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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:CDH23-NSD1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CDH23-NSD1
FusionPDB ID: 15062
FusionGDB2.0 ID: 15062
HgeneTgene
Gene symbol

CDH23

NSD1

Gene ID

64072

64324

Gene namecadherin related 23nuclear receptor binding SET domain protein 1
SynonymsCDHR23|PITA5|USH1DARA267|KMT3B|SOTOS|SOTOS1|STO
Cytomap

10q22.1

5q35.3

Type of geneprotein-codingprotein-coding
Descriptioncadherin-23cadherin-like 23cadherin-related family member 23otocadherinhistone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specificH3-K36-HMTaseH4-K20-HMTaseNR-binding SET domain-containing proteinandrogen receptor coactivator 267 kDa proteinandrogen receptor-associated coregulator 267androgen receptor-as
Modification date2020032020200321
UniProtAcc

Q9H251

Main function of 5'-partner protein: FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells. CDH23 is required for establishing and/or maintaining the proper organization of the stereocilia bundle of hair cells in the cochlea and the vestibule during late embryonic/early postnatal development. It is part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A that mediates mechanotransduction in cochlear hair cells. Required for normal hearing. {ECO:0000269|PubMed:11138009, ECO:0000269|PubMed:16679490}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000224721, ENST00000299366, 
ENST00000398788, ENST00000398809, 
ENST00000398842, ENST00000461841, 
ENST00000475158, 		ENST00000361032, 
ENST00000511258, ENST00000347982, 
ENST00000354179, ENST00000439151, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 7 X 2=9812 X 14 X 7=1176
# samples 717
** MAII scorelog2(7/98*10)=-0.485426827170242
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1176*10)=-2.79028140869866
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CDH23 [Title/Abstract] AND NSD1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CDH23 [Title/Abstract] AND NSD1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NSD1(176563031)-CDH23(73434869), # samples:3
CDH23(73501678)-NSD1(176618885), # samples:2
Anticipated loss of major functional domain due to fusion event.CDH23-NSD1 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.
CDH23-NSD1 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.
CDH23-NSD1 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.
CDH23-NSD1 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
TgeneNSD1

GO:0045893

positive regulation of transcription, DNA-templated

11509567



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/chr10:176563031/chr5:73434869)
- 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 CDH23 (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 NSD1 (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)
ENST00000224721CDH23chr1073501678+ENST00000354179NSD1chr5176618885+1678048655120284007
ENST00000224721CDH23chr1073501678+ENST00000439151NSD1chr5176618885+1678548655120284007
ENST00000224721CDH23chr1073501678+ENST00000347982NSD1chr5176618885+1233248655120284007

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
ENST00000224721ENST00000354179CDH23chr1073501678+NSD1chr5176618885+0.0002619530.99973804
ENST00000224721ENST00000439151CDH23chr1073501678+NSD1chr5176618885+0.0002619960.99973804
ENST00000224721ENST00000347982CDH23chr1073501678+NSD1chr5176618885+0.0005037950.9994962

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 CDH23-NSD1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CDH23chr1073501678NSD1chr517661888548651618HLVATVEDEGTPTLSCQPKKKSTPLK

