014
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(32/9750*10)=-4.92925840863697
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: KANSL1 [Title/Abstract] AND PHF20 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: KANSL1 [Title/Abstract] AND PHF20 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KANSL1(44171925)-PHF20(34515701), # samples:1
Anticipated loss of major functional domain due to fusion event.KANSL1-PHF20 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.
KANSL1-PHF20 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.
KANSL1-PHF20 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.
KANSL1-PHF20 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.
KANSL1-PHF20 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KANSL1-PHF20 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
KANSL1-PHF20 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
KANSL1-PHF20 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
KANSL1-PHF20 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
HgeneKANSL1

GO:0043981

histone H4-K5 acetylation

20018852

HgeneKANSL1

GO:0043982

histone H4-K8 acetylation

20018852

HgeneKANSL1

GO:0043984

histone H4-K16 acetylation

20018852

TgenePHF20

GO:0043981

histone H4-K5 acetylation

20018852

TgenePHF20

GO:0043982

histone H4-K8 acetylation

20018852

TgenePHF20

GO:0043984

histone H4-K16 acetylation

20018852



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/chr17:44171925/chr20:34515701)
- 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 KANSL1 (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 PHF20 (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)
ENST00000574590KANSL1chr1744171925-ENST00000374012PHF20chr2034515701+544716582272692821
ENST00000575318KANSL1chr1744171925-ENST00000374012PHF20chr2034515701+52541465342499821
ENST00000432791KANSL1chr1744171925-ENST00000374012PHF20chr2034515701+53051516852550821

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
ENST00000574590ENST00000374012KANSL1chr1744171925-PHF20chr2034515701+0.001406260.99859375
ENST00000575318ENST00000374012KANSL1chr1744171925-PHF20chr2034515701+0.001513660.9984863
ENST00000432791ENST00000374012KANSL1chr1744171925-PHF20chr2034515701+0.0015625680.99843746

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 KANSL1-PHF20

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
KANSL1chr1744171925PHF20chr20345157011465477QQTDIYKQIRANKCEECQCWQHGVCM
KANSL1chr1744171925PHF20chr20345157011516477QQTDIYKQIRANKCEECQCWQHGVCM
KANSL1chr1744171925PHF20chr20345157011658477QQTDIYKQIRANKCEECQCWQHGVCM

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Potential FusionNeoAntigen Information of KANSL1-PHF20 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of KANSL1-PHF20 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.
KANSL1-PHF20_44171925_34515701.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)
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0101QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0101TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0101QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0103QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0103TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0103QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0105QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0105TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0105QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0107QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0107TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0107QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0109QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0109TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0109QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0111QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0111TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0111QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0113QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0113TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0113QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0115QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0115TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0115QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0117QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0117TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0117QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0119QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0119TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0119QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0121QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0121TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0121QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0125QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0125TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0125QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0127QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0127TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0127QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0129QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0129TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0129QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0131QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0131TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0131QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-0447QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1001QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1003QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1130QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1446QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1515QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1527QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1534QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1601QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1601TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1601QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1602QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1603QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1603TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1603QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1604QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1604TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1605QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1607QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1608QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1608TDIYKQIRANKCEEC217
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1608QQTDIYKQIRANKCE015
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1609QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1610QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1611QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1612QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1614QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB1-1616QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB3-0217QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB5-0102QTDIYKQIRANKCEE116
KANSL1-PHF20chr1744171925chr20345157011516DRB5-0108NQTDIYKQIRANKCEE116

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Fusion breakpoint peptide structures of KANSL1-PHF20

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KANSL1-PHF20

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of KANSL1-PHF20

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

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
KANSL1-PHF20chr1744171925chr2034515701015QQTDIYKQIRANKCECAGCAAACAGACATTTACAAACAGATACGTGCTAATAAGTGTGAA
KANSL1-PHF20chr1744171925chr2034515701116QTDIYKQIRANKCEECAAACAGACATTTACAAACAGATACGTGCTAATAAGTGTGAAGAG
KANSL1-PHF20chr1744171925chr2034515701217TDIYKQIRANKCEECACAGACATTTACAAACAGATACGTGCTAATAAGTGTGAAGAGTGC

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Information of the samples that have these potential fusion neoantigens of KANSL1-PHF20

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for KANSL1-PHF20

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 KANSL1-PHF20

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 KANSL1-PHF20

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