FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use
Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ATP6V1C1-PML

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ATP6V1C1-PML
FusionPDB ID: 8158
FusionGDB2.0 ID: 8158
HgeneTgene
Gene symbol

ATP6V1C1

PML

Gene ID

528

5371

Gene nameATPase H+ transporting V1 subunit C1promyelocytic leukemia
SynonymsATP6C|ATP6D|VATC|Vma5MYL|PP8675|RNF71|TRIM19
Cytomap

8q22.3

15q24.1

Type of geneprotein-codingprotein-coding
DescriptionV-type proton ATPase subunit C 1ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1H(+)-transporting two-sector ATPase, subunit CH+ -ATPase C subunitH+-transporting ATPase chain C, vacuolarV-ATPase C subunitV-ATPase subunit C 1subunit C of vacuprotein PMLPML/RARA fusionRING finger protein 71probable transcription factor PMLpromyelocytic leukemia proteinpromyelocytic leukemia, inducer oftripartite motif protein TRIM19tripartite motif-containing protein 19
Modification date2020031320200313
UniProtAcc

P21283

Main function of 5'-partner protein: FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.

PRAM1

Main function of 5'-partner protein: 670
Ensembl transtripts involved in fusion geneENST idsENST00000395862, ENST00000518738, 
ENST00000521514, ENST00000518857, 
ENST00000569161, ENST00000268058, 
ENST00000268059, ENST00000354026, 
ENST00000359928, ENST00000395132, 
ENST00000395135, ENST00000435786, 
ENST00000436891, ENST00000563500, 
ENST00000564428, ENST00000565898, 
ENST00000567543, ENST00000569477, 
ENST00000569965, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 7 X 6=3789 X 24 X 6=1296
# samples 1128
** MAII scorelog2(11/378*10)=-1.78088271069641
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(28/1296*10)=-2.21056698593966
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ATP6V1C1 [Title/Abstract] AND PML [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ATP6V1C1 [Title/Abstract] AND PML [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ATP6V1C1(104054635)-PML(74315168), # samples:1
ATP6V1C1(104054635)-PML(74315169), # samples:1
Anticipated loss of major functional domain due to fusion event.ATP6V1C1-PML 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.
ATP6V1C1-PML 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.
ATP6V1C1-PML 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.
ATP6V1C1-PML 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
TgenePML

