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:EPS15L1-CLNS1A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EPS15L1-CLNS1A
FusionPDB ID: 27069
FusionGDB2.0 ID: 27069
HgeneTgene
Gene symbol

EPS15L1

CLNS1A

Gene ID

58513

1207

Gene nameepidermal growth factor receptor pathway substrate 15 like 1chloride nucleotide-sensitive channel 1A
SynonymsEPS15RCLCI|CLNS1B|ICln
Cytomap

19p13.11

11q14.1

Type of geneprotein-codingprotein-coding
Descriptionepidermal growth factor receptor substrate 15-like 1epidermal growth factor receptor substrate EPS15Reps15-related proteinmethylosome subunit pIClnchloride channel regulatory proteinchloride channel, nucleotide sensitive 1Achloride conductance regulatory protein IClnchloride ion current inducer proteini(Cln)reticulocyte pIClnreticulocyte protein ICln
Modification date2020031320200313
UniProtAcc

Q9UBC2

Main function of 5'-partner protein: FUNCTION: Seems to be a constitutive component of clathrin-coated pits that is required for receptor-mediated endocytosis. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR seems to require association with DAB2. {ECO:0000269|PubMed:22648170, ECO:0000269|PubMed:9407958}.

P54105

Main function of 5'-partner protein: FUNCTION: Involved in both the assembly of spliceosomal snRNPs and the methylation of Sm proteins (PubMed:21081503, PubMed:18984161). Chaperone that regulates the assembly of spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Thereby, plays an important role in the splicing of cellular pre-mRNAs. Most spliceosomal snRNPs contain a common set of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP. In the cytosol, the Sm proteins SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG are trapped in an inactive 6S pICln-Sm complex by the chaperone CLNS1A that controls the assembly of the core snRNP. Dissociation by the SMN complex of CLNS1A from the trapped Sm proteins and their transfer to an SMN-Sm complex triggers the assembly of core snRNPs and their transport to the nucleus. May also indirectly participate in cellular volume control by activation of a swelling-induced chloride conductance pathway. {ECO:0000269|PubMed:10330151, ECO:0000269|PubMed:11713266, ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:21081503}.
Ensembl transtripts involved in fusion geneENST idsENST00000248070, ENST00000455140, 
ENST00000535753, ENST00000594975, 
ENST00000597937, ENST00000602009, 
ENST00000533957, ENST00000263309, 
ENST00000525064, ENST00000525428, 
ENST00000528364, ENST00000532069, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 17 X 14=547410 X 8 X 6=480
# samples 3413
** MAII scorelog2(34/5474*10)=-4.00898878322726
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/480*10)=-1.88452278258006
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: EPS15L1 [Title/Abstract] AND CLNS1A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: EPS15L1 [Title/Abstract] AND CLNS1A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EPS15L1(16552703)-CLNS1A(77330740), # samples:3
Anticipated loss of major functional domain due to fusion event.EPS15L1-CLNS1A 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.
EPS15L1-CLNS1A 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
TgeneCLNS1A

