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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:CHD9-RAD51B

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CHD9-RAD51B
FusionPDB ID: 16409
FusionGDB2.0 ID: 16409
HgeneTgene
Gene symbol

CHD9

RAD51B

Gene ID

80205

5890

Gene namechromodomain helicase DNA binding protein 9RAD51 paralog B
SynonymsAD013|CHD-9|CReMM|KISH2|PRIC320R51H2|RAD51L1|REC2
Cytomap

16q12.2

14q24.1

Type of geneprotein-codingprotein-coding
Descriptionchromodomain-helicase-DNA-binding protein 9ATP-dependent helicase CHD9PPAR-alpha-interacting complex protein 320 kDaPPAR{gamma}-interacting cofactor 320 kDachromatin remodeling factor CHROM1chromatin-related mesenchymal modulatorciprofibrate bound pDNA repair protein RAD51 homolog 2RAD51 homolog BRecA-like proteinrecombination repair protein
Modification date2020032020200313
UniProtAcc

Q3L8U1

Main function of 5'-partner protein: FUNCTION: Acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. Proposed to be a ATP-dependent chromatin remodeling protein. Has DNA-dependent ATPase activity and binds to A/T-rich DNA. Associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis (By similarity). {ECO:0000250, ECO:0000269|PubMed:16095617, ECO:0000269|PubMed:16554032}.

O15315

Main function of 5'-partner protein: FUNCTION: Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents. May promote the assembly of presynaptic RAD51 nucleoprotein filaments. Binds single-stranded DNA and double-stranded DNA and has DNA-dependent ATPase activity. Part of the RAD21 paralog protein complex BCDX2 which acts in the BRCA1-BRCA2-dependent HR pathway. Upon DNA damage, BCDX2 acts downstream of BRCA2 recruitment and upstream of RAD51 recruitment. BCDX2 binds predominantly to the intersection of the four duplex arms of the Holliday junction and to junction of replication forks. The BCDX2 complex was originally reported to bind single-stranded DNA, single-stranded gaps in duplex DNA and specifically to nicks in duplex DNA. The BCDX2 subcomplex RAD51B:RAD51C exhibits single-stranded DNA-dependent ATPase activity suggesting an involvement in early stages of the HR pathway. {ECO:0000269|PubMed:11751635, ECO:0000269|PubMed:11751636, ECO:0000269|PubMed:11842113, ECO:0000269|PubMed:12441335, ECO:0000269|PubMed:23108668, ECO:0000269|PubMed:23149936}.
Ensembl transtripts involved in fusion geneENST idsENST00000398510, ENST00000447540, 
ENST00000564845, ENST00000566029, 
ENST00000564582, 		ENST00000469165, 
ENST00000390683, ENST00000471583, 
ENST00000487270, ENST00000487861, 
ENST00000488612, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 6=70241 X 23 X 12=11316
# samples 1356
** MAII scorelog2(13/702*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(56/11316*10)=-4.33679344445129
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CHD9 [Title/Abstract] AND RAD51B [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CHD9 [Title/Abstract] AND RAD51B [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CHD9(53191453)-RAD51B(68758601), # samples:3
Anticipated loss of major functional domain due to fusion event.CHD9-RAD51B 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.
CHD9-RAD51B 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.
CHD9-RAD51B 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.
CHD9-RAD51B 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/chr16:53191453/chr14:68758601)
- 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 CHD9 (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 RAD51B (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)
ENST00000447540CHD9chr1653191453+ENST00000487861RAD51Bchr1468758601+250116612092182657
ENST00000447540CHD9chr1653191453+ENST00000471583RAD51Bchr1468758601+239316612091957582
ENST00000447540CHD9chr1653191453+ENST00000487270RAD51Bchr1468758601+345316612092059616
ENST00000447540CHD9chr1653191453+ENST00000488612RAD51Bchr1468758601+242816612092005598
ENST00000447540CHD9chr1653191453+ENST00000390683RAD51Bchr1468758601+200616612092005599
ENST00000566029CHD9chr1653191453+ENST00000487861RAD51Bchr1468758601+250116612092182657
ENST00000566029CHD9chr1653191453+ENST00000471583RAD51Bchr1468758601+239316612091957582
ENST00000566029CHD9chr1653191453+ENST00000487270RAD51Bchr1468758601+345316612092059616
ENST00000566029CHD9chr1653191453+ENST00000488612RAD51Bchr1468758601+242816612092005598
ENST00000566029CHD9chr1653191453+ENST00000390683RAD51Bchr1468758601+200616612092005599
ENST00000564845CHD9chr1653191453+ENST00000487861RAD51Bchr1468758601+259417543022275657
ENST00000564845CHD9chr1653191453+ENST00000471583RAD51Bchr1468758601+248617543022050582
ENST00000564845CHD9chr1653191453+ENST00000487270RAD51Bchr1468758601+354617543022152616
ENST00000564845CHD9chr1653191453+ENST00000488612RAD51Bchr1468758601+252117543022098598
ENST00000564845CHD9chr1653191453+ENST00000390683RAD51Bchr1468758601+209917543022098599
ENST00000398510CHD9chr1653191453+ENST00000487861RAD51Bchr1468758601+23791539872060657
ENST00000398510CHD9chr1653191453+ENST00000471583RAD51Bchr1468758601+22711539871835582
ENST00000398510CHD9chr1653191453+ENST00000487270RAD51Bchr1468758601+33311539871937616
ENST00000398510CHD9chr1653191453+ENST00000488612RAD51Bchr1468758601+23061539871883598
ENST00000398510CHD9chr1653191453+ENST00000390683RAD51Bchr1468758601+18841539871883598