GO:0001666

response to hypoxia

16915281

TgenePML

GO:0030308

negative regulation of cell growth

9448006

TgenePML

GO:0034097

response to cytokine

9412458

TgenePML

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

22406621

TgenePML

GO:0045087

innate immune response

18248090

TgenePML

GO:0045892

negative regulation of transcription, DNA-templated

9448006

TgenePML

GO:0051457

maintenance of protein location in nucleus

17332504

TgenePML

GO:0065003

protein-containing complex assembly

12915590

TgenePML

GO:0090398

cellular senescence

22002537|22117195|23431171

TgenePML

GO:1902187

negative regulation of viral release from host cell

18248090



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/chr8:104054635/chr15:74315168)
- 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 ATP6V1C1 (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 PML (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000395862ATP6V1C1chr8104054635+ENST00000395135PMLchr1574315168+18163591351658507
ENST00000395862ATP6V1C1chr8104054635+ENST00000395132PMLchr1574315168+13993591292321323
ENST00000395862ATP6V1C1chr8104054635+ENST00000268059PMLchr1574315168+26903591352246703
ENST00000395862ATP6V1C1chr8104054635+ENST00000354026PMLchr1574315168+25463591352102655
ENST00000395862ATP6V1C1chr8104054635+ENST00000268058PMLchr1574315168+41693591352405756
ENST00000395862ATP6V1C1chr8104054635+ENST00000565898PMLchr1574315168+50663591352261708
ENST00000395862ATP6V1C1chr8104054635+ENST00000569477PMLchr1574315168+19263591351682515
ENST00000395862ATP6V1C1chr8104054635+ENST00000569965PMLchr1574315168+18253591351439434
ENST00000395862ATP6V1C1chr8104054635+ENST00000567543PMLchr1574315168+10923591351028297
ENST00000395862ATP6V1C1chr8104054635+ENST00000435786PMLchr1574315168+33313591351592485
ENST00000395862ATP6V1C1chr8104054635+ENST00000436891PMLchr1574315168+26983591351439434
ENST00000395862ATP6V1C1chr8104054635+ENST00000564428PMLchr1574315168+16733591351514459
ENST00000395862ATP6V1C1chr8104054635+ENST00000359928PMLchr1574315168+14143591351028297
ENST00000395862ATP6V1C1chr8104054635+ENST00000563500PMLchr1574315168+42493591351463442
ENST00000518738ATP6V1C1chr8104054635+ENST00000395135PMLchr1574315168+18203631391662507
ENST00000518738ATP6V1C1chr8104054635+ENST00000395132PMLchr1574315168+14033631296325323
ENST00000518738ATP6V1C1chr8104054635+ENST00000268059PMLchr1574315168+26943631392250703
ENST00000518738ATP6V1C1chr8104054635+ENST00000354026PMLchr1574315168+25503631392106655
ENST00000518738ATP6V1C1chr8104054635+ENST00000268058PMLchr1574315168+41733631392409756
ENST00000518738ATP6V1C1chr8104054635+ENST00000565898PMLchr1574315168+50703631392265708
ENST00000518738ATP6V1C1chr8104054635+ENST00000569477PMLchr1574315168+19303631391686515
ENST00000518738ATP6V1C1chr8104054635+ENST00000569965PMLchr1574315168+18293631391443434
ENST00000518738ATP6V1C1chr8104054635+ENST00000567543PMLchr1574315168+10963631391032297
