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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:PCDHGB3-JMJD1C

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PCDHGB3-JMJD1C
FusionPDB ID: 63258
FusionGDB2.0 ID: 63258
HgeneTgene
Gene symbol

PCDHGB3

JMJD1C

Gene ID

56102

221037

Gene nameprotocadherin gamma subfamily B, 3jumonji domain containing 1C
SynonymsPCDH-GAMMA-B3KDM3C|TRIP-8|TRIP8
Cytomap

5q31.3

10q21.3

Type of geneprotein-codingprotein-coding
Descriptionprotocadherin gamma-B3probable JmjC domain-containing histone demethylation protein 2CTR-interacting protein 8thyroid hormone receptor interactor 8thyroid receptor-interacting protein 8
Modification date2020031320200313
UniProtAcc.

Q15652

Main function of 5'-partner protein: FUNCTION: Probable histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May be involved in hormone-dependent transcriptional activation, by participating in recruitment to androgen-receptor target genes (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000576222, ENST00000399251, 
ENST00000489372, ENST00000542921, 
ENST00000402544, ENST00000399262, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score1 X 1 X 1=119 X 16 X 5=1520
# samples 117
** MAII scorelog2(1/1*10)=3.32192809488736log2(17/1520*10)=-3.16046467219325
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PCDHGB3 [Title/Abstract] AND JMJD1C [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PCDHGB3 [Title/Abstract] AND JMJD1C [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PCDHGB3(140752376)-JMJD1C(65024524), # samples:1
Anticipated loss of major functional domain due to fusion event.PCDHGB3-JMJD1C 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.
PCDHGB3-JMJD1C 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


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/chr5:140752376/chr10:65024524)
- 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 PCDHGB3 (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 JMJD1C (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)
ENST00000576222PCDHGB3chr5140752376+ENST00000399262JMJD1Cchr1065024524-10660254613198353234

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
ENST00000576222ENST00000399262PCDHGB3chr5140752376+JMJD1Cchr1065024524-0.0003286710.99967134

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 PCDHGB3-JMJD1C

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PCDHGB3chr5140752376JMJD1Cchr10650245242546805NPEMPSNSGNLQKTFKPLVERNIPSS

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Potential FusionNeoAntigen Information of PCDHGB3-JMJD1C 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.
PCDHGB3-JMJD1C_140752376_65024524.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)
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:09KTFKPLVER0.99810.67081221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:11KTFKPLVER0.99810.67081221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:03KTFKPLVER0.99810.67081221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A30:08KTFKPLVER0.99790.79461221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B08:01NLQKTFKPL0.99180.6812918
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A31:02KTFKPLVER0.93930.67941221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B13:02LQKTFKPLV0.520.86931019
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B52:01LQKTFKPLV0.05560.98171019
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:09KTFKPLVERN0.96860.66331222
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:11KTFKPLVERN0.96860.66331222
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:03KTFKPLVERN0.96860.66331222
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A31:02QKTFKPLVER0.91060.53451121
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:03QKTFKPLVER0.85820.50581121
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:09QKTFKPLVER0.85820.50581121
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:11QKTFKPLVER0.85820.50581121
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:11LQKTFKPLVER0.99250.63131021
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:03LQKTFKPLVER0.99250.63131021
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:09LQKTFKPLVER0.99250.63131021
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A31:01KTFKPLVER0.99810.62421221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B15:04LQKTFKPLV0.78260.95851019
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B51:07LQKTFKPLV0.02490.87091019
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A31:01KTFKPLVERN0.95180.59081222
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A31:01LQKTFKPLVER0.99430.6191021
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:01KTFKPLVER0.99810.67081221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A30:01KTFKPLVER0.99770.88331221
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B08:18NLQKTFKPL0.99180.6812918
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-B08:12NLQKTFKPL0.63220.8824918
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:01KTFKPLVERN0.96860.66331222
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:01QKTFKPLVER0.85820.50581121
PCDHGB3-JMJD1Cchr5140752376chr10650245242546HLA-A74:01LQKTFKPLVER0.99250.63131021

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Potential FusionNeoAntigen Information of PCDHGB3-JMJD1C 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.
PCDHGB3-JMJD1C_140752376_65024524.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)
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0103QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0103LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0109QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0115QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0115LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0807QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0807LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0807NLQKTFKPLVERNIP924
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0819QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0819LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0825QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0825LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0832QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0832LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0834QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0834LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0905QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-0905LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1216QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1216LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1216NLQKTFKPLVERNIP924
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1222QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1222LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1222NLQKTFKPLVERNIP924
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-13100QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-13100LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1346QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1346LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1401SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1401NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1404SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1407SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1426SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1426NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1428SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1428NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1435SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1438SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1438NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1439SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1439NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1450SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1454SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1454NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1458SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1458NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1460SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1460NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1461SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1462SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1462NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1470SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1470NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1471SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1471NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1475SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1475NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1482SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1482NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1486SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1486NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1487SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1487NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1488SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1488NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1490SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1490NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1497SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1497NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1499SGNLQKTFKPLVERN722
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1499NSGNLQKTFKPLVER621
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1515QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1515LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1529QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1601QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1601LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1602QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1603QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1603LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1604QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1604LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1605QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1607QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1608QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1608LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1609QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1609LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1609NLQKTFKPLVERNIP924
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1610QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1610LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1611QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1612QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1614QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1614LQKTFKPLVERNIPS1025
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB1-1616QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB5-0102QKTFKPLVERNIPSS1126
PCDHGB3-JMJD1Cchr5140752376chr10650245242546DRB5-0108NQKTFKPLVERNIPSS1126

