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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:PTPN12-CCDC146

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTPN12-CCDC146
FusionPDB ID: 70187
FusionGDB2.0 ID: 70187
HgeneTgene
Gene symbol

PTPN12

CCDC146

Gene ID

5782

57639

Gene nameprotein tyrosine phosphatase non-receptor type 12coiled-coil domain containing 146
SynonymsPTP-PEST|PTPG1MBO2
Cytomap

7q11.23

7q11.23

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 12protein-tyrosine phosphatase G1coiled-coil domain-containing protein 146
Modification date2020032920200327
UniProtAcc.

Q8IYE0

Main function of 5'-partner protein:
Ensembl transtripts involved in fusion geneENST idsENST00000248594, ENST00000415482, 
ENST00000435495, 		ENST00000415740, 
ENST00000285871, ENST00000431197, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score22 X 21 X 16=73925 X 11 X 8=440
# samples 4412
** MAII scorelog2(44/7392*10)=-4.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/440*10)=-1.87446911791614
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PTPN12 [Title/Abstract] AND CCDC146 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PTPN12 [Title/Abstract] AND CCDC146 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CCDC146(76924255)-PTPN12(77200395), # samples:1
PTPN12(77166962)-CCDC146(76903010), # samples:1
PTPN12(77200503)-CCDC146(76796974), # samples:1
PTPN12(77230123)-CCDC146(76922268), # samples:1
PTPN12(77166962)-CCDC146(76903011), # samples:1
PTPN12(77168162)-CCDC146(76903011), # samples:1
PTPN12(77200503)-CCDC146(76796975), # samples:1
PTPN12(77214898)-CCDC146(76958713), # samples:1
PTPN12(77166962)-CCDC146(76908069), # samples:1
PTPN12(77193512)-CCDC146(76908069), # samples:1
PTPN12(77230123)-CCDC146(76922269), # samples:1
PTPN12(77227218)-CCDC146(76922269), # samples:1
Anticipated loss of major functional domain due to fusion event.PTPN12-CCDC146 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.
PTPN12-CCDC146 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.
PTPN12-CCDC146 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.
PTPN12-CCDC146 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.
PTPN12-CCDC146 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PTPN12-CCDC146 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted 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
HgenePTPN12

GO:0006470

protein dephosphorylation

27134172

HgenePTPN12

GO:0035335

peptidyl-tyrosine dephosphorylation

27134172



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/chr7:76924255/chr7:77200395)
- 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 PTPN12 (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 CCDC146 (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)
ENST00000248594PTPN12chr777166962+ENST00000431197CCDC146chr776908069+213737121798598
ENST00000248594PTPN12chr777166962+ENST00000285871CCDC146chr776908069+213737121798598
ENST00000248594PTPN12chr777227218+ENST00000431197CCDC146chr776922269+161582421276424
ENST00000248594PTPN12chr777227218+ENST00000285871CCDC146chr776922269+161582421276424
ENST00000415482PTPN12chr777227218+ENST00000431197CCDC146chr776922269+131652584977297
ENST00000415482PTPN12chr777227218+ENST00000285871CCDC146chr776922269+131652584977297
ENST00000435495PTPN12chr777227218+ENST00000431197CCDC146chr776922269+118639550847265
ENST00000435495PTPN12chr777227218+ENST00000285871CCDC146chr776922269+118639550847265

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
ENST00000248594ENST00000431197PTPN12chr777166962+CCDC146chr776908069+0.0019389460.998061
ENST00000248594ENST00000285871PTPN12chr777166962+CCDC146chr776908069+0.0019389460.998061
ENST00000248594ENST00000431197PTPN12chr777227218+CCDC146chr776922269+0.000473220.99952674
ENST00000248594ENST00000285871PTPN12chr777227218+CCDC146chr776922269+0.000473220.99952674
ENST00000415482ENST00000431197PTPN12chr777227218+CCDC146chr776922269+0.000817450.9991825
ENST00000415482ENST00000285871PTPN12chr777227218+CCDC146chr776922269+0.000817450.9991825
ENST00000435495ENST00000431197PTPN12chr777227218+CCDC146chr776922269+0.0016432190.99835676
ENST00000435495ENST00000285871PTPN12chr777227218+CCDC146chr776922269+0.0016432190.99835676