ENST00000518738ATP6V1C1chr8104054635+ENST00000435786PMLchr1574315168+33353631391596485
ENST00000518738ATP6V1C1chr8104054635+ENST00000436891PMLchr1574315168+27023631391443434
ENST00000518738ATP6V1C1chr8104054635+ENST00000564428PMLchr1574315168+16773631391518459
ENST00000518738ATP6V1C1chr8104054635+ENST00000359928PMLchr1574315168+14183631391032297
ENST00000518738ATP6V1C1chr8104054635+ENST00000563500PMLchr1574315168+42533631391467442
ENST00000395862ATP6V1C1chr8104054635+ENST00000395135PMLchr1574315169+18163591351658507
ENST00000395862ATP6V1C1chr8104054635+ENST00000395132PMLchr1574315169+13993591292321323
ENST00000395862ATP6V1C1chr8104054635+ENST00000268059PMLchr1574315169+26903591352246703
ENST00000395862ATP6V1C1chr8104054635+ENST00000354026PMLchr1574315169+25463591352102655
ENST00000395862ATP6V1C1chr8104054635+ENST00000268058PMLchr1574315169+41693591352405756
ENST00000395862ATP6V1C1chr8104054635+ENST00000565898PMLchr1574315169+50663591352261708
ENST00000395862ATP6V1C1chr8104054635+ENST00000569477PMLchr1574315169+19263591351682515
ENST00000395862ATP6V1C1chr8104054635+ENST00000569965PMLchr1574315169+18253591351439434
ENST00000395862ATP6V1C1chr8104054635+ENST00000567543PMLchr1574315169+10923591351028297
ENST00000395862ATP6V1C1chr8104054635+ENST00000435786PMLchr1574315169+33313591351592485
ENST00000395862ATP6V1C1chr8104054635+ENST00000436891PMLchr1574315169+26983591351439434
ENST00000395862ATP6V1C1chr8104054635+ENST00000564428PMLchr1574315169+16733591351514459
ENST00000395862ATP6V1C1chr8104054635+ENST00000359928PMLchr1574315169+14143591351028297
ENST00000395862ATP6V1C1chr8104054635+ENST00000563500PMLchr1574315169+42493591351463442
ENST00000518738ATP6V1C1chr8104054635+ENST00000395135PMLchr1574315169+18203631391662507
ENST00000518738ATP6V1C1chr8104054635+ENST00000395132PMLchr1574315169+14033631296325323
ENST00000518738ATP6V1C1chr8104054635+ENST00000268059PMLchr1574315169+26943631392250703
ENST00000518738ATP6V1C1chr8104054635+ENST00000354026PMLchr1574315169+25503631392106655
ENST00000518738ATP6V1C1chr8104054635+ENST00000268058PMLchr1574315169+41733631392409756
ENST00000518738ATP6V1C1chr8104054635+ENST00000565898PMLchr1574315169+50703631392265708
ENST00000518738ATP6V1C1chr8104054635+ENST00000569477PMLchr1574315169+19303631391686515
ENST00000518738ATP6V1C1chr8104054635+ENST00000569965PMLchr1574315169+18293631391443434
ENST00000518738ATP6V1C1chr8104054635+ENST00000567543PMLchr1574315169+10963631391032297
ENST00000518738ATP6V1C1chr8104054635+ENST00000435786PMLchr1574315169+33353631391596485
ENST00000518738ATP6V1C1chr8104054635+ENST00000436891PMLchr1574315169+27023631391443434
ENST00000518738ATP6V1C1chr8104054635+ENST00000564428PMLchr1574315169+16773631391518459
ENST00000518738ATP6V1C1chr8104054635+ENST00000359928PMLchr1574315169+14183631391032297
ENST00000518738ATP6V1C1chr8104054635+ENST00000563500PMLchr1574315169+42533631391467442