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Potential FusionNeoAntigen Information of CDH23-NSD1 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.
CDH23-NSD1_73501678_176618885.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)
CDH23-NSD1chr1073501678chr51766188854865HLA-B13:01VEDEGTPTL0.97560.9535514
CDH23-NSD1chr1073501678chr51766188854865HLA-B50:02VEDEGTPTL0.91760.5541514
CDH23-NSD1chr1073501678chr51766188854865HLA-B44:03VEDEGTPTL0.73590.9527514
CDH23-NSD1chr1073501678chr51766188854865HLA-B45:01VEDEGTPTL0.62310.7338514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:01VEDEGTPTL0.59220.9596514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:13VEDEGTPTL0.58230.9678514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:01VEDEGTPTL0.58170.9637514
CDH23-NSD1chr1073501678chr51766188854865HLA-B38:01VEDEGTPTL0.53840.9649514
CDH23-NSD1chr1073501678chr51766188854865HLA-B38:02VEDEGTPTL0.51960.9692514
CDH23-NSD1chr1073501678chr51766188854865HLA-B15:37VEDEGTPTL0.46690.7529514
CDH23-NSD1chr1073501678chr51766188854865HLA-B15:10VEDEGTPTL0.33550.6787514
CDH23-NSD1chr1073501678chr51766188854865HLA-B41:01VEDEGTPTL0.30560.8675514
CDH23-NSD1chr1073501678chr51766188854865HLA-B50:01VEDEGTPTL0.29070.7848514
CDH23-NSD1chr1073501678chr51766188854865HLA-B35:04VEDEGTPTL0.21890.9802514
CDH23-NSD1chr1073501678chr51766188854865HLA-B35:02VEDEGTPTL0.21890.9802514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:13TVEDEGTPTL0.48990.9647414
CDH23-NSD1chr1073501678chr51766188854865HLA-B41:01TVEDEGTPTL0.25790.8851414
CDH23-NSD1chr1073501678chr51766188854865HLA-A02:21TVEDEGTPTL0.23010.6314414
CDH23-NSD1chr1073501678chr51766188854865HLA-B41:01ATVEDEGTPTL0.93860.9059314
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:13ATVEDEGTPTL0.9220.9581314
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:08EDEGTPTL0.94350.7302614
CDH23-NSD1chr1073501678chr51766188854865HLA-C05:09VEDEGTPTL0.99970.9218514
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:07VEDEGTPTL0.99960.7167514
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:10VEDEGTPTL0.99960.7182514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:15VEDEGTPTL0.99950.957514
CDH23-NSD1chr1073501678chr51766188854865HLA-B40:06VEDEGTPTL0.99860.7286514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:03VEDEGTPTL0.88840.971514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:13VEDEGTPTL0.77850.9669514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:04VEDEGTPTL0.77850.9669514
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:14VEDEGTPTL0.69910.7441514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:09VEDEGTPTL0.6920.71514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:08VEDEGTPTL0.68270.8017514
CDH23-NSD1chr1073501678chr51766188854865HLA-B14:03VEDEGTPTL0.64680.8914514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:10VEDEGTPTL0.60370.9535514
CDH23-NSD1chr1073501678chr51766188854865HLA-C07:13VEDEGTPTL0.58240.961514
CDH23-NSD1chr1073501678chr51766188854865HLA-C07:29VEDEGTPTL0.52850.9604514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:05VEDEGTPTL0.50550.9559514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:12VEDEGTPTL0.48750.9664514
CDH23-NSD1chr1073501678chr51766188854865HLA-B35:12VEDEGTPTL0.21890.9802514
CDH23-NSD1chr1073501678chr51766188854865HLA-B51:07VEDEGTPTL0.0250.9186514
CDH23-NSD1chr1073501678chr51766188854865HLA-C05:09TVEDEGTPTL0.99990.9271414
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:10TVEDEGTPTL0.99990.7434414
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:15TVEDEGTPTL0.99990.9631414
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:06TVEDEGTPTL0.95540.9268414
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:04TVEDEGTPTL0.92420.9748414
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:13TVEDEGTPTL0.92420.9748414
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:08TVEDEGTPTL0.86310.8565414
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:03TVEDEGTPTL0.78950.9685414
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:08VEDEGTPTLS0.75570.774515
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:09TVEDEGTPTL0.67050.703414
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:05TVEDEGTPTL0.45440.9477414
CDH23-NSD1chr1073501678chr51766188854865HLA-A02:07TVEDEGTPTL0.20410.5168414
CDH23-NSD1chr1073501678chr51766188854865HLA-C05:09ATVEDEGTPTL10.9359314
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:15ATVEDEGTPTL10.973314
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:08ATVEDEGTPTL0.99610.8569314