GO:0000387

spliceosomal snRNP assembly

18984161



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/chr19:16552703/chr11:77330740)
- 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 EPS15L1 (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 CLNS1A (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)
ENST00000455140EPS15L1chr1916552703-ENST00000525428CLNS1Achr1177330740-248823267507146
ENST00000455140EPS15L1chr1916552703-ENST00000263309CLNS1Achr1177330740-82323267507146
ENST00000455140EPS15L1chr1916552703-ENST00000525064CLNS1Achr1177330740-82323267507146
ENST00000455140EPS15L1chr1916552703-ENST00000532069CLNS1Achr1177330740-61423267507146
ENST00000455140EPS15L1chr1916552703-ENST00000528364CLNS1Achr1177330740-4772326733689
ENST00000248070EPS15L1chr1916552703-ENST00000525428CLNS1Achr1177330740-25613052580192
ENST00000248070EPS15L1chr1916552703-ENST00000263309CLNS1Achr1177330740-8963052580192
ENST00000248070EPS15L1chr1916552703-ENST00000525064CLNS1Achr1177330740-8963052580192
ENST00000248070EPS15L1chr1916552703-ENST00000532069CLNS1Achr1177330740-6873052580192
ENST00000248070EPS15L1chr1916552703-ENST00000528364CLNS1Achr1177330740-5503052409135
ENST00000535753EPS15L1chr1916552703-ENST00000525428CLNS1Achr1177330740-245219631471146
ENST00000535753EPS15L1chr1916552703-ENST00000263309CLNS1Achr1177330740-78719631471146
ENST00000535753EPS15L1chr1916552703-ENST00000525064CLNS1Achr1177330740-78719631471146
ENST00000535753EPS15L1chr1916552703-ENST00000532069CLNS1Achr1177330740-57819631471146
ENST00000535753EPS15L1chr1916552703-ENST00000528364CLNS1Achr1177330740-4411963130089
ENST00000594975EPS15L1chr1916552703-ENST00000525428CLNS1Achr1177330740-25613052580192
ENST00000594975EPS15L1chr1916552703-ENST00000263309CLNS1Achr1177330740-8963052580192
ENST00000594975EPS15L1chr1916552703-ENST00000525064CLNS1Achr1177330740-8963052580192
ENST00000594975EPS15L1chr1916552703-ENST00000532069CLNS1Achr1177330740-6873052580192
ENST00000594975EPS15L1chr1916552703-ENST00000528364CLNS1Achr1177330740-5503052409135
ENST00000597937EPS15L1chr1916552703-ENST00000525428CLNS1Achr1177330740-24261705445146
ENST00000597937EPS15L1chr1916552703-ENST00000263309CLNS1Achr1177330740-7611705445146
ENST00000597937EPS15L1chr1916552703-ENST00000525064CLNS1Achr1177330740-7611705445146