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
ENST00000395862ENST00000395135ATP6V1C1chr8104054635+PMLchr1574315168+0.0191162360.9808837
ENST00000395862ENST00000395132ATP6V1C1chr8104054635+PMLchr1574315168+0.0126921750.98730785
ENST00000395862ENST00000268059ATP6V1C1chr8104054635+PMLchr1574315168+0.0505315660.9494685
ENST00000395862ENST00000354026ATP6V1C1chr8104054635+PMLchr1574315168+0.074023720.9259763
ENST00000395862ENST00000268058ATP6V1C1chr8104054635+PMLchr1574315168+0.0089171140.9910829
ENST00000395862ENST00000565898ATP6V1C1chr8104054635+PMLchr1574315168+0.0062386180.99376136
ENST00000395862ENST00000569477ATP6V1C1chr8104054635+PMLchr1574315168+0.0261032620.97389674
ENST00000395862ENST00000569965ATP6V1C1chr8104054635+PMLchr1574315168+0.0184839670.981516
ENST00000395862ENST00000567543ATP6V1C1chr8104054635+PMLchr1574315168+0.008529950.99147004
ENST00000395862ENST00000435786ATP6V1C1chr8104054635+PMLchr1574315168+0.0152796410.98472035
ENST00000395862ENST00000436891ATP6V1C1chr8104054635+PMLchr1574315168+0.0177408270.98225915
ENST00000395862ENST00000564428ATP6V1C1chr8104054635+PMLchr1574315168+0.0177404020.98225963
ENST00000395862ENST00000359928ATP6V1C1chr8104054635+PMLchr1574315168+0.0110555790.9889444
ENST00000395862ENST00000563500ATP6V1C1chr8104054635+PMLchr1574315168+0.0164794570.98352057
ENST00000518738ENST00000395135ATP6V1C1chr8104054635+PMLchr1574315168+0.018103730.9818963
ENST00000518738ENST00000395132ATP6V1C1chr8104054635+PMLchr1574315168+0.0118096490.9881904
ENST00000518738ENST00000268059ATP6V1C1chr8104054635+PMLchr1574315168+0.048980150.9510198
ENST00000518738ENST00000354026ATP6V1C1chr8104054635+PMLchr1574315168+0.0726233050.9273767
ENST00000518738ENST00000268058ATP6V1C1chr8104054635+PMLchr1574315168+0.0087362090.99126387
ENST00000518738ENST00000565898ATP6V1C1chr8104054635+PMLchr1574315168+0.0061097830.99389017
ENST00000518738ENST00000569477ATP6V1C1chr8104054635+PMLchr1574315168+0.0250296870.97497034
ENST00000518738ENST00000569965ATP6V1C1chr8104054635+PMLchr1574315168+0.0175964250.98240364
ENST00000518738ENST00000567543ATP6V1C1chr8104054635+PMLchr1574315168+0.0082607740.99173915
ENST00000518738ENST00000435786ATP6V1C1chr8104054635+PMLchr1574315168+0.0148629710.985137
ENST00000518738ENST00000436891ATP6V1C1chr8104054635+PMLchr1574315168+0.0169629180.98303705
ENST00000518738ENST00000564428ATP6V1C1chr8104054635+PMLchr1574315168+0.0172591060.9827408
ENST00000518738ENST00000359928ATP6V1C1chr8104054635+PMLchr1574315168+0.0104609190.9895391
ENST00000518738ENST00000563500ATP6V1C1chr8104054635+PMLchr1574315168+0.0159170680.9840829
ENST00000395862ENST00000395135ATP6V1C1chr8104054635+PMLchr1574315169+0.0191162360.9808837
ENST00000395862ENST00000395132ATP6V1C1chr8104054635+PMLchr1574315169+0.0126921750.98730785
ENST00000395862ENST00000268059ATP6V1C1chr8104054635+PMLchr1574315169+0.0505315660.9494685
ENST00000395862ENST00000354026ATP6V1C1chr8104054635+PMLchr1574315169+0.074023720.9259763
ENST00000395862ENST00000268058ATP6V1C1chr8104054635+PMLchr1574315169+0.0089171140.9910829
ENST00000395862ENST00000565898ATP6V1C1chr8104054635+PMLchr1574315169+0.0062386180.99376136
ENST00000395862ENST00000569477ATP6V1C1chr8104054635+PMLchr1574315169+0.0261032620.97389674
ENST00000395862ENST00000569965ATP6V1C1chr8104054635+PMLchr1574315169+0.0184839670.981516
ENST00000395862ENST00000567543ATP6V1C1chr8104054635+PMLchr1574315169+0.008529950.99147004
ENST00000395862ENST00000435786ATP6V1C1chr8104054635+PMLchr1574315169+0.0152796410.98472035
ENST00000395862ENST00000436891ATP6V1C1chr8104054635+PMLchr1574315169+0.0177408270.98225915
ENST00000395862ENST00000564428ATP6V1C1chr8104054635+PMLchr1574315169+0.0177404020.98225963
ENST00000395862ENST00000359928ATP6V1C1chr8104054635+PMLchr1574315169+0.0110555790.9889444
ENST00000395862ENST00000563500ATP6V1C1chr8104054635+PMLchr1574315169+0.0164794570.98352057
ENST00000518738ENST00000395135ATP6V1C1chr8104054635+PMLchr1574315169+0.018103730.9818963
ENST00000518738ENST00000395132ATP6V1C1chr8104054635+PMLchr1574315169+0.0118096490.9881904
ENST00000518738ENST00000268059ATP6V1C1chr8104054635+PMLchr1574315169+0.048980150.9510198
ENST00000518738ENST00000354026ATP6V1C1chr8104054635+PMLchr1574315169+0.0726233050.9273767
ENST00000518738ENST00000268058ATP6V1C1chr8104054635+PMLchr1574315169+0.0087362090.99126387
ENST00000518738ENST00000565898ATP6V1C1chr8104054635+PMLchr1574315169+0.0061097830.99389017
ENST00000518738ENST00000569477ATP6V1C1chr8104054635+PMLchr1574315169+0.0250296870.97497034
ENST00000518738ENST00000569965ATP6V1C1chr8104054635+PMLchr1574315169+0.0175964250.98240364
ENST00000518738ENST00000567543ATP6V1C1chr8104054635+PMLchr1574315169+0.0082607740.99173915
ENST00000518738ENST00000435786ATP6V1C1chr8104054635+PMLchr1574315169+0.0148629710.985137
ENST00000518738ENST00000436891ATP6V1C1chr8104054635+PMLchr1574315169+0.0169629180.98303705
ENST00000518738ENST00000564428ATP6V1C1chr8104054635+PMLchr1574315169+0.0172591060.9827408
ENST00000518738ENST00000359928ATP6V1C1chr8104054635+PMLchr1574315169+0.0104609190.9895391
ENST00000518738ENST00000563500ATP6V1C1chr8104054635+PMLchr1574315169+0.0159170680.9840829