CDH23-NSD1chr1073501678chr51766188854865HLA-B48:03ATVEDEGTPTL0.95390.5065314
CDH23-NSD1chr1073501678chr51766188854865HLA-B44:10ATVEDEGTPTL0.83610.6622314
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:11EDEGTPTL0.94550.6807614
CDH23-NSD1chr1073501678chr51766188854865HLA-C05:01VEDEGTPTL0.99970.9218514
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:03VEDEGTPTL0.99970.7552514
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:01VEDEGTPTL0.99960.7167514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:02VEDEGTPTL0.99950.957514
CDH23-NSD1chr1073501678chr51766188854865HLA-C18:01VEDEGTPTL0.99950.7087514
CDH23-NSD1chr1073501678chr51766188854865HLA-B40:04VEDEGTPTL0.99880.7607514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:01VEDEGTPTL0.88840.971514
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:04VEDEGTPTL0.78710.8822514
CDH23-NSD1chr1073501678chr51766188854865HLA-B44:26VEDEGTPTL0.73590.9527514
CDH23-NSD1chr1073501678chr51766188854865HLA-B44:13VEDEGTPTL0.73590.9527514
CDH23-NSD1chr1073501678chr51766188854865HLA-B44:07VEDEGTPTL0.73590.9527514
CDH23-NSD1chr1073501678chr51766188854865HLA-C03:67VEDEGTPTL0.68410.9889514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:02VEDEGTPTL0.64250.969514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:07VEDEGTPTL0.62480.9327514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:11VEDEGTPTL0.62240.7472514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:05VEDEGTPTL0.59220.9596514
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:31VEDEGTPTL0.59220.9633514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:04VEDEGTPTL0.59220.9626514
CDH23-NSD1chr1073501678chr51766188854865HLA-B38:05VEDEGTPTL0.53840.9649514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:06VEDEGTPTL0.52930.9647514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:08VEDEGTPTL0.52580.9524514
CDH23-NSD1chr1073501678chr51766188854865HLA-C07:04VEDEGTPTL0.51860.8914514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:03VEDEGTPTL0.50860.9536514
CDH23-NSD1chr1073501678chr51766188854865HLA-B18:11VEDEGTPTL0.50110.9249514
CDH23-NSD1chr1073501678chr51766188854865HLA-B41:03VEDEGTPTL0.48930.5024514
CDH23-NSD1chr1073501678chr51766188854865HLA-A02:14VEDEGTPTL0.39820.5386514
CDH23-NSD1chr1073501678chr51766188854865HLA-B48:02VEDEGTPTL0.37360.9455514
CDH23-NSD1chr1073501678chr51766188854865HLA-B35:13VEDEGTPTL0.36170.9271514
CDH23-NSD1chr1073501678chr51766188854865HLA-B50:05VEDEGTPTL0.29070.7848514
CDH23-NSD1chr1073501678chr51766188854865HLA-B50:04VEDEGTPTL0.29070.7848514
CDH23-NSD1chr1073501678chr51766188854865HLA-B35:09VEDEGTPTL0.21890.9802514
CDH23-NSD1chr1073501678chr51766188854865HLA-B15:09VEDEGTPTL0.21720.6939514
CDH23-NSD1chr1073501678chr51766188854865HLA-B35:20VEDEGTPTL0.13680.9598514
CDH23-NSD1chr1073501678chr51766188854865HLA-B07:13VEDEGTPTL0.00760.7281514
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:02TVEDEGTPTL0.99990.9631414
CDH23-NSD1chr1073501678chr51766188854865HLA-C05:01TVEDEGTPTL0.99990.9271414
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:03TVEDEGTPTL0.99990.7865414
CDH23-NSD1chr1073501678chr51766188854865HLA-C03:06TVEDEGTPTL0.85660.9958414
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:11TVEDEGTPTL0.83010.8124414
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:01TVEDEGTPTL0.78950.9685414
CDH23-NSD1chr1073501678chr51766188854865HLA-B07:13TVEDEGTPTL0.73860.811414
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:02TVEDEGTPTL0.65380.9661414
CDH23-NSD1chr1073501678chr51766188854865HLA-B40:04TVEDEGTPTL0.43340.7628414
CDH23-NSD1chr1073501678chr51766188854865HLA-B41:03TVEDEGTPTL0.38890.5443414
CDH23-NSD1chr1073501678chr51766188854865HLA-A69:01TVEDEGTPTL0.30080.6953414
CDH23-NSD1chr1073501678chr51766188854865HLA-A02:14TVEDEGTPTL0.24040.5205414
CDH23-NSD1chr1073501678chr51766188854865HLA-A02:06TVEDEGTPTL0.23010.6314414
CDH23-NSD1chr1073501678chr51766188854865HLA-C08:02ATVEDEGTPTL10.973314
CDH23-NSD1chr1073501678chr51766188854865HLA-C04:03ATVEDEGTPTL10.8104314
CDH23-NSD1chr1073501678chr51766188854865HLA-C05:01ATVEDEGTPTL10.9359314
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:11ATVEDEGTPTL0.98480.8143314
CDH23-NSD1chr1073501678chr51766188854865HLA-B40:21ATVEDEGTPTL0.9820.536314
CDH23-NSD1chr1073501678chr51766188854865HLA-B40:04ATVEDEGTPTL0.98120.765314
CDH23-NSD1chr1073501678chr51766188854865HLA-B41:03ATVEDEGTPTL0.95840.5682314
CDH23-NSD1chr1073501678chr51766188854865HLA-B40:12ATVEDEGTPTL0.95390.5065314
CDH23-NSD1chr1073501678chr51766188854865HLA-B39:02ATVEDEGTPTL0.94860.9574314