ENST00000597937EPS15L1chr1916552703-ENST00000532069CLNS1Achr1177330740-5521705445146
ENST00000597937EPS15L1chr1916552703-ENST00000528364CLNS1Achr1177330740-415170527489
ENST00000455140EPS15L1chr1916552702-ENST00000525428CLNS1Achr1177330740-248823267507146
ENST00000455140EPS15L1chr1916552702-ENST00000263309CLNS1Achr1177330740-82323267507146
ENST00000455140EPS15L1chr1916552702-ENST00000525064CLNS1Achr1177330740-82323267507146
ENST00000455140EPS15L1chr1916552702-ENST00000532069CLNS1Achr1177330740-61423267507146
ENST00000455140EPS15L1chr1916552702-ENST00000528364CLNS1Achr1177330740-4772326733689
ENST00000248070EPS15L1chr1916552702-ENST00000525428CLNS1Achr1177330740-25613052580192
ENST00000248070EPS15L1chr1916552702-ENST00000263309CLNS1Achr1177330740-8963052580192
ENST00000248070EPS15L1chr1916552702-ENST00000525064CLNS1Achr1177330740-8963052580192
ENST00000248070EPS15L1chr1916552702-ENST00000532069CLNS1Achr1177330740-6873052580192
ENST00000248070EPS15L1chr1916552702-ENST00000528364CLNS1Achr1177330740-5503052409135
ENST00000535753EPS15L1chr1916552702-ENST00000525428CLNS1Achr1177330740-245219631471146
ENST00000535753EPS15L1chr1916552702-ENST00000263309CLNS1Achr1177330740-78719631471146
ENST00000535753EPS15L1chr1916552702-ENST00000525064CLNS1Achr1177330740-78719631471146
ENST00000535753EPS15L1chr1916552702-ENST00000532069CLNS1Achr1177330740-57819631471146
ENST00000535753EPS15L1chr1916552702-ENST00000528364CLNS1Achr1177330740-4411963130089
ENST00000594975EPS15L1chr1916552702-ENST00000525428CLNS1Achr1177330740-25613052580192
ENST00000594975EPS15L1chr1916552702-ENST00000263309CLNS1Achr1177330740-8963052580192
ENST00000594975EPS15L1chr1916552702-ENST00000525064CLNS1Achr1177330740-8963052580192
ENST00000594975EPS15L1chr1916552702-ENST00000532069CLNS1Achr1177330740-6873052580192
ENST00000594975EPS15L1chr1916552702-ENST00000528364CLNS1Achr1177330740-5503052409135
ENST00000597937EPS15L1chr1916552702-ENST00000525428CLNS1Achr1177330740-24261705445146
ENST00000597937EPS15L1chr1916552702-ENST00000263309CLNS1Achr1177330740-7611705445146
ENST00000597937EPS15L1chr1916552702-ENST00000525064CLNS1Achr1177330740-7611705445146
ENST00000597937EPS15L1chr1916552702-ENST00000532069CLNS1Achr1177330740-5521705445146
ENST00000597937EPS15L1chr1916552702-ENST00000528364CLNS1Achr1177330740-415170527489