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

Top

Fusion Protein Breakpoint Sequences for ATP6V1C1-PML

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ATP6V1C1chr8104054635PMLchr157431516835975SDELAKLDAFVEGIYCRGCSKPLCCS
ATP6V1C1chr8104054635PMLchr157431516836375SDELAKLDAFVEGIYCRGCSKPLCCS
ATP6V1C1chr8104054635PMLchr157431516935975SDELAKLDAFVEGIYCRGCSKPLCCS
ATP6V1C1chr8104054635PMLchr157431516936375SDELAKLDAFVEGIYCRGCSKPLCCS

Top

Potential FusionNeoAntigen Information of ATP6V1C1-PML 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.
ATP6V1C1-PML_104054635_74315168.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)
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:60KLDAFVEGI0.99520.6061514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:67KLDAFVEGI0.99510.5645514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:30KLDAFVEGI0.99510.5645514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:24KLDAFVEGI0.99510.5645514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:11KLDAFVEGI0.99490.6111514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:04KLDAFVEGI0.99390.7646514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:21KLDAFVEGI0.99360.6784514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:17KLDAFVEGI0.9910.5701514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:22KLDAFVEGI0.99020.5624514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:27KLDAFVEGI0.98930.6229514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:16KLDAFVEGI0.98910.5059514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:13KLDAFVEGI0.98510.7189514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:38KLDAFVEGI0.98340.6983514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A31:02AFVEGIYCR0.96460.5211817
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:35KLDAFVEGI0.92730.5855514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:29KLDAFVEGI0.91280.5665514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:20KLDAFVEGI0.87180.5705514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-B15:03AKLDAFVEGIY0.97710.8532415
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-C05:09KLDAFVEGI0.99970.9552514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:07KLDAFVEGI0.99530.592514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:01KLDAFVEGI0.99510.5645514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-B35:24DAFVEGIY0.99290.9142715
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-B18:04DAFVEGIY0.99030.9018715
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-B18:07DAFVEGIY0.97520.8341715
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-C05:01KLDAFVEGI0.99970.9552514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-C04:03KLDAFVEGI0.99970.907514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:14KLDAFVEGI0.99390.5823514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-A02:06KLDAFVEGI0.99360.6784514
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-B78:02DAFVEGIYC0.8150.5765716
ATP6V1C1-PMLchr8104054635chr1574315168359HLA-B48:02AKLDAFVEGIY0.97920.9276415

Top

Potential FusionNeoAntigen Information of ATP6V1C1-PML 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)

Top

Fusion breakpoint peptide structures of ATP6V1C1-PML

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
4830LDAFVEGIYCRGCSATP6V1C1PMLchr8104054635chr1574315168359

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATP6V1C1-PML

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-B14:023BVN4830LDAFVEGIYCRGCS-7.15543-7.26883
HLA-B14:023BVN4830LDAFVEGIYCRGCS-4.77435-5.80965
HLA-B52:013W394830LDAFVEGIYCRGCS-6.80875-6.92215
HLA-B52:013W394830LDAFVEGIYCRGCS-4.20386-5.23916
HLA-A11:014UQ24830LDAFVEGIYCRGCS-7.5194-8.5547
HLA-A11:014UQ24830LDAFVEGIYCRGCS-6.9601-7.0735
HLA-A24:025HGA4830LDAFVEGIYCRGCS-7.52403-7.63743
HLA-A24:025HGA4830LDAFVEGIYCRGCS-5.82433-6.85963
HLA-B27:056PYJ4830LDAFVEGIYCRGCS-3.28285-4.31815
HLA-B44:053DX84830LDAFVEGIYCRGCS-5.91172-6.94702
HLA-B44:053DX84830LDAFVEGIYCRGCS-4.24346-4.35686

Top

Vaccine Design for the FusionNeoAntigens of ATP6V1C1-PML

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
ATP6V1C1-PMLchr8104054635chr1574315168415AKLDAFVEGIYGGCTAAACTGGATGCATTTGTAGAAGGCATCTA
ATP6V1C1-PMLchr8104054635chr1574315168514KLDAFVEGITAAACTGGATGCATTTGTAGAAGGCAT
ATP6V1C1-PMLchr8104054635chr1574315168715DAFVEGIYGGATGCATTTGTAGAAGGCATCTA
ATP6V1C1-PMLchr8104054635chr1574315168716DAFVEGIYCGGATGCATTTGTAGAAGGCATCTACTG
ATP6V1C1-PMLchr8104054635chr1574315168817AFVEGIYCRTGCATTTGTAGAAGGCