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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:NNT-PRLR

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NNT-PRLR
FusionPDB ID: 59493
FusionGDB2.0 ID: 59493
HgeneTgene
Gene symbol

NNT

PRLR

Gene ID

23530

5618

Gene namenicotinamide nucleotide transhydrogenaseprolactin receptor
SynonymsGCCD4HPRL|MFAB|RI-PRLR|hPRLrI
Cytomap

5p12

5p13.2

Type of geneprotein-codingprotein-coding
DescriptionNAD(P) transhydrogenase, mitochondrialpyridine nucleotide transhydrogenaseprolactin receptorhPRL receptorsecreted prolactin binding protein
Modification date2020031320200329
UniProtAcc

Q13423

Main function of 5'-partner protein: FUNCTION: The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane (By similarity). May play a role in reactive oxygen species (ROS) detoxification in the adrenal gland (PubMed:22634753). {ECO:0000250|UniProtKB:P07001, ECO:0000269|PubMed:22634753}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000264663, ENST00000344920, 
ENST00000512996, 		ENST00000509934, 
ENST00000231423, ENST00000310101, 
ENST00000342362, ENST00000348262, 
ENST00000382002, ENST00000397391, 
ENST00000511486, ENST00000513753, 
ENST00000542609, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 3 X 4=488 X 7 X 5=280
# samples 58
** MAII scorelog2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(8/280*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NNT [Title/Abstract] AND PRLR [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NNT [Title/Abstract] AND PRLR [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NNT(43628489)-PRLR(35072846), # samples:2
Anticipated loss of major functional domain due to fusion event.NNT-PRLR 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.
NNT-PRLR 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.
NNT-PRLR 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.
NNT-PRLR 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
TgenePRLR

GO:0007171

activation of transmembrane receptor protein tyrosine kinase activity

10585417

TgenePRLR

GO:0042976

activation of Janus kinase activity

10585417

TgenePRLR

GO:0043066

negative regulation of apoptotic process

10585417



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/chr5:43628489/chr5:35072846)
- 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 NNT (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 PRLR (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)
ENST00000264663NNTchr543628489+ENST00000342362PRLRchr535072846-1207011851492680843
ENST00000264663NNTchr543628489+ENST00000382002PRLRchr535072846-1206511851492680843
ENST00000264663NNTchr543628489+ENST00000231423PRLRchr535072846-247411851491942597
ENST00000264663NNTchr543628489+ENST00000513753PRLRchr535072846-232011851491678509
ENST00000264663NNTchr543628489+ENST00000397391PRLRchr535072846-213411851491618489
ENST00000264663NNTchr543628489+ENST00000348262PRLRchr535072846-213411851491618489
ENST00000264663NNTchr543628489+ENST00000542609PRLRchr535072846-188111851491741530
ENST00000264663NNTchr543628489+ENST00000310101PRLRchr535072846-210911851491861570
ENST00000264663NNTchr543628489+ENST00000511486PRLRchr535072846-268111851492680844
ENST00000344920NNTchr543628489+ENST00000342362PRLRchr535072846-1207011852032680825
ENST00000344920NNTchr543628489+ENST00000382002PRLRchr535072846-1206511852032680825
ENST00000344920NNTchr543628489+ENST00000231423PRLRchr535072846-247411852031942579
ENST00000344920NNTchr543628489+ENST00000513753PRLRchr535072846-232011852031678491
ENST00000344920NNTchr543628489+ENST00000397391PRLRchr535072846-213411852031618471
ENST00000344920NNTchr543628489+ENST00000348262PRLRchr535072846-213411852031618471
ENST00000344920NNTchr543628489+ENST00000542609PRLRchr535072846-188111852031741512
ENST00000344920NNTchr543628489+ENST00000310101PRLRchr535072846-210911852031861552
ENST00000344920NNTchr543628489+ENST00000511486PRLRchr535072846-268111852032680826
ENST00000512996NNTchr543628489+ENST00000342362PRLRchr535072846-117949091132404763
ENST00000512996NNTchr543628489+ENST00000382002PRLRchr535072846-117899091132404763
ENST00000512996NNTchr543628489+ENST00000231423PRLRchr535072846-21989091131666517
ENST00000512996NNTchr543628489+ENST00000513753PRLRchr535072846-20449091131402429
ENST00000512996NNTchr543628489+ENST00000397391PRLRchr535072846-18589091131342409
ENST00000512996NNTchr543628489+ENST00000348262PRLRchr535072846-18589091131342409
ENST00000512996NNTchr543628489+ENST00000542609PRLRchr535072846-16059091131465450
ENST00000512996NNTchr543628489+ENST00000310101PRLRchr535072846-18339091131585490
ENST00000512996NNTchr543628489+ENST00000511486PRLRchr535072846-24059091132404764

