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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:ASAP1-CDKN2B

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ASAP1-CDKN2B
FusionPDB ID: 6952
FusionGDB2.0 ID: 6952
HgeneTgene
Gene symbol

ASAP1

CDKN2B

Gene ID

50807

1030

Gene nameArfGAP with SH3 domain, ankyrin repeat and PH domain 1cyclin dependent kinase inhibitor 2B
SynonymsAMAP1|CENTB4|DDEF1|PAG2|PAP|ZG14PCDK4I|INK4B|MTS2|P15|TP15|p15INK4b
Cytomap

8q24.21-q24.22

9p21.3

Type of geneprotein-codingprotein-coding
Descriptionarf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 1130 kDa phosphatidylinositol 4,5-biphosphate-dependent ARF1 GTPase-activating protein130 kDa phosphatidylinositol 4,5-bisphosphate-dependent ARF1 GTPase-activating proteinADP-ribosylcyclin-dependent kinase 4 inhibitor BCDK inhibitory proteinCDK4B inhibitorMTS-2cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)cyclin-dependent kinases 4 and 6 binding proteinmultiple tumor suppressor 2p14-INK4bp14_CDK inhibitorp14_INK4B
Modification date2020032720200322
UniProtAcc

Q9ULH1

Main function of 5'-partner protein: FUNCTION: Possesses phosphatidylinositol 4,5-bisphosphate-dependent GTPase-activating protein activity for ARF1 (ADP ribosylation factor 1) and ARF5 and a lesser activity towards ARF6. May coordinate membrane trafficking with cell growth or actin cytoskeleton remodeling by binding to both SRC and PIP2. May function as a signal transduction protein involved in the differentiation of fibroblasts into adipocytes and possibly other cell types (By similarity). Plays a role in ciliogenesis. {ECO:0000250, ECO:0000269|PubMed:20393563}.

P42772

Main function of 5'-partner protein: FUNCTION: Interacts strongly with CDK4 and CDK6. Potent inhibitor. Potential effector of TGF-beta induced cell cycle arrest.
Ensembl transtripts involved in fusion geneENST idsENST00000357668, ENST00000518721, 
ENST00000520625, 
ENST00000380142, 
ENST00000539462, ENST00000276925, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score25 X 17 X 13=55251 X 1 X 1=1
# samples 281
** MAII scorelog2(28/5525*10)=-4.30247573222119
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Fusion gene context

PubMed: ASAP1 [Title/Abstract] AND CDKN2B [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ASAP1 [Title/Abstract] AND CDKN2B [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ASAP1(131370263)-CDKN2B(22006246), # samples:2
Anticipated loss of major functional domain due to fusion event.ASAP1-CDKN2B 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.
ASAP1-CDKN2B 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.
ASAP1-CDKN2B seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ASAP1-CDKN2B seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneCDKN2B

GO:0000079

regulation of cyclin-dependent protein serine/threonine kinase activity

8078588

TgeneCDKN2B

GO:0042326

negative regulation of phosphorylation

8078588



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/chr8:131370263/chr9:22006246)
- 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 ASAP1 (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 CDKN2B (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)
ENST00000518721ASAP1chr8131370263-ENST00000276925CDKN2Bchr922006246-3759414228674148

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
ENST00000518721ENST00000276925ASAP1chr8131370263-CDKN2Bchr922006246-0.0191511380.98084885

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 ASAP1-CDKN2B

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ASAP1chr8131370263CDKN2Bchr92200624641462LHNCRNTVTLLEEVMMMGSARVAELL