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Potential FusionNeoAntigen Information of CDH23-NSD1 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 CDH23-NSD1

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
1578EDEGTPTLSCQPKKCDH23NSD1chr1073501678chr51766188854865

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CDH23-NSD1

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-B14:023BVN1578EDEGTPTLSCQPKK-7.69222-7.69942
HLA-B52:013W391578EDEGTPTLSCQPKK-7.60148-7.60868
HLA-A11:014UQ21578EDEGTPTLSCQPKK-6.66327-6.67047
HLA-A24:025HGA1578EDEGTPTLSCQPKK-9.4375-9.4447
HLA-B27:056PYJ1578EDEGTPTLSCQPKK-4.77117-4.77837
HLA-B44:053DX81578EDEGTPTLSCQPKK-6.68497-6.69217

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Vaccine Design for the FusionNeoAntigens of CDH23-NSD1

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
CDH23-NSD1chr1073501678chr5176618885314ATVEDEGTPTLGTGGAGGACGAGGGCACCCCAACCCTGTCGTGT
CDH23-NSD1chr1073501678chr5176618885414TVEDEGTPTLGAGGACGAGGGCACCCCAACCCTGTCGTGT
CDH23-NSD1chr1073501678chr5176618885514VEDEGTPTLGACGAGGGCACCCCAACCCTGTCGTGT
CDH23-NSD1chr1073501678chr5176618885515VEDEGTPTLSGACGAGGGCACCCCAACCCTGTCGTGTCAA
CDH23-NSD1chr1073501678chr5176618885614EDEGTPTLGAGGGCACCCCAACCCTGTCGTGT

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 CDH23-NSD1

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
BRCACDH23-NSD1chr1073501678ENST00000224721chr5176618885ENST00000347982TCGA-AN-A0FJ-01A

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Potential target of CAR-T therapy development for CDH23-NSD1

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 CDH23-NSD1

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 CDH23-NSD1

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