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 PTPN12-CCDC146

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PTPN12chr777166962CCDC146chr776908069371121SPDHNGEDNFARDFMQKYTNIVKEMK
PTPN12chr777227218CCDC146chr776922269395115DYFIRTLLLEFQNMNGYQRRIKNATE
PTPN12chr777227218CCDC146chr776922269525147DYFIRTLLLEFQNMNGYQRRIKNATE
PTPN12chr777227218CCDC146chr776922269824274DYFIRTLLLEFQNMNGYQRRIKNATE

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Potential FusionNeoAntigen Information of PTPN12-CCDC146 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.
PTPN12-CCDC146_77166962_76908069.msa
PTPN12-CCDC146_77227218_76922269.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)
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:01FARDFMQKY0.99910.956918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:25FARDFMQKY0.9990.9437918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:02FARDFMQKY0.99810.9517918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:08FARDFMQKY0.9940.9104918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:17FARDFMQKY0.98950.9131918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:01FARDFMQKY0.9890.9275918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:05FARDFMQKY0.97860.6917918
PTPN12-CCDC146chr777166962chr776908069371HLA-B08:01DFMQKYTNI0.97160.53381221
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:03FARDFMQKY0.96360.8677918
PTPN12-CCDC146chr777166962chr776908069371HLA-B08:09DFMQKYTNI0.94980.62371221
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:16FARDFMQKY0.940.8492918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:95ARDFMQKY0.99860.74791018
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:46ARDFMQKY0.99120.92861018
PTPN12-CCDC146chr777166962chr776908069371HLA-C12:16ARDFMQKY0.91140.97541018
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:07FARDFMQKY0.99910.8269918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:21FARDFMQKY0.99820.9423918
PTPN12-CCDC146chr777166962chr776908069371HLA-C12:16FARDFMQKY0.99550.9585918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:05FARDFMQKY0.99520.9038918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:31FARDFMQKY0.990.9128918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:04FARDFMQKY0.85620.9707918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:19FARDFMQKY0.8020.6745918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:95FARDFMQKY0.76420.64918
PTPN12-CCDC146chr777166962chr776908069371HLA-C15:04FARDFMQKY0.73330.8576918
PTPN12-CCDC146chr777166962chr776908069371HLA-C12:04FARDFMQKY0.69890.994918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:67FARDFMQKY0.6970.9445918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:80FARDFMQKY0.6970.9445918
PTPN12-CCDC146chr777166962chr776908069371HLA-C06:03FARDFMQKY0.69490.9932918
PTPN12-CCDC146chr777166962chr776908069371HLA-C12:12FARDFMQKY0.69450.9318918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:05FARDFMQKY0.68870.9465918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:10FARDFMQKY0.65920.952918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:27FARDFMQKY0.63760.9417918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:46FARDFMQKY0.57820.8819918
PTPN12-CCDC146chr777166962chr776908069371HLA-C03:14FARDFMQKY0.41540.9743918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:01ARDFMQKY0.99860.74021018
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:17ARDFMQKY0.99320.96781018
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:125FARDFMQKY0.99910.956918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:34FARDFMQKY0.99910.956918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:27FARDFMQKY0.99910.9662918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:33FARDFMQKY0.99910.956918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:135FARDFMQKY0.9990.9593918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:50FARDFMQKY0.99870.9316918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:35FARDFMQKY0.99860.9638918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:53FARDFMQKY0.99830.9513918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:11FARDFMQKY0.99820.941918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:08FARDFMQKY0.99810.9427918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:39FARDFMQKY0.99790.9008918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:24FARDFMQKY0.99790.9481918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:43FARDFMQKY0.99770.9433918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:11FARDFMQKY0.99750.9425918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:12FARDFMQKY0.99570.9108918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:20FARDFMQKY0.9950.9301918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:28FARDFMQKY0.99310.9348918