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Potential FusionNeoAntigen Information of ASAP1-CDKN2B 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.
ASAP1-CDKN2B_131370263_22006246.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)
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:24EVMMMGSAR0.99910.72251221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:03EVMMMGSAR0.99880.69821221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A66:01EVMMMGSAR0.99790.68051221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-B45:01EEVMMMGSA0.9940.97431120
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:06EVMMMGSAR0.98870.69251221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:24TLLEEVMMM0.98860.6553817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:67TLLEEVMMM0.98860.6553817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:30TLLEEVMMM0.98860.6553817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A33:01EVMMMGSAR0.98820.66641221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A33:05EVMMMGSAR0.98820.66641221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:22TLLEEVMMM0.98810.758817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:60TLLEEVMMM0.98790.6498817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:11TLLEEVMMM0.98570.6877817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:21TLLEEVMMM0.98310.7702817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-B50:02EEVMMMGSA0.97990.79851120
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A26:03EVMMMGSAR0.97750.72361221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:08EVMMMGSAR0.97470.68711221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:05EVMMMGSAR0.97350.72191221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:27TLLEEVMMM0.97110.7604817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:16TLLEEVMMM0.96940.6915817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:38TLLEEVMMM0.96830.761817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:04TLLEEVMMM0.96820.8543817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:21NTVTLLEEV0.96250.8007514
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:17TLLEEVMMM0.95840.7526817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:13TLLEEVMMM0.94750.8303817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:35TLLEEVMMM0.90710.6791817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:29TLLEEVMMM0.88540.6578817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:19TLLEEVMMM0.87050.6903817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:20TLLEEVMMM0.86220.6607817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A34:01EVMMMGSAR0.8310.58881221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A34:05EVMMMGSAR0.8310.58881221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A34:02EVMMMGSAR0.77440.57161221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-B13:01TLLEEVMMM0.03770.9966817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:01EVMMMGSAR0.99910.72251221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:07TLLEEVMMM0.98910.6636817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:02TLLEEVMMM0.98870.6394817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:01TLLEEVMMM0.98860.6553817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:05TLLEEVMMM0.98440.7676817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:05NTVTLLEEV0.98430.669514
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A33:03EVMMMGSAR0.94460.5441221
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A68:02NTVTLLEEV0.99930.8406514
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A69:01NTVTLLEEV0.99860.826514
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:06TLLEEVMMM0.98310.7702817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:14TLLEEVMMM0.98260.7365817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:03TLLEEVMMM0.97330.8163817
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-A02:06NTVTLLEEV0.96250.8007514
ASAP1-CDKN2Bchr8131370263chr922006246414HLA-B40:21TLLEEVMMM0.03010.6993817

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Potential FusionNeoAntigen Information of ASAP1-CDKN2B 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 ASAP1-CDKN2B

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
9741TVTLLEEVMMMGSAASAP1CDKN2Bchr8131370263chr922006246414

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ASAP1-CDKN2B

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-B14:023BVN9741TVTLLEEVMMMGSA-6.00367-7.03897
HLA-B14:023BVN9741TVTLLEEVMMMGSA-5.39279-5.50619
HLA-B52:013W399741TVTLLEEVMMMGSA-6.37513-6.48853
HLA-B52:013W399741TVTLLEEVMMMGSA-5.71942-6.75472
HLA-A11:014UQ29741TVTLLEEVMMMGSA-11.5708-11.6842
HLA-A11:014UQ29741TVTLLEEVMMMGSA-8.11091-9.14621
HLA-A24:025HGA9741TVTLLEEVMMMGSA-6.75661-6.87001
HLA-A24:025HGA9741TVTLLEEVMMMGSA-5.30147-6.33677
HLA-B27:056PYJ9741TVTLLEEVMMMGSA-4.27108-5.30638
HLA-B44:053DX89741TVTLLEEVMMMGSA-6.47731-6.59071
HLA-B44:053DX89741TVTLLEEVMMMGSA-3.23433-4.26963

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Vaccine Design for the FusionNeoAntigens of ASAP1-CDKN2B

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
ASAP1-CDKN2Bchr8131370263chr9220062461120EEVMMMGSAGAGGAGGTCATGATGATGGGCAGCGCC
ASAP1-CDKN2Bchr8131370263chr9220062461221EVMMMGSARGAGGTCATGATGATGGGCAGCGCCCGC
ASAP1-CDKN2Bchr8131370263chr922006246514NTVTLLEEVAACACCGTCACGCTGCTGGAGGAGGTC
ASAP1-CDKN2Bchr8131370263chr922006246817TLLEEVMMMACGCTGCTGGAGGAGGTCATGATGATG

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 ASAP1-CDKN2B

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
SKCMASAP1-CDKN2Bchr8131370263ENST00000518721chr922006246ENST00000276925TCGA-FS-A1ZE-06A

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Potential target of CAR-T therapy development for ASAP1-CDKN2B

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 ASAP1-CDKN2B

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 ASAP1-CDKN2B

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