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
ENST00000447540ENST00000487861CHD9chr1653191453+RAD51Bchr1468758601+0.003785940.9962141
ENST00000447540ENST00000471583CHD9chr1653191453+RAD51Bchr1468758601+0.0013885350.99861145
ENST00000447540ENST00000487270CHD9chr1653191453+RAD51Bchr1468758601+0.0017740750.998226
ENST00000447540ENST00000488612CHD9chr1653191453+RAD51Bchr1468758601+0.0018130290.998187
ENST00000447540ENST00000390683CHD9chr1653191453+RAD51Bchr1468758601+0.0018774480.9981225
ENST00000566029ENST00000487861CHD9chr1653191453+RAD51Bchr1468758601+0.003785940.9962141
ENST00000566029ENST00000471583CHD9chr1653191453+RAD51Bchr1468758601+0.0013885350.99861145
ENST00000566029ENST00000487270CHD9chr1653191453+RAD51Bchr1468758601+0.0017740750.998226
ENST00000566029ENST00000488612CHD9chr1653191453+RAD51Bchr1468758601+0.0018130290.998187
ENST00000566029ENST00000390683CHD9chr1653191453+RAD51Bchr1468758601+0.0018774480.9981225
ENST00000564845ENST00000487861CHD9chr1653191453+RAD51Bchr1468758601+0.0039545660.9960454
ENST00000564845ENST00000471583CHD9chr1653191453+RAD51Bchr1468758601+0.0013072060.9986928
ENST00000564845ENST00000487270CHD9chr1653191453+RAD51Bchr1468758601+0.0018931640.99810684
ENST00000564845ENST00000488612CHD9chr1653191453+RAD51Bchr1468758601+0.0019190240.99808097
ENST00000564845ENST00000390683CHD9chr1653191453+RAD51Bchr1468758601+0.0018060.99819404
ENST00000398510ENST00000487861CHD9chr1653191453+RAD51Bchr1468758601+0.0042271010.9957729
ENST00000398510ENST00000471583CHD9chr1653191453+RAD51Bchr1468758601+0.0014457510.9985543
ENST00000398510ENST00000487270CHD9chr1653191453+RAD51Bchr1468758601+0.0018486470.99815136
ENST00000398510ENST00000488612CHD9chr1653191453+RAD51Bchr1468758601+0.0020273920.99797255
ENST00000398510ENST00000390683CHD9chr1653191453+RAD51Bchr1468758601+0.0021360170.99786395

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 CHD9-RAD51B

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CHD9chr1653191453RAD51Bchr14687586011539483QHLHDRNHLCLQRQVILTNQITTHLS
CHD9chr1653191453RAD51Bchr14687586011661483QHLHDRNHLCLQRQVILTNQITTHLS
CHD9chr1653191453RAD51Bchr14687586011754483QHLHDRNHLCLQRQVILTNQITTHLS