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
ENST00000455140ENST00000525428EPS15L1chr1916552703-CLNS1Achr1177330740-0.0181232190.98187673
ENST00000455140ENST00000263309EPS15L1chr1916552703-CLNS1Achr1177330740-0.015883030.984117
ENST00000455140ENST00000525064EPS15L1chr1916552703-CLNS1Achr1177330740-0.015883030.984117
ENST00000455140ENST00000532069EPS15L1chr1916552703-CLNS1Achr1177330740-0.0158252960.98417467
ENST00000455140ENST00000528364EPS15L1chr1916552703-CLNS1Achr1177330740-0.103799850.8962001
ENST00000248070ENST00000525428EPS15L1chr1916552703-CLNS1Achr1177330740-0.022863840.97713614
ENST00000248070ENST00000263309EPS15L1chr1916552703-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000248070ENST00000525064EPS15L1chr1916552703-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000248070ENST00000532069EPS15L1chr1916552703-CLNS1Achr1177330740-0.022370.97763
ENST00000248070ENST00000528364EPS15L1chr1916552703-CLNS1Achr1177330740-0.114671390.8853286
ENST00000535753ENST00000525428EPS15L1chr1916552703-CLNS1Achr1177330740-0.032460240.9675397
ENST00000535753ENST00000263309EPS15L1chr1916552703-CLNS1Achr1177330740-0.0157014470.9842986
ENST00000535753ENST00000525064EPS15L1chr1916552703-CLNS1Achr1177330740-0.0157014470.9842986
ENST00000535753ENST00000532069EPS15L1chr1916552703-CLNS1Achr1177330740-0.0119562530.9880437
ENST00000535753ENST00000528364EPS15L1chr1916552703-CLNS1Achr1177330740-0.102689780.89731026
ENST00000594975ENST00000525428EPS15L1chr1916552703-CLNS1Achr1177330740-0.022863840.97713614
ENST00000594975ENST00000263309EPS15L1chr1916552703-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000594975ENST00000525064EPS15L1chr1916552703-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000594975ENST00000532069EPS15L1chr1916552703-CLNS1Achr1177330740-0.022370.97763
ENST00000594975ENST00000528364EPS15L1chr1916552703-CLNS1Achr1177330740-0.114671390.8853286
ENST00000597937ENST00000525428EPS15L1chr1916552703-CLNS1Achr1177330740-0.0192413830.9807586
ENST00000597937ENST00000263309EPS15L1chr1916552703-CLNS1Achr1177330740-0.0132769670.986723
ENST00000597937ENST00000525064EPS15L1chr1916552703-CLNS1Achr1177330740-0.0132769670.986723
ENST00000597937ENST00000532069EPS15L1chr1916552703-CLNS1Achr1177330740-0.0131967460.98680323
ENST00000597937ENST00000528364EPS15L1chr1916552703-CLNS1Achr1177330740-0.093059970.90694
ENST00000455140ENST00000525428EPS15L1chr1916552702-CLNS1Achr1177330740-0.0181232190.98187673
ENST00000455140ENST00000263309EPS15L1chr1916552702-CLNS1Achr1177330740-0.015883030.984117
ENST00000455140ENST00000525064EPS15L1chr1916552702-CLNS1Achr1177330740-0.015883030.984117
ENST00000455140ENST00000532069EPS15L1chr1916552702-CLNS1Achr1177330740-0.0158252960.98417467
ENST00000455140ENST00000528364EPS15L1chr1916552702-CLNS1Achr1177330740-0.103799850.8962001
ENST00000248070ENST00000525428EPS15L1chr1916552702-CLNS1Achr1177330740-0.022863840.97713614
ENST00000248070ENST00000263309EPS15L1chr1916552702-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000248070ENST00000525064EPS15L1chr1916552702-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000248070ENST00000532069EPS15L1chr1916552702-CLNS1Achr1177330740-0.022370.97763
ENST00000248070ENST00000528364EPS15L1chr1916552702-CLNS1Achr1177330740-0.114671390.8853286
ENST00000535753ENST00000525428EPS15L1chr1916552702-CLNS1Achr1177330740-0.032460240.9675397
ENST00000535753ENST00000263309EPS15L1chr1916552702-CLNS1Achr1177330740-0.0157014470.9842986
ENST00000535753ENST00000525064EPS15L1chr1916552702-CLNS1Achr1177330740-0.0157014470.9842986
ENST00000535753ENST00000532069EPS15L1chr1916552702-CLNS1Achr1177330740-0.0119562530.9880437
ENST00000535753ENST00000528364EPS15L1chr1916552702-CLNS1Achr1177330740-0.102689780.89731026
ENST00000594975ENST00000525428EPS15L1chr1916552702-CLNS1Achr1177330740-0.022863840.97713614
ENST00000594975ENST00000263309EPS15L1chr1916552702-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000594975ENST00000525064EPS15L1chr1916552702-CLNS1Achr1177330740-0.0177674820.9822326
ENST00000594975ENST00000532069EPS15L1chr1916552702-CLNS1Achr1177330740-0.022370.97763
ENST00000594975ENST00000528364EPS15L1chr1916552702-CLNS1Achr1177330740-0.114671390.8853286
ENST00000597937ENST00000525428EPS15L1chr1916552702-CLNS1Achr1177330740-0.0192413830.9807586
ENST00000597937ENST00000263309EPS15L1chr1916552702-CLNS1Achr1177330740-0.0132769670.986723
ENST00000597937ENST00000525064EPS15L1chr1916552702-CLNS1Achr1177330740-0.0132769670.986723
ENST00000597937ENST00000532069EPS15L1chr1916552702-CLNS1Achr1177330740-0.0131967460.98680323
ENST00000597937ENST00000528364EPS15L1chr1916552702-CLNS1Achr1177330740-0.093059970.90694