PTPN12-CCDC146chr777166962chr776908069371HLA-C03:02FARDFMQKY0.99130.9781918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:23FARDFMQKY0.98950.9299918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:20FARDFMQKY0.98930.9414918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:17FARDFMQKY0.9890.8604918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:77FARDFMQKY0.9890.9275918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:30FARDFMQKY0.9890.8604918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:54FARDFMQKY0.98510.9409918
PTPN12-CCDC146chr777166962chr776908069371HLA-C12:02FARDFMQKY0.98310.967918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:13FARDFMQKY0.97830.669918
PTPN12-CCDC146chr777166962chr776908069371HLA-B08:18DFMQKYTNI0.97160.53381221
PTPN12-CCDC146chr777166962chr776908069371HLA-C03:67FARDFMQKY0.96340.9773918
PTPN12-CCDC146chr777166962chr776908069371HLA-B35:24FARDFMQKY0.94760.9395918
PTPN12-CCDC146chr777166962chr776908069371HLA-B58:06FARDFMQKY0.92990.9101918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:22FARDFMQKY0.9180.7543918
PTPN12-CCDC146chr777166962chr776908069371HLA-A25:01FARDFMQKY0.89240.8353918
PTPN12-CCDC146chr777166962chr776908069371HLA-B15:68FARDFMQKY0.88640.7632918
PTPN12-CCDC146chr777166962chr776908069371HLA-C12:03FARDFMQKY0.83760.9804918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:01FARDFMQKY0.77670.6083918
PTPN12-CCDC146chr777166962chr776908069371HLA-C15:09FARDFMQKY0.73330.8576918
PTPN12-CCDC146chr777166962chr776908069371HLA-C16:04FARDFMQKY0.69930.9823918
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:02FARDFMQKY0.6970.9445918
PTPN12-CCDC146chr777166962chr776908069371HLA-B08:12DFMQKYTNI0.69460.67011221
PTPN12-CCDC146chr777166962chr776908069371HLA-C07:17FARDFMQKY0.67810.9569918
PTPN12-CCDC146chr777166962chr776908069371HLA-C03:05FARDFMQKY0.61680.9105918
PTPN12-CCDC146chr777166962chr776908069371HLA-C06:02FARDFMQKY0.6070.9929918
PTPN12-CCDC146chr777166962chr776908069371HLA-C06:17FARDFMQKY0.6070.9929918
PTPN12-CCDC146chr777166962chr776908069371HLA-B18:04FARDFMQKY0.59750.9338918
PTPN12-CCDC146chr777166962chr776908069371HLA-C06:06FARDFMQKY0.48470.9866918
PTPN12-CCDC146chr777166962chr776908069371HLA-C02:02FARDFMQKY0.3340.981918
PTPN12-CCDC146chr777166962chr776908069371HLA-C02:10FARDFMQKY0.3340.981918
PTPN12-CCDC146chr777166962chr776908069371HLA-B18:07FARDFMQKY0.31150.8795918
PTPN12-CCDC146chr777166962chr776908069371HLA-C16:01FARDFMQKY0.26960.9654918
PTPN12-CCDC146chr777166962chr776908069371HLA-C16:02FARDFMQKY0.18670.9857918
PTPN12-CCDC146chr777166962chr776908069371HLA-C06:08FARDFMQKY0.15280.9923918
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:01LEFQNMNGY0.99540.8574817
PTPN12-CCDC146chr777227218chr776922269824HLA-B44:03LEFQNMNGY0.98960.9482817
PTPN12-CCDC146chr777227218chr776922269824HLA-B15:03LEFQNMNGY0.0750.7418817
PTPN12-CCDC146chr777227218chr776922269824HLA-A33:01EFQNMNGYQRR0.99290.518920
PTPN12-CCDC146chr777227218chr776922269824HLA-A33:05EFQNMNGYQRR0.99290.518920
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:04LEFQNMNGY0.99760.874817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:07LEFQNMNGY0.99630.8179817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:08LEFQNMNGY0.99560.7742817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:05LEFQNMNGY0.99540.8574817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:06LEFQNMNGY0.99370.8719817
PTPN12-CCDC146chr777227218chr776922269824HLA-B44:13LEFQNMNGY0.98960.9482817
PTPN12-CCDC146chr777227218chr776922269824HLA-B44:26LEFQNMNGY0.98960.9482817
PTPN12-CCDC146chr777227218chr776922269824HLA-B44:07LEFQNMNGY0.98960.9482817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:03LEFQNMNGY0.98940.8463817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:11LEFQNMNGY0.87710.8378817
PTPN12-CCDC146chr777227218chr776922269824HLA-B15:12LEFQNMNGY0.77130.8389817
PTPN12-CCDC146chr777227218chr776922269824HLA-B35:28LEFQNMNGY0.64720.8836817
PTPN12-CCDC146chr777227218chr776922269824HLA-B35:20LEFQNMNGY0.58990.9012817
PTPN12-CCDC146chr777227218chr776922269824HLA-B15:53LEFQNMNGY0.57810.8123817
PTPN12-CCDC146chr777227218chr776922269824HLA-B15:54LEFQNMNGY0.12230.7745817
PTPN12-CCDC146chr777227218chr776922269824HLA-B48:02LEFQNMNGY0.09130.8639817
PTPN12-CCDC146chr777227218chr776922269824HLA-B18:11LLEFQNMNGY0.56730.8735717

