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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:CHPT1-TXNRD1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CHPT1-TXNRD1
FusionPDB ID: 16631
FusionGDB2.0 ID: 16631
HgeneTgene
Gene symbol

CHPT1

TXNRD1

Gene ID

56994

7296

Gene namecholine phosphotransferase 1thioredoxin reductase 1
SynonymsCPT|CPT1GRIM-12|TR|TR1|TRXR1|TXNR
Cytomap

12q23.2

12q23.3

Type of geneprotein-codingprotein-coding
Descriptioncholinephosphotransferase 1AAPT1-like proteincholinephosphotransferase 1 alphadiacylglycerol cholinephosphotransferase 1hCPT1phosphatidylcholine synthesizing enzymethioredoxin reductase 1, cytoplasmicKM-102-derived reductase-like factorgene associated with retinoic and IFN-induced mortality 12 proteingene associated with retinoic and interferon-induced mortality 12 proteinoxidoreductasetestis tissue sperm-bindi
Modification date2020031320200313
UniProtAcc

Q8WUD6

Main function of 5'-partner protein: FUNCTION: Catalyzes phosphatidylcholine biosynthesis from CDP-choline. It thereby plays a central role in the formation and maintenance of vesicular membranes. {ECO:0000269|PubMed:10893425}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000229266, ENST00000549872, 
ENST00000550385, 		ENST00000378070, 
ENST00000397736, ENST00000427956, 
ENST00000524698, ENST00000526950, 
ENST00000529546, ENST00000540716, 
ENST00000542918, ENST00000526006, 
ENST00000354940, ENST00000388854, 
ENST00000429002, ENST00000503506, 
ENST00000525566, ENST00000526390, 
ENST00000526691, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 10 X 6=78011 X 11 X 4=484
# samples 1412
** MAII scorelog2(14/780*10)=-2.47804729680464
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/484*10)=-2.01197264166608
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: CHPT1 [Title/Abstract] AND TXNRD1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: CHPT1 [Title/Abstract] AND TXNRD1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CHPT1(102091912)-TXNRD1(104707023), # samples:3
Anticipated loss of major functional domain due to fusion event.CHPT1-TXNRD1 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.
CHPT1-TXNRD1 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.
CHPT1-TXNRD1 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.
CHPT1-TXNRD1 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
HgeneCHPT1

GO:0006656

phosphatidylcholine biosynthetic process

10893425

HgeneCHPT1

GO:0006663

platelet activating factor biosynthetic process

10893425



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/chr12:102091912/chr12:104707023)
- 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 CHPT1 (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 TXNRD1 (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)
ENST00000229266CHPT1chr12102091912+ENST00000525566TXNRD1chr12104707023+3783508851914609
ENST00000229266CHPT1chr12102091912+ENST00000429002TXNRD1chr12104707023+3777508851914609
ENST00000229266CHPT1chr12102091912+ENST00000503506TXNRD1chr12104707023+3777508851914609
ENST00000229266CHPT1chr12102091912+ENST00000526691TXNRD1chr12104707023+3783508851914609
ENST00000229266CHPT1chr12102091912+ENST00000388854TXNRD1chr12104707023+3777508851914609
ENST00000229266CHPT1chr12102091912+ENST00000354940TXNRD1chr12104707023+3777508851914609
ENST00000229266CHPT1chr12102091912+ENST00000526390TXNRD1chr12104707023+3774508851914609
ENST00000549872CHPT1chr12102091912+ENST00000525566TXNRD1chr12104707023+3738463401869609
ENST00000549872CHPT1chr12102091912+ENST00000429002TXNRD1chr12104707023+3732463401869609
ENST00000549872CHPT1chr12102091912+ENST00000503506TXNRD1chr12104707023+3732463401869609
ENST00000549872CHPT1chr12102091912+ENST00000526691TXNRD1chr12104707023+3738463401869609
ENST00000549872CHPT1chr12102091912+ENST00000388854TXNRD1chr12104707023+3732463401869609
ENST00000549872CHPT1chr12102091912+ENST00000354940TXNRD1chr12104707023+3732463401869609
ENST00000549872CHPT1chr12102091912+ENST00000526390TXNRD1chr12104707023+3729463401869609