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
ENST00000264663ENST00000342362NNTchr543628489+PRLRchr535072846-0.0001786450.99982136
ENST00000264663ENST00000382002NNTchr543628489+PRLRchr535072846-0.0001785990.9998215
ENST00000264663ENST00000231423NNTchr543628489+PRLRchr535072846-0.0004486510.99955136
ENST00000264663ENST00000513753NNTchr543628489+PRLRchr535072846-0.0004328460.9995671
ENST00000264663ENST00000397391NNTchr543628489+PRLRchr535072846-0.0004933490.9995066
ENST00000264663ENST00000348262NNTchr543628489+PRLRchr535072846-0.0004933490.9995066
ENST00000264663ENST00000542609NNTchr543628489+PRLRchr535072846-0.0005148210.99948514
ENST00000264663ENST00000310101NNTchr543628489+PRLRchr535072846-0.0008898170.99911016
ENST00000264663ENST00000511486NNTchr543628489+PRLRchr535072846-0.0006765980.99932337
ENST00000344920ENST00000342362NNTchr543628489+PRLRchr535072846-0.0001795570.9998204
ENST00000344920ENST00000382002NNTchr543628489+PRLRchr535072846-0.0001794940.99982053
ENST00000344920ENST00000231423NNTchr543628489+PRLRchr535072846-0.0005172980.99948263
ENST00000344920ENST00000513753NNTchr543628489+PRLRchr535072846-0.0004946680.9995053
ENST00000344920ENST00000397391NNTchr543628489+PRLRchr535072846-0.0006135580.9993864
ENST00000344920ENST00000348262NNTchr543628489+PRLRchr535072846-0.0006135580.9993864
ENST00000344920ENST00000542609NNTchr543628489+PRLRchr535072846-0.0006202550.99937975
ENST00000344920ENST00000310101NNTchr543628489+PRLRchr535072846-0.001150810.99884915
ENST00000344920ENST00000511486NNTchr543628489+PRLRchr535072846-0.0007851570.99921477
ENST00000512996ENST00000342362NNTchr543628489+PRLRchr535072846-0.0002751170.9997249
ENST00000512996ENST00000382002NNTchr543628489+PRLRchr535072846-0.0002749330.99972504
ENST00000512996ENST00000231423NNTchr543628489+PRLRchr535072846-0.0007602330.9992398
ENST00000512996ENST00000513753NNTchr543628489+PRLRchr535072846-0.000832760.9991672
ENST00000512996ENST00000397391NNTchr543628489+PRLRchr535072846-0.0011525880.99884737
ENST00000512996ENST00000348262NNTchr543628489+PRLRchr535072846-0.0011525880.99884737
ENST00000512996ENST00000542609NNTchr543628489+PRLRchr535072846-0.0015319920.998468
ENST00000512996ENST00000310101NNTchr543628489+PRLRchr535072846-0.0016072750.99839264
ENST00000512996ENST00000511486NNTchr543628489+PRLRchr535072846-0.0016487610.9983512

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 NNT-PRLR

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NNTchr543628489PRLRchr5350728461185327KEVDILISTALIPVQPDPPLELAVEV
NNTchr543628489PRLRchr5350728461185345KEVDILISTALIPVQPDPPLELAVEV
NNTchr543628489PRLRchr535072846909265KEVDILISTALIPVQPDPPLELAVEV

