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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:TLK2-PITPNC1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TLK2-PITPNC1
FusionPDB ID: 91161
FusionGDB2.0 ID: 91161
HgeneTgene
Gene symbol

TLK2

PITPNC1

Gene ID

11011

26207

Gene nametousled like kinase 2phosphatidylinositol transfer protein cytoplasmic 1
SynonymsHsHPK|MRD57|PKU-ALPHAM-RDGB-beta|MRDGBbeta|RDGB-BETA|RDGBB|RDGBB1
Cytomap

17q23.2

17q24.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase tousled-like 2cytoplasmic phosphatidylinositol transfer protein 1M-rdgB betamammalian rdgB homolog betaretinal degeneration B beta 1retinal degeneration B homolog beta
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000577616, ENST00000582809, 
ENST00000326270, ENST00000343388, 
ENST00000346027, ENST00000542523, 
ENST00000299954, ENST00000335257, 
ENST00000580974, ENST00000581322, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 11 X 9=178231 X 22 X 12=8184
# samples 2452
** MAII scorelog2(24/1782*10)=-2.8923910259134
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(52/8184*10)=-3.97622261671687
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: TLK2 [Title/Abstract] AND PITPNC1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TLK2 [Title/Abstract] AND PITPNC1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TLK2(60558567)-PITPNC1(65528918), # samples:2
Anticipated loss of major functional domain due to fusion event.TLK2-PITPNC1 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.
TLK2-PITPNC1 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
HgeneTLK2

GO:0001672

regulation of chromatin assembly or disassembly

12660173

HgeneTLK2

GO:0006468

protein phosphorylation

12660173

HgeneTLK2

GO:0006974

cellular response to DNA damage stimulus

12660173

HgeneTLK2

GO:0018105

peptidyl-serine phosphorylation

20016786

HgeneTLK2

GO:0035556

intracellular signal transduction

12660173

HgeneTLK2

GO:0071480

cellular response to gamma radiation

12660173

TgenePITPNC1

GO:0015914

phospholipid transport

22822086



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/chr17:60558567/chr17:65528918)
- 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 TLK2 (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 PITPNC1 (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)
ENST00000326270TLK2chr1760558567+ENST00000580974PITPNC1chr1765528918+57873491211107328
ENST00000326270TLK2chr1760558567+ENST00000299954PITPNC1chr1765528918+20603491211107328
ENST00000326270TLK2chr1760558567+ENST00000335257PITPNC1chr1765528918+19413491211299392
ENST00000326270TLK2chr1760558567+ENST00000581322PITPNC1chr1765528918+14253491211299392
ENST00000346027TLK2chr1760558567+ENST00000580974PITPNC1chr1765528918+57903521211110329
ENST00000346027TLK2chr1760558567+ENST00000299954PITPNC1chr1765528918+20633521211110329
ENST00000346027TLK2chr1760558567+ENST00000335257PITPNC1chr1765528918+19443521211302393
ENST00000346027TLK2chr1760558567+ENST00000581322PITPNC1chr1765528918+14283521211302393
ENST00000343388TLK2chr1760558567+ENST00000580974PITPNC1chr1765528918+566522750985311
ENST00000343388TLK2chr1760558567+ENST00000299954PITPNC1chr1765528918+193822750985311
ENST00000343388TLK2chr1760558567+ENST00000335257PITPNC1chr1765528918+1819227501177375
ENST00000343388TLK2chr1760558567+ENST00000581322PITPNC1chr1765528918+1303227501177375
ENST00000542523TLK2chr1760558567+ENST00000580974PITPNC1chr1765528918+554410625864279
ENST00000542523TLK2chr1760558567+ENST00000299954PITPNC1chr1765528918+181710625864279
ENST00000542523TLK2chr1760558567+ENST00000335257PITPNC1chr1765528918+1698106251056343
ENST00000542523TLK2chr1760558567+ENST00000581322PITPNC1chr1765528918+1182106251056343
ENST00000326270TLK2chr1760558567+ENST00000580974PITPNC1chr1765528917+57873491211107328
ENST00000326270TLK2chr1760558567+ENST00000299954PITPNC1chr1765528917+20603491211107328
ENST00000326270TLK2chr1760558567+ENST00000335257PITPNC1chr1765528917+19413491211299392
ENST00000326270TLK2chr1760558567+ENST00000581322PITPNC1chr1765528917+14253491211299392
ENST00000346027TLK2chr1760558567+ENST00000580974PITPNC1chr1765528917+57903521211110329
ENST00000346027TLK2chr1760558567+ENST00000299954PITPNC1chr1765528917+20633521211110329
ENST00000346027TLK2chr1760558567+ENST00000335257PITPNC1chr1765528917+19443521211302393
ENST00000346027TLK2chr1760558567+ENST00000581322PITPNC1chr1765528917+14283521211302393
ENST00000343388TLK2chr1760558567+ENST00000580974PITPNC1chr1765528917+566522750985311
ENST00000343388TLK2chr1760558567+ENST00000299954PITPNC1chr1765528917+193822750985311
ENST00000343388TLK2chr1760558567+ENST00000335257PITPNC1chr1765528917+1819227501177375
ENST00000343388TLK2chr1760558567+ENST00000581322PITPNC1chr1765528917+1303227501177375
ENST00000542523TLK2chr1760558567+ENST00000580974PITPNC1chr1765528917+554410625864279
ENST00000542523TLK2chr1760558567+ENST00000299954PITPNC1chr1765528917+181710625864279
ENST00000542523TLK2chr1760558567+ENST00000335257PITPNC1chr1765528917+1698106251056343
ENST00000542523TLK2chr1760558567+ENST00000581322PITPNC1chr1765528917+1182106251056343