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
ENST00000229266ENST00000525566CHPT1chr12102091912+TXNRD1chr12104707023+0.0007386610.9992613
ENST00000229266ENST00000429002CHPT1chr12102091912+TXNRD1chr12104707023+0.000775180.9992248
ENST00000229266ENST00000503506CHPT1chr12102091912+TXNRD1chr12104707023+0.000775180.9992248
ENST00000229266ENST00000526691CHPT1chr12102091912+TXNRD1chr12104707023+0.0007386610.9992613
ENST00000229266ENST00000388854CHPT1chr12102091912+TXNRD1chr12104707023+0.000775180.9992248
ENST00000229266ENST00000354940CHPT1chr12102091912+TXNRD1chr12104707023+0.000775180.9992248
ENST00000229266ENST00000526390CHPT1chr12102091912+TXNRD1chr12104707023+0.0007727680.9992273
ENST00000549872ENST00000525566CHPT1chr12102091912+TXNRD1chr12104707023+0.0007212240.99927884
ENST00000549872ENST00000429002CHPT1chr12102091912+TXNRD1chr12104707023+0.0007594050.99924064
ENST00000549872ENST00000503506CHPT1chr12102091912+TXNRD1chr12104707023+0.0007594050.99924064
ENST00000549872ENST00000526691CHPT1chr12102091912+TXNRD1chr12104707023+0.0007212240.99927884
ENST00000549872ENST00000388854CHPT1chr12102091912+TXNRD1chr12104707023+0.0007594050.99924064
ENST00000549872ENST00000354940CHPT1chr12102091912+TXNRD1chr12104707023+0.0007594050.99924064
ENST00000549872ENST00000526390CHPT1chr12102091912+TXNRD1chr12104707023+0.0007602740.9992398

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 CHPT1-TXNRD1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
CHPT1chr12102091912TXNRD1chr12104707023463141LVLISYCPTATEEEAAQYGKKVMVLD
CHPT1chr12102091912TXNRD1chr12104707023508141LVLISYCPTATEEEAAQYGKKVMVLD

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Potential FusionNeoAntigen Information of CHPT1-TXNRD1 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.
CHPT1-TXNRD1_102091912_104707023.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)
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:01TEEEAAQY0.99560.84221018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B35:08TATEEEAAQY0.97470.8548818
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B35:01TATEEEAAQY0.9260.8303818
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B44:09TEEEAAQY0.99830.5071018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:05TEEEAAQY0.99560.84221018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:08TEEEAAQY0.99540.86061018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:06TEEEAAQY0.99410.85281018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:04TEEEAAQY0.9930.85311018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:03TEEEAAQY0.95220.83171018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B18:11TEEEAAQY0.9510.76771018
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B35:77TATEEEAAQY0.9260.8303818
CHPT1-TXNRD1chr12102091912chr12104707023508HLA-B35:23TATEEEAAQY0.91730.8806818

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Potential FusionNeoAntigen Information of CHPT1-TXNRD1 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 CHPT1-TXNRD1

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
904CPTATEEEAAQYGKCHPT1TXNRD1chr12102091912chr12104707023508

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CHPT1-TXNRD1

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-B51:011E28904CPTATEEEAAQYGK-4.74014-4.74014
HLA-A03:012XPG904CPTATEEEAAQYGK-5.24919-5.24919
HLA-B14:023BVN904CPTATEEEAAQYGK-4.30965-4.30965
HLA-B18:014JQV904CPTATEEEAAQYGK-4.49786-4.49786
HLA-A11:014UQ2904CPTATEEEAAQYGK-4.61939-4.61939
HLA-A24:025HGA904CPTATEEEAAQYGK-5.27587-5.27587
HLA-B57:015VUD904CPTATEEEAAQYGK-4.50519-4.50519
HLA-C08:026JTP904CPTATEEEAAQYGK-5.64713-5.64713
HLA-B27:056PYJ904CPTATEEEAAQYGK-3.60727-3.60727
HLA-B27:036PZ5904CPTATEEEAAQYGK-5.44172-5.44172

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Vaccine Design for the FusionNeoAntigens of CHPT1-TXNRD1

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
CHPT1-TXNRD1chr12102091912chr121047070231018TEEEAAQYACCGAAGAGGAGGCAGCCCAATAT
CHPT1-TXNRD1chr12102091912chr12104707023818TATEEEAAQYACGGCCACCGAAGAGGAGGCAGCCCAATAT

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 CHPT1-TXNRD1

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
SARCCHPT1-TXNRD1chr12102091912ENST00000229266chr12104707023ENST00000354940TCGA-DX-A2IZ-01A

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Potential target of CAR-T therapy development for CHPT1-TXNRD1

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
HgeneCHPT1chr12:102091912chr12:104707023ENST00000229266+1966_8691407.0TransmembraneHelical

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 CHPT1-TXNRD1

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 CHPT1-TXNRD1

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