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Fusion breakpoint peptide structures of PCDHGB3-JMJD1C

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
6374NSGNLQKTFKPLVEPCDHGB3JMJD1Cchr5140752376chr10650245242546

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PCDHGB3-JMJD1C

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-B14:023BVN6374NSGNLQKTFKPLVE-7.15543-7.26883
HLA-B14:023BVN6374NSGNLQKTFKPLVE-4.77435-5.80965
HLA-B52:013W396374NSGNLQKTFKPLVE-6.80875-6.92215
HLA-B52:013W396374NSGNLQKTFKPLVE-4.20386-5.23916
HLA-A11:014UQ26374NSGNLQKTFKPLVE-7.5194-8.5547
HLA-A11:014UQ26374NSGNLQKTFKPLVE-6.9601-7.0735
HLA-A24:025HGA6374NSGNLQKTFKPLVE-7.52403-7.63743
HLA-A24:025HGA6374NSGNLQKTFKPLVE-5.82433-6.85963
HLA-B27:056PYJ6374NSGNLQKTFKPLVE-3.28285-4.31815
HLA-B44:053DX86374NSGNLQKTFKPLVE-5.91172-6.94702
HLA-B44:053DX86374NSGNLQKTFKPLVE-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of PCDHGB3-JMJD1C

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
PCDHGB3-JMJD1Cchr5140752376chr10650245241019LQKTFKPLVTTGCAAAAGACTTTCAAACCTCTGGTT
PCDHGB3-JMJD1Cchr5140752376chr10650245241021LQKTFKPLVERTTGCAAAAGACTTTCAAACCTCTGGTTGAAAGA
PCDHGB3-JMJD1Cchr5140752376chr10650245241121QKTFKPLVERCAAAAGACTTTCAAACCTCTGGTTGAAAGA
PCDHGB3-JMJD1Cchr5140752376chr10650245241221KTFKPLVERAAGACTTTCAAACCTCTGGTTGAAAGA
PCDHGB3-JMJD1Cchr5140752376chr10650245241222KTFKPLVERNAAGACTTTCAAACCTCTGGTTGAAAGAAAT
PCDHGB3-JMJD1Cchr5140752376chr1065024524918NLQKTFKPLAATTTGCAAAAGACTTTCAAACCTCTG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PCDHGB3-JMJD1Cchr5140752376chr10650245241025LQKTFKPLVERNIPSTTGCAAAAGACTTTCAAACCTCTGGTTGAAAGAAATATACCCAGT
PCDHGB3-JMJD1Cchr5140752376chr10650245241126QKTFKPLVERNIPSSCAAAAGACTTTCAAACCTCTGGTTGAAAGAAATATACCCAGTTCA
PCDHGB3-JMJD1Cchr5140752376chr1065024524621NSGNLQKTFKPLVERAATTCAGGCAATTTGCAAAAGACTTTCAAACCTCTGGTTGAAAGA
PCDHGB3-JMJD1Cchr5140752376chr1065024524722SGNLQKTFKPLVERNTCAGGCAATTTGCAAAAGACTTTCAAACCTCTGGTTGAAAGAAAT
PCDHGB3-JMJD1Cchr5140752376chr1065024524924NLQKTFKPLVERNIPAATTTGCAAAAGACTTTCAAACCTCTGGTTGAAAGAAATATACCC

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Information of the samples that have these potential fusion neoantigens of PCDHGB3-JMJD1C

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
SKCMPCDHGB3-JMJD1Cchr5140752376ENST00000576222chr1065024524ENST00000399262TCGA-EE-A20I-06A

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Potential target of CAR-T therapy development for PCDHGB3-JMJD1C

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
HgenePCDHGB3chr5:140752376chr10:65024524ENST00000576222+14692_712805930.0TransmembraneHelical

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 PCDHGB3-JMJD1C

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 PCDHGB3-JMJD1C

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
TgeneJMJD1CC0004352Autistic Disorder1CTD_human
TgeneJMJD1CC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneJMJD1CC0012236DiGeorge Syndrome1ORPHANET
TgeneJMJD1CC0087031Juvenile-Onset Still Disease1CTD_human
TgeneJMJD1CC0220704Shprintzen syndrome1ORPHANET
TgeneJMJD1CC0431406Asymmetric crying face association1ORPHANET
TgeneJMJD1CC0795907CONOTRUNCAL ANOMALY FACE SYNDROME1ORPHANET
TgeneJMJD1CC1333813Central Nervous System Germinoma1ORPHANET
TgeneJMJD1CC293634622q11 Deletion Syndrome1ORPHANET
TgeneJMJD1CC326610122q11 partial monosomy syndrome1ORPHANET
TgeneJMJD1CC3495559Juvenile arthritis1CTD_human
TgeneJMJD1CC3714758Juvenile psoriatic arthritis1CTD_human
TgeneJMJD1CC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneJMJD1CC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human