FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:SKAP1-ZNF74

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SKAP1-ZNF74
FusionPDB ID: 82071
FusionGDB2.0 ID: 82071
HgeneTgene
Gene symbol

SKAP1

ZNF74

Gene ID

8631

7625

Gene namesrc kinase associated phosphoprotein 1zinc finger protein 74
SynonymsHEL-S-81p|SCAP1|SKAP55COS52|ZFP520|ZNF520|hZNF7
Cytomap

17q21.32

22q11.21

Type of geneprotein-codingprotein-coding
Descriptionsrc kinase-associated phosphoprotein 1SKAP-55epididymis secretory sperm binding protein Li 81ppp55src family-associated phosphoprotein 1src kinase-associated phosphoprotein of 55 kDazinc finger protein 74zinc finger protein 520
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000336915, ENST00000584924, 
ENST00000357502, ENST00000403682, 
ENST00000356671, ENST00000400451, 
ENST00000405993, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score26 X 10 X 10=26002 X 3 X 2=12
# samples 354
** MAII scorelog2(35/2600*10)=-2.89308479608349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/12*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: SKAP1 [Title/Abstract] AND ZNF74 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SKAP1 [Title/Abstract] AND ZNF74 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SKAP1(46474042)-ZNF74(20754922), # samples:2
Anticipated loss of major functional domain due to fusion event.SKAP1-ZNF74 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.
SKAP1-ZNF74 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.
SKAP1-ZNF74 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.
SKAP1-ZNF74 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.
SKAP1-ZNF74 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
SKAP1-ZNF74 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
SKAP1-ZNF74 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
HgeneSKAP1

GO:0002821

positive regulation of adaptive immune response

12652296

HgeneSKAP1

GO:0033625

positive regulation of integrin activation

12652296

HgeneSKAP1

GO:0034116

positive regulation of heterotypic cell-cell adhesion

12652296

HgeneSKAP1

GO:0045944

positive regulation of transcription by RNA polymerase II

11909961

HgeneSKAP1

GO:1903039

positive regulation of leukocyte cell-cell adhesion

12652296



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/chr17:46474042/chr22:20754922)
- 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 SKAP1 (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 ZNF74 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000336915SKAP1chr1746474042-ENST00000400451ZNF74chr2220754922+27472223002036578
ENST00000336915SKAP1chr1746474042-ENST00000356671ZNF74chr2220754922+23932223002036578
ENST00000336915SKAP1chr1746474042-ENST00000405993ZNF74chr2220754922+19412223001940546
ENST00000336915SKAP1chr1746474041-ENST00000400451ZNF74chr2220754921+27472223002036578
ENST00000336915SKAP1chr1746474041-ENST00000356671ZNF74chr2220754921+23932223002036578
ENST00000336915SKAP1chr1746474041-ENST00000405993ZNF74chr2220754921+19412223001940546

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
ENST00000336915ENST00000400451SKAP1chr1746474042-ZNF74chr2220754922+0.0906684550.90933156
ENST00000336915ENST00000356671SKAP1chr1746474042-ZNF74chr2220754922+0.1038193850.8961806
ENST00000336915ENST00000405993SKAP1chr1746474042-ZNF74chr2220754922+0.1112588940.88874114
ENST00000336915ENST00000400451SKAP1chr1746474041-ZNF74chr2220754921+0.0906684550.90933156
ENST00000336915ENST00000356671SKAP1chr1746474041-ZNF74chr2220754921+0.1038193850.8961806
ENST00000336915ENST00000405993SKAP1chr1746474041-ZNF74chr2220754921+0.1112588940.88874114

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

Top

Fusion Protein Breakpoint Sequences for SKAP1-ZNF74

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SKAP1chr1746474041ZNF74chr2220754921222137ASTPSEPEKFPQVRRQRGAGAGEGEF
SKAP1chr1746474041ZNF74chr2220754921222169ASTPSEPEKFPQVRRQRGAGAGEGEF
SKAP1chr1746474042ZNF74chr2220754922222137ASTPSEPEKFPQVRRQRGAGAGEGEF
SKAP1chr1746474042ZNF74chr2220754922222169ASTPSEPEKFPQVRRQRGAGAGEGEF

Top

Potential FusionNeoAntigen Information of SKAP1-ZNF74 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.
SKAP1-ZNF74_46474041_20754921.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)
SKAP1-ZNF74chr1746474041chr2220754921222HLA-A31:02KFPQVRRQR0.91040.6205817
SKAP1-ZNF74chr1746474041chr2220754921222HLA-A31:01KFPQVRRQR0.9550.5731817

Top

Potential FusionNeoAntigen Information of SKAP1-ZNF74 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)

Top

Fusion breakpoint peptide structures of SKAP1-ZNF74

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
6582PEKFPQVRRQRGAGSKAP1ZNF74chr1746474041chr2220754921222

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SKAP1-ZNF74

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-B14:023BVN6582PEKFPQVRRQRGAG-7.37157-7.48337
HLA-B14:023BVN6582PEKFPQVRRQRGAG-5.75216-6.79526
HLA-B52:013W396582PEKFPQVRRQRGAG-7.36854-7.48034
HLA-B52:013W396582PEKFPQVRRQRGAG-4.42371-5.46681
HLA-A11:014UQ26582PEKFPQVRRQRGAG-8.60667-9.64977
HLA-A11:014UQ26582PEKFPQVRRQRGAG-5.54504-5.65684
HLA-A24:025HGA6582PEKFPQVRRQRGAG-7.65859-7.77039
HLA-A24:025HGA6582PEKFPQVRRQRGAG-6.03094-7.07404
HLA-B44:053DX86582PEKFPQVRRQRGAG-5.82315-5.93495
HLA-B44:053DX86582PEKFPQVRRQRGAG-2.98805-4.03115

Top

Vaccine Design for the FusionNeoAntigens of SKAP1-ZNF74

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
SKAP1-ZNF74chr1746474041chr2220754921817KFPQVRRQRGCAAATCAAAGCCAGGAATCGGTGAGT

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

Top

Information of the samples that have these potential fusion neoantigens of SKAP1-ZNF74

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
OVSKAP1-ZNF74chr1746474041ENST00000336915chr2220754921ENST00000356671TCGA-24-1467

Top

Potential target of CAR-T therapy development for SKAP1-ZNF74

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

Top

Related Drugs to SKAP1-ZNF74

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to SKAP1-ZNF74

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