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Potential FusionNeoAntigen Information of CHD9-RAD51B 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.
CHD9-RAD51B_53191453_68758601.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)
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B39:06NHLCLQRQV0.9980.8663615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B39:24NHLCLQRQV0.99690.5699615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B38:02NHLCLQRQV0.99610.9787615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:10NHLCLQRQV0.9670.6442615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B48:01RQVILTNQI0.94340.50931221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B13:02RQVILTNQI0.88610.80621221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B13:01RQVILTNQI0.75850.96711221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:37NHLCLQRQV0.69310.6816615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B39:13RQVILTNQI0.36570.97051221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B52:01RQVILTNQI0.04190.96321221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:04LQRQVILT0.99490.75341018
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B39:05NHLCLQRQV0.99550.9221615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:04RQVILTNQI0.8620.97641221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:09NHLCLQRQV0.98770.7498615
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:73RQVILTNQI0.81230.93181221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B15:30RQVILTNQI0.66970.9581221
CHD9-RAD51Bchr1653191453chr14687586011539HLA-B39:02RQVILTNQI0.43660.97181221

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Potential FusionNeoAntigen Information of CHD9-RAD51B 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 CHD9-RAD51B

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
6181NHLCLQRQVILTNQCHD9RAD51Bchr1653191453chr14687586011539

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CHD9-RAD51B

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-B14:023BVN6181NHLCLQRQVILTNQ-7.9962-8.1096
HLA-B14:023BVN6181NHLCLQRQVILTNQ-5.70842-6.74372
HLA-B52:013W396181NHLCLQRQVILTNQ-6.83737-6.95077
HLA-B52:013W396181NHLCLQRQVILTNQ-4.4836-5.5189
HLA-A11:014UQ26181NHLCLQRQVILTNQ-10.0067-10.1201
HLA-A11:014UQ26181NHLCLQRQVILTNQ-9.03915-10.0745
HLA-A24:025HGA6181NHLCLQRQVILTNQ-6.56204-6.67544
HLA-A24:025HGA6181NHLCLQRQVILTNQ-5.42271-6.45801
HLA-B44:053DX86181NHLCLQRQVILTNQ-7.85648-8.89178
HLA-B44:053DX86181NHLCLQRQVILTNQ-5.3978-5.5112
HLA-A02:016TDR6181NHLCLQRQVILTNQ-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of CHD9-RAD51B

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
CHD9-RAD51Bchr1653191453chr14687586011018LQRQVILTCAGCGACAGGTTATCTTGACGAAT
CHD9-RAD51Bchr1653191453chr14687586011221RQVILTNQICAGGTTATCTTGACGAATCAGATTACA
CHD9-RAD51Bchr1653191453chr1468758601615NHLCLQRQVCACCTATGTTTACAGCGACAGGTTATC

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 CHD9-RAD51B

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
BRCACHD9-RAD51Bchr1653191453ENST00000398510chr1468758601ENST00000390683TCGA-B6-A0RU-01A

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Potential target of CAR-T therapy development for CHD9-RAD51B

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 CHD9-RAD51B

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 CHD9-RAD51B

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
TgeneRAD51BC0006142Malignant neoplasm of breast1CTD_human
TgeneRAD51BC0013146Drug abuse1CTD_human
TgeneRAD51BC0013170Drug habituation1CTD_human
TgeneRAD51BC0013222Drug Use Disorders1CTD_human
TgeneRAD51BC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneRAD51BC0038580Substance Dependence1CTD_human
TgeneRAD51BC0038586Substance Use Disorders1CTD_human
TgeneRAD51BC0236969Substance-Related Disorders1CTD_human
TgeneRAD51BC0238033Carcinoma of Male Breast1CTD_human
TgeneRAD51BC0242788Breast Neoplasms, Male1CTD_human
TgeneRAD51BC0678222Breast Carcinoma1CTD_human
TgeneRAD51BC0740858Substance abuse problem1CTD_human
TgeneRAD51BC1257931Mammary Neoplasms, Human1CTD_human
TgeneRAD51BC1458155Mammary Neoplasms1CTD_human
TgeneRAD51BC1510472Drug Dependence1CTD_human
TgeneRAD51BC4316881Prescription Drug Abuse1CTD_human
TgeneRAD51BC4704874Mammary Carcinoma, Human1CTD_human