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
ENST00000326270ENST00000580974TLK2chr1760558567+PITPNC1chr1765528918+0.0001795340.99982053
ENST00000326270ENST00000299954TLK2chr1760558567+PITPNC1chr1765528918+0.0004778220.9995222
ENST00000326270ENST00000335257TLK2chr1760558567+PITPNC1chr1765528918+0.0002740360.999726
ENST00000326270ENST00000581322TLK2chr1760558567+PITPNC1chr1765528918+0.0006710410.999329
ENST00000346027ENST00000580974TLK2chr1760558567+PITPNC1chr1765528918+0.0001809930.999819
ENST00000346027ENST00000299954TLK2chr1760558567+PITPNC1chr1765528918+0.0004914680.9995085
ENST00000346027ENST00000335257TLK2chr1760558567+PITPNC1chr1765528918+0.0002900110.99971
ENST00000346027ENST00000581322TLK2chr1760558567+PITPNC1chr1765528918+0.0007252540.9992748
ENST00000343388ENST00000580974TLK2chr1760558567+PITPNC1chr1765528918+0.0001821560.9998179
ENST00000343388ENST00000299954TLK2chr1760558567+PITPNC1chr1765528918+0.0003867620.9996132
ENST00000343388ENST00000335257TLK2chr1760558567+PITPNC1chr1765528918+0.0002278220.99977213
ENST00000343388ENST00000581322TLK2chr1760558567+PITPNC1chr1765528918+0.0004949620.99950504
ENST00000542523ENST00000580974TLK2chr1760558567+PITPNC1chr1765528918+0.0001761080.99982387
ENST00000542523ENST00000299954TLK2chr1760558567+PITPNC1chr1765528918+0.0003504980.9996495
ENST00000542523ENST00000335257TLK2chr1760558567+PITPNC1chr1765528918+0.0001860590.999814
ENST00000542523ENST00000581322TLK2chr1760558567+PITPNC1chr1765528918+0.0003997540.99960023
ENST00000326270ENST00000580974TLK2chr1760558567+PITPNC1chr1765528917+0.0001795340.99982053
ENST00000326270ENST00000299954TLK2chr1760558567+PITPNC1chr1765528917+0.0004778220.9995222
ENST00000326270ENST00000335257TLK2chr1760558567+PITPNC1chr1765528917+0.0002740360.999726
ENST00000326270ENST00000581322TLK2chr1760558567+PITPNC1chr1765528917+0.0006710410.999329
ENST00000346027ENST00000580974TLK2chr1760558567+PITPNC1chr1765528917+0.0001809930.999819
ENST00000346027ENST00000299954TLK2chr1760558567+PITPNC1chr1765528917+0.0004914680.9995085
ENST00000346027ENST00000335257TLK2chr1760558567+PITPNC1chr1765528917+0.0002900110.99971
ENST00000346027ENST00000581322TLK2chr1760558567+PITPNC1chr1765528917+0.0007252540.9992748
ENST00000343388ENST00000580974TLK2chr1760558567+PITPNC1chr1765528917+0.0001821560.9998179
ENST00000343388ENST00000299954TLK2chr1760558567+PITPNC1chr1765528917+0.0003867620.9996132
ENST00000343388ENST00000335257TLK2chr1760558567+PITPNC1chr1765528917+0.0002278220.99977213
ENST00000343388ENST00000581322TLK2chr1760558567+PITPNC1chr1765528917+0.0004949620.99950504
ENST00000542523ENST00000580974TLK2chr1760558567+PITPNC1chr1765528917+0.0001761080.99982387
ENST00000542523ENST00000299954TLK2chr1760558567+PITPNC1chr1765528917+0.0003504980.9996495
ENST00000542523ENST00000335257TLK2chr1760558567+PITPNC1chr1765528917+0.0001860590.999814
ENST00000542523ENST00000581322TLK2chr1760558567+PITPNC1chr1765528917+0.0003997540.99960023