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Potential FusionNeoAntigen Information of NNT-PRLR 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.
NNT-PRLR_43628489_35072846.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)
NNT-PRLRchr543628489chr5350728461185HLA-B35:03IPVQPDPPL0.99170.92221120
NNT-PRLRchr543628489chr5350728461185HLA-B35:01IPVQPDPPL0.9880.93181120
NNT-PRLRchr543628489chr5350728461185HLA-B35:08IPVQPDPPL0.98460.87041120
NNT-PRLRchr543628489chr5350728461185HLA-B35:04IPVQPDPPL0.96570.97661120
NNT-PRLRchr543628489chr5350728461185HLA-B35:02IPVQPDPPL0.96570.97661120
NNT-PRLRchr543628489chr5350728461185HLA-B35:05IPVQPDPPL0.96150.73761120
NNT-PRLRchr543628489chr5350728461185HLA-B35:03LIPVQPDPPL0.80180.93721020
NNT-PRLRchr543628489chr5350728461185HLA-B35:02LIPVQPDPPL0.65220.98621020
NNT-PRLRchr543628489chr5350728461185HLA-B35:04LIPVQPDPPL0.65220.98621020
NNT-PRLRchr543628489chr5350728461185HLA-B35:03IPVQPDPPLEL0.99730.89421122
NNT-PRLRchr543628489chr5350728461185HLA-B51:01IPVQPDPPLEL0.99560.52021122
NNT-PRLRchr543628489chr5350728461185HLA-B35:05IPVQPDPPLEL0.99520.70991122
NNT-PRLRchr543628489chr5350728461185HLA-B35:02IPVQPDPPLEL0.99120.96981122
NNT-PRLRchr543628489chr5350728461185HLA-B35:04IPVQPDPPLEL0.99120.96981122
NNT-PRLRchr543628489chr5350728461185HLA-B35:12IPVQPDPPL0.96570.97661120
NNT-PRLRchr543628489chr5350728461185HLA-B39:10IPVQPDPPL0.82890.95741120
NNT-PRLRchr543628489chr5350728461185HLA-B51:08IPVQPDPPL0.81360.51891120
NNT-PRLRchr543628489chr5350728461185HLA-B42:02IPVQPDPPL0.65240.64881120
NNT-PRLRchr543628489chr5350728461185HLA-B42:01IPVQPDPPL0.56890.63721120
NNT-PRLRchr543628489chr5350728461185HLA-B35:12LIPVQPDPPL0.65220.98621020
NNT-PRLRchr543628489chr5350728461185HLA-C01:17IPVQPDPPLEL0.99930.95171122
NNT-PRLRchr543628489chr5350728461185HLA-C01:30IPVQPDPPLEL0.99840.96451122
NNT-PRLRchr543628489chr5350728461185HLA-B35:12IPVQPDPPLEL0.99120.96981122
NNT-PRLRchr543628489chr5350728461185HLA-B42:02IPVQPDPPLEL0.98360.81181122
NNT-PRLRchr543628489chr5350728461185HLA-B51:08IPVQPDPPLEL0.9810.6271122
NNT-PRLRchr543628489chr5350728461185HLA-C07:29IPVQPDPPLEL0.97650.95911122
NNT-PRLRchr543628489chr5350728461185HLA-B42:01IPVQPDPPLEL0.97150.80341122
NNT-PRLRchr543628489chr5350728461185HLA-C07:13IPVQPDPPLEL0.95930.95111122
NNT-PRLRchr543628489chr5350728461185HLA-B39:10IPVQPDPPLEL0.94380.97291122
NNT-PRLRchr543628489chr5350728461185HLA-B07:12ALIPVQPDPPL0.84380.7068920
NNT-PRLRchr543628489chr5350728461185HLA-B35:13IPVQPDPPL0.98960.9251120
NNT-PRLRchr543628489chr5350728461185HLA-B35:77IPVQPDPPL0.9880.93181120
NNT-PRLRchr543628489chr5350728461185HLA-B35:23IPVQPDPPL0.98590.91861120
NNT-PRLRchr543628489chr5350728461185HLA-B35:09IPVQPDPPL0.96570.97661120
NNT-PRLRchr543628489chr5350728461185HLA-B35:17IPVQPDPPL0.96320.84691120
NNT-PRLRchr543628489chr5350728461185HLA-B35:30IPVQPDPPL0.96320.84691120
NNT-PRLRchr543628489chr5350728461185HLA-B35:24IPVQPDPPL0.95540.96061120
NNT-PRLRchr543628489chr5350728461185HLA-B35:11IPVQPDPPL0.95380.91141120
NNT-PRLRchr543628489chr5350728461185HLA-B78:02IPVQPDPPL0.9490.56451120
NNT-PRLRchr543628489chr5350728461185HLA-B51:14IPVQPDPPL0.9280.50671120
NNT-PRLRchr543628489chr5350728461185HLA-B67:01IPVQPDPPL0.83790.81631120
NNT-PRLRchr543628489chr5350728461185HLA-B35:43IPVQPDPPL0.13990.8691120
NNT-PRLRchr543628489chr5350728461185HLA-B15:08IPVQPDPPL0.11940.86751120
NNT-PRLRchr543628489chr5350728461185HLA-B35:09LIPVQPDPPL0.65220.98621020
NNT-PRLRchr543628489chr5350728461185HLA-B67:01LIPVQPDPPL0.47910.9391020
NNT-PRLRchr543628489chr5350728461185HLA-C01:02IPVQPDPPLEL0.99930.951122
NNT-PRLRchr543628489chr5350728461185HLA-C01:03IPVQPDPPLEL0.99760.95521122
NNT-PRLRchr543628489chr5350728461185HLA-B51:29IPVQPDPPLEL0.99760.51181122
NNT-PRLRchr543628489chr5350728461185HLA-B35:13IPVQPDPPLEL0.99720.89611122
NNT-PRLRchr543628489chr5350728461185HLA-B35:30IPVQPDPPLEL0.99580.78341122
NNT-PRLRchr543628489chr5350728461185HLA-B35:17IPVQPDPPLEL0.99580.78341122
NNT-PRLRchr543628489chr5350728461185HLA-B35:09IPVQPDPPLEL0.99120.96981122
NNT-PRLRchr543628489chr5350728461185HLA-B51:09IPVQPDPPLEL0.9910.57591122
NNT-PRLRchr543628489chr5350728461185HLA-B55:04IPVQPDPPLEL0.98920.53661122
NNT-PRLRchr543628489chr5350728461185HLA-B51:21IPVQPDPPLEL0.97630.53561122
NNT-PRLRchr543628489chr5350728461185HLA-B67:01IPVQPDPPLEL0.95380.95731122
NNT-PRLRchr543628489chr5350728461185HLA-B67:01ALIPVQPDPPL0.57410.9682920