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 EPS15L1-CLNS1A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
EPS15L1chr1916552702CLNS1Achr117733074017055LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552702CLNS1Achr117733074019655LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552702CLNS1Achr117733074023255LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552702CLNS1Achr1177330740305101LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552703CLNS1Achr117733074017055LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552703CLNS1Achr117733074019655LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552703CLNS1Achr117733074023255LKKSGLSDIILGKMGWRWIPHQQLLD
EPS15L1chr1916552703CLNS1Achr1177330740305101LKKSGLSDIILGKMGWRWIPHQQLLD

Top

Potential FusionNeoAntigen Information of EPS15L1-CLNS1A 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.
EPS15L1-CLNS1A_16552702_77330740.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)
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:01ILGKMGWRW0.97330.9962918
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A32:13ILGKMGWRW0.9630.9969918
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A31:08ILGKMGWRW0.95510.8782918
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B58:01ILGKMGWRW0.94680.992918
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:01IILGKMGWRW0.99960.991818
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A33:01DIILGKMGWR0.99540.7359717
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A33:05DIILGKMGWR0.99540.7359717
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A32:13IILGKMGWRW0.97170.9953818
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A02:04GLSDIILGKM0.96020.6878414
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:01LSDIILGKMGW10.9877516
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B58:01LSDIILGKMGW0.99960.981516
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:03LSDIILGKMGW0.99940.993516
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C05:09LSDIILGKM0.99990.8802514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C08:15LSDIILGKM0.99970.9581514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C04:06LSDIILGKM0.98350.885514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C08:04LSDIILGKM0.89590.8926514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C08:13LSDIILGKM0.89590.8926514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B44:08SDIILGKMGW0.99050.5481616
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C04:03LSDIILGKM0.99990.8501514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C05:01LSDIILGKM0.99990.8802514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-C08:02LSDIILGKM0.99970.9581514
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A25:01DIILGKMGW0.99430.984716
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B53:02DIILGKMGW0.97370.7807716
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:10ILGKMGWRW0.97330.9962918
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-A32:01ILGKMGWRW0.96920.9965918
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B15:13DIILGKMGW0.73860.7878716
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:10IILGKMGWRW0.99960.991818
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:10LSDIILGKMGW10.9877516
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:04LSDIILGKMGW0.99980.8761516
EPS15L1-CLNS1Achr1916552702chr1177330740305HLA-B57:02LSDIILGKMGW0.99960.9769516

Top

Potential FusionNeoAntigen Information of EPS15L1-CLNS1A 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 EPS15L1-CLNS1A

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
8471SDIILGKMGWRWIPEPS15L1CLNS1Achr1916552702chr1177330740305

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EPS15L1-CLNS1A

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-B14:023BVN8471SDIILGKMGWRWIP-7.15543-7.26883
HLA-B14:023BVN8471SDIILGKMGWRWIP-4.77435-5.80965
HLA-B52:013W398471SDIILGKMGWRWIP-6.80875-6.92215
HLA-B52:013W398471SDIILGKMGWRWIP-4.20386-5.23916
HLA-A11:014UQ28471SDIILGKMGWRWIP-7.5194-8.5547
HLA-A11:014UQ28471SDIILGKMGWRWIP-6.9601-7.0735
HLA-A24:025HGA8471SDIILGKMGWRWIP-7.52403-7.63743
HLA-A24:025HGA8471SDIILGKMGWRWIP-5.82433-6.85963
HLA-B27:056PYJ8471SDIILGKMGWRWIP-3.28285-4.31815
HLA-B44:053DX88471SDIILGKMGWRWIP-5.91172-6.94702
HLA-B44:053DX88471SDIILGKMGWRWIP-4.24346-4.35686

Top

Vaccine Design for the FusionNeoAntigens of EPS15L1-CLNS1A

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
EPS15L1-CLNS1Achr1916552702chr1177330740414GLSDIILGKMGGCCTCTCGGACATTATCCTTGGGAAGATG
EPS15L1-CLNS1Achr1916552702chr1177330740514LSDIILGKMCTCTCGGACATTATCCTTGGGAAGATG
EPS15L1-CLNS1Achr1916552702chr1177330740516LSDIILGKMGWCTCTCGGACATTATCCTTGGGAAGATGGGATGG
EPS15L1-CLNS1Achr1916552702chr1177330740616SDIILGKMGWTCGGACATTATCCTTGGGAAGATGGGATGG
EPS15L1-CLNS1Achr1916552702chr1177330740716DIILGKMGWGACATTATCCTTGGGAAGATGGGATGG
EPS15L1-CLNS1Achr1916552702chr1177330740717DIILGKMGWRGACATTATCCTTGGGAAGATGGGATGGAGG
EPS15L1-CLNS1Achr1916552702chr1177330740818IILGKMGWRWATTATCCTTGGGAAGATGGGATGGAGGTGG
EPS15L1-CLNS1Achr1916552702chr1177330740918ILGKMGWRWATCCTTGGGAAGATGGGATGGAGGTGG

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 EPS15L1-CLNS1A

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
BRCAEPS15L1-CLNS1Achr1916552702ENST00000248070chr1177330740ENST00000263309TCGA-C8-A12Q

Top

Potential target of CAR-T therapy development for EPS15L1-CLNS1A

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 EPS15L1-CLNS1A

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

Top

Related Diseases to EPS15L1-CLNS1A

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