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 TLK2-PITPNC1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TLK2chr1760558567PITPNC1chr176552891710627LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891722759LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891734976LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891735277LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891810627LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891822759LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891834976LLEARFTGVGVSKYKIGQLYMISKHS
TLK2chr1760558567PITPNC1chr176552891835277LLEARFTGVGVSKYKIGQLYMISKHS

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Potential FusionNeoAntigen Information of TLK2-PITPNC1 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.
TLK2-PITPNC1_60558567_65528917.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)
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:17FTGVGVSKY0.9620.9817514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:16FTGVGVSKY0.810.9623514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-A80:01FTGVGVSKY0.69760.5509514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:25SKYKIGQLY0.47730.56031120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B46:01FTGVGVSKY0.37450.6603514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B57:01VSKYKIGQLY0.99740.72291020
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:17VSKYKIGQLY0.98930.5791020
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:05ARFTGVGVSKY10.8536314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:02ARFTGVGVSKY10.6378314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:04ARFTGVGVSKY10.853314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C06:03VSKYKIGQL0.94390.94631019
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C12:04VSKYKIGQL0.9370.94631019
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:27SKYKIGQLY0.91980.73031120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:05SKYKIGQLY0.83340.71091120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:67SKYKIGQLY0.75880.68071120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:80SKYKIGQLY0.75880.68071120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:10SKYKIGQLY0.74870.74031120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:46SKYKIGQLY0.74270.50231120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C15:04FTGVGVSKY0.66830.964514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:29KYKIGQLYM0.54010.78291221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:05KYKIGQLYM0.49750.84151221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:67KYKIGQLYM0.47790.79821221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:80KYKIGQLYM0.47790.79821221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:10KYKIGQLYM0.4650.86471221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:27KYKIGQLYM0.45260.84221221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:21SKYKIGQLY0.40390.54131120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:46KYKIGQLYM0.34530.67631221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C03:14FTGVGVSKY0.20120.9891514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:04SKYKIGQLY0.14670.55331120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C12:04FTGVGVSKY0.06180.9974514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C12:16SKYKIGQLY0.03150.73871120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C06:03SKYKIGQLY0.0040.8871120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C15:04VSKYKIGQLY0.98450.60131020
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:14ARFTGVGVSKY0.99990.7667314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:03ARFTGVGVSKY0.99980.8674314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:46ARFTGVGVSKY0.99590.9045314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C14:02KYKIGQLY0.61460.80661220
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C14:03KYKIGQLY0.61460.80661220
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C03:02FTGVGVSKY0.87330.9848514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:17SKYKIGQLY0.76010.79131120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:02SKYKIGQLY0.75880.68071120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-A25:01FTGVGVSKY0.69470.9721514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-A30:01KYKIGQLYM0.68050.70461221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C15:09FTGVGVSKY0.66830.964514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:02KYKIGQLYM0.47790.79821221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:17KYKIGQLYM0.44990.86331221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:27SKYKIGQLY0.40520.55911120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:135SKYKIGQLY0.38930.56641120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B35:28SKYKIGQLY0.31830.56651120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C12:02FTGVGVSKY0.24430.9886514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B48:02SKYKIGQLY0.23840.53351120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C06:06KYKIGQLYM0.22190.9581221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C16:04FTGVGVSKY0.21580.9914514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B18:04SKYKIGQLY0.17780.59951120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C06:08SKYKIGQLY0.14930.79891120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C14:03KYKIGQLYM0.13560.85061221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C14:02KYKIGQLYM0.13560.85061221
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B18:03SKYKIGQLY0.08110.55731120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C16:02FTGVGVSKY0.08080.9947514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B18:06SKYKIGQLY0.07570.56561120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C12:02SKYKIGQLY0.00740.73171120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C06:17SKYKIGQLY0.00680.88591120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C06:02SKYKIGQLY0.00680.88591120
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C02:02FTGVGVSKY0.00340.9933514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C02:10FTGVGVSKY0.00340.9933514
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:135VSKYKIGQLY0.99870.56751020
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B57:10VSKYKIGQLY0.99740.72291020
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C15:09VSKYKIGQLY0.98450.60131020
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:10ARFTGVGVSKY10.936314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:08ARFTGVGVSKY10.7476314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B27:09ARFTGVGVSKY0.99970.8242314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:01ARFTGVGVSKY0.99960.7952314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-C07:22ARFTGVGVSKY0.99720.8048314
TLK2-PITPNC1chr1760558567chr1765528917349HLA-B15:68ARFTGVGVSKY0.96890.7488314