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Potential FusionNeoAntigen Information of NNT-PRLR 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.
NNT-PRLR_43628489_35072846.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)
NNT-PRLRchr543628489chr5350728461185DRB1-0301LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0310LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0310ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB1-0313LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0318LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0320LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0322LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0326LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0328LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0330LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0332LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0334LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0336LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0342LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0344LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0346LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0350LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0352LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-0354LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-1476LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-1476ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB1-1479LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB1-1479ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0101LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0101ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0104LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0104ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0105LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0105ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0108LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0108ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0109LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0111LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0111ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0112LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0112ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0113LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0113ALIPVQPDPPLELAV924
NNT-PRLRchr543628489chr5350728461185DRB3-0114LIPVQPDPPLELAVE1025
NNT-PRLRchr543628489chr5350728461185DRB3-0114ALIPVQPDPPLELAV924

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Fusion breakpoint peptide structures of NNT-PRLR

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
4004ISTALIPVQPDPPLNNTPRLRchr543628489chr5350728461185

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NNT-PRLR

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-B14:023BVN4004ISTALIPVQPDPPL-7.15543-7.26883
HLA-B14:023BVN4004ISTALIPVQPDPPL-4.77435-5.80965
HLA-B52:013W394004ISTALIPVQPDPPL-6.80875-6.92215
HLA-B52:013W394004ISTALIPVQPDPPL-4.20386-5.23916
HLA-A11:014UQ24004ISTALIPVQPDPPL-7.5194-8.5547
HLA-A11:014UQ24004ISTALIPVQPDPPL-6.9601-7.0735
HLA-A24:025HGA4004ISTALIPVQPDPPL-7.52403-7.63743
HLA-A24:025HGA4004ISTALIPVQPDPPL-5.82433-6.85963
HLA-B27:056PYJ4004ISTALIPVQPDPPL-3.28285-4.31815
HLA-B44:053DX84004ISTALIPVQPDPPL-5.91172-6.94702
HLA-B44:053DX84004ISTALIPVQPDPPL-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of NNT-PRLR

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
NNT-PRLRchr543628489chr5350728461020LIPVQPDPPLTTATTCCAGTTCAGCCAGACCCTCCTTTGG
NNT-PRLRchr543628489chr5350728461120IPVQPDPPLTTCCAGTTCAGCCAGACCCTCCTTTGG
NNT-PRLRchr543628489chr5350728461122IPVQPDPPLELTTCCAGTTCAGCCAGACCCTCCTTTGGAGCTGG
NNT-PRLRchr543628489chr535072846920ALIPVQPDPPLCACTTATTCCAGTTCAGCCAGACCCTCCTTTGG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
NNT-PRLRchr543628489chr5350728461025LIPVQPDPPLELAVETTATTCCAGTTCAGCCAGACCCTCCTTTGGAGCTGGCTGTGGAAG
NNT-PRLRchr543628489chr535072846924ALIPVQPDPPLELAVCACTTATTCCAGTTCAGCCAGACCCTCCTTTGGAGCTGGCTGTGG

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Information of the samples that have these potential fusion neoantigens of NNT-PRLR

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
COADNNT-PRLRchr543628489ENST00000264663chr535072846ENST00000231423TCGA-D5-6924-01A

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Potential target of CAR-T therapy development for NNT-PRLR

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
TgenePRLRchr5:43628489chr5:35072846ENST0000023142329235_2580377.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST0000031010129235_2580350.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST0000034236228235_2580522.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST0000034826226235_2580269.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST00000382002410235_2580623.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST0000051148606235_2580522.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST0000051375328235_2580289.0TransmembraneHelical
TgenePRLRchr5:43628489chr5:35072846ENST0000054260928235_2580310.0TransmembraneHelical

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 NNT-PRLR

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 NNT-PRLR

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