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Potential FusionNeoAntigen Information of PTPN12-CCDC146 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.
PTPN12-CCDC146_77166962_76908069.msa
PTPN12-CCDC146_77227218_76922269.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)
PTPN12-CCDC146chr777166962chr776908069371DRB1-0103ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0103FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0803FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0807FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0807ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0808FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0808ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0811FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0811ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0813FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0813ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0814FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0815ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0815FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0819FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0819ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0823FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0827FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0830ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0830FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0833FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0834FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0834ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0835FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0836FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0837FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-0837ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-0838FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-1331FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-1367ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-1367FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-1463FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-1463ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-1467ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777166962chr776908069371DRB1-1467FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-1489FARDFMQKYTNIVKE924
PTPN12-CCDC146chr777166962chr776908069371DRB1-1489ARDFMQKYTNIVKEM1025
PTPN12-CCDC146chr777227218chr776922269824DRB5-0101LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0101LLLEFQNMNGYQRRI621
PTPN12-CCDC146chr777227218chr776922269824DRB5-0101LEFQNMNGYQRRIKN823
PTPN12-CCDC146chr777227218chr776922269824DRB5-0102LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0103LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0104LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0105LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0105LLLEFQNMNGYQRRI621
PTPN12-CCDC146chr777227218chr776922269824DRB5-0105LEFQNMNGYQRRIKN823
PTPN12-CCDC146chr777227218chr776922269824DRB5-0108NLLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0111LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0113LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0113LLLEFQNMNGYQRRI621
PTPN12-CCDC146chr777227218chr776922269824DRB5-0113LEFQNMNGYQRRIKN823
PTPN12-CCDC146chr777227218chr776922269824DRB5-0114LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0114LLLEFQNMNGYQRRI621
PTPN12-CCDC146chr777227218chr776922269824DRB5-0114LEFQNMNGYQRRIKN823
PTPN12-CCDC146chr777227218chr776922269824DRB5-0203LLEFQNMNGYQRRIK722
PTPN12-CCDC146chr777227218chr776922269824DRB5-0203LLLEFQNMNGYQRRI621

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Fusion breakpoint peptide structures of PTPN12-CCDC146

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
1603EDNFARDFMQKYTNPTPN12CCDC146chr777166962chr776908069371
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
5239LLLEFQNMNGYQRRPTPN12CCDC146chr777227218chr776922269824