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Potential FusionNeoAntigen Information of TLK2-PITPNC1 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 TLK2-PITPNC1

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
9381TGVGVSKYKIGQLYTLK2PITPNC1chr1760558567chr1765528917349

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TLK2-PITPNC1

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-B14:023BVN9381TGVGVSKYKIGQLY-7.15543-7.26883
HLA-B14:023BVN9381TGVGVSKYKIGQLY-4.77435-5.80965
HLA-B52:013W399381TGVGVSKYKIGQLY-6.80875-6.92215
HLA-B52:013W399381TGVGVSKYKIGQLY-4.20386-5.23916
HLA-A11:014UQ29381TGVGVSKYKIGQLY-7.5194-8.5547
HLA-A11:014UQ29381TGVGVSKYKIGQLY-6.9601-7.0735
HLA-A24:025HGA9381TGVGVSKYKIGQLY-7.52403-7.63743
HLA-A24:025HGA9381TGVGVSKYKIGQLY-5.82433-6.85963
HLA-B27:056PYJ9381TGVGVSKYKIGQLY-3.28285-4.31815
HLA-B44:053DX89381TGVGVSKYKIGQLY-5.91172-6.94702
HLA-B44:053DX89381TGVGVSKYKIGQLY-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of TLK2-PITPNC1

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
TLK2-PITPNC1chr1760558567chr17655289171019VSKYKIGQLGTTAGTAAGTACAAAATTGGACAGCTG
TLK2-PITPNC1chr1760558567chr17655289171020VSKYKIGQLYGTTAGTAAGTACAAAATTGGACAGCTGTAC
TLK2-PITPNC1chr1760558567chr17655289171120SKYKIGQLYAGTAAGTACAAAATTGGACAGCTGTAC
TLK2-PITPNC1chr1760558567chr17655289171220KYKIGQLYAAGTACAAAATTGGACAGCTGTAC
TLK2-PITPNC1chr1760558567chr17655289171221KYKIGQLYMAAGTACAAAATTGGACAGCTGTACATG
TLK2-PITPNC1chr1760558567chr1765528917314ARFTGVGVSKYGCCAGGTTTACTGGAGTAGGTGTTAGTAAGTAC
TLK2-PITPNC1chr1760558567chr1765528917514FTGVGVSKYTTTACTGGAGTAGGTGTTAGTAAGTAC

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 TLK2-PITPNC1

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
BRCATLK2-PITPNC1chr1760558567ENST00000326270chr1765528917ENST00000299954TCGA-D8-A27G

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Potential target of CAR-T therapy development for TLK2-PITPNC1

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 TLK2-PITPNC1

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 TLK2-PITPNC1

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