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPN12-CCDC146

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-B14:023BVN1603EDNFARDFMQKYTN-8.23912-8.35832
HLA-B14:023BVN1603EDNFARDFMQKYTN-5.08293-6.12403
HLA-B52:013W391603EDNFARDFMQKYTN-6.5481-6.6673
HLA-B52:013W391603EDNFARDFMQKYTN-5.02074-6.06184
HLA-A11:014UQ21603EDNFARDFMQKYTN-7.38354-7.50274
HLA-A11:014UQ21603EDNFARDFMQKYTN-7.16929-8.21039
HLA-A24:025HGA1603EDNFARDFMQKYTN-6.56855-7.60965
HLA-A24:025HGA1603EDNFARDFMQKYTN-6.17952-6.29872
HLA-B44:053DX81603EDNFARDFMQKYTN-6.51906-6.63826
HLA-B44:053DX81603EDNFARDFMQKYTN-4.19587-5.23697
HLA-A02:016TDR1603EDNFARDFMQKYTN-2.91211-3.95321
HLA-A02:016TDR1603EDNFARDFMQKYTN-2.59402-2.71322
HLA-B14:023BVN5239LLLEFQNMNGYQRR-5.68508-5.79848
HLA-B14:023BVN5239LLLEFQNMNGYQRR-4.48181-5.51711
HLA-B52:013W395239LLLEFQNMNGYQRR-6.58333-6.69673
HLA-B52:013W395239LLLEFQNMNGYQRR-5.63259-6.66789
HLA-A11:014UQ25239LLLEFQNMNGYQRR-10.3303-10.4437
HLA-A11:014UQ25239LLLEFQNMNGYQRR-6.29447-7.32977
HLA-A24:025HGA5239LLLEFQNMNGYQRR-7.77035-7.88375
HLA-A24:025HGA5239LLLEFQNMNGYQRR-5.35627-6.39157
HLA-B27:056PYJ5239LLLEFQNMNGYQRR-3.97515-5.01045
HLA-B44:053DX85239LLLEFQNMNGYQRR-5.81963-5.93303
HLA-B44:053DX85239LLLEFQNMNGYQRR-4.86027-5.89557
HLA-A02:016TDR5239LLLEFQNMNGYQRR-5.17978-6.21508
HLA-A02:016TDR5239LLLEFQNMNGYQRR-5.36237-5.47577

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Vaccine Design for the FusionNeoAntigens of PTPN12-CCDC146

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
PTPN12-CCDC146chr777166962chr7769080691018ARDFMQKYGACTTCATGCAAAAATACACCAAC
PTPN12-CCDC146chr777166962chr7769080691221DFMQKYTNIATGCAAAAATACACCAACATTGTTAAA
PTPN12-CCDC146chr777166962chr776908069918FARDFMQKYCGGGACTTCATGCAAAAATACACCAAC
PTPN12-CCDC146chr777227218chr776922269717LLEFQNMNGYTTACTTGAATTTCAAAATATGAATGGCTAT
PTPN12-CCDC146chr777227218chr776922269817LEFQNMNGYCTTGAATTTCAAAATATGAATGGCTAT
PTPN12-CCDC146chr777227218chr776922269920EFQNMNGYQRRGAATTTCAAAATATGAATGGCTATCAAAGAAGG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PTPN12-CCDC146chr777166962chr7769080691025ARDFMQKYTNIVKEMGACTTCATGCAAAAATACACCAACATTGTTAAAGAAATGAAAGCA
PTPN12-CCDC146chr777166962chr776908069924FARDFMQKYTNIVKECGGGACTTCATGCAAAAATACACCAACATTGTTAAAGAAATGAAA
PTPN12-CCDC146chr777227218chr776922269621LLLEFQNMNGYQRRICTCTTACTTGAATTTCAAAATATGAATGGCTATCAAAGAAGGATC
PTPN12-CCDC146chr777227218chr776922269722LLEFQNMNGYQRRIKTTACTTGAATTTCAAAATATGAATGGCTATCAAAGAAGGATCAAA
PTPN12-CCDC146chr777227218chr776922269823LEFQNMNGYQRRIKNCTTGAATTTCAAAATATGAATGGCTATCAAAGAAGGATCAAAAAT

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Information of the samples that have these potential fusion neoantigens of PTPN12-CCDC146

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
SKCMPTPN12-CCDC146chr777166962ENST00000248594chr776908069ENST00000285871TCGA-ER-A19T-01A
STADPTPN12-CCDC146chr777227218ENST00000248594chr776922269ENST00000285871TCGA-HU-A4GH-01A

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Potential target of CAR-T therapy development for PTPN12-CCDC146

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 PTPN12-CCDC146

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 PTPN12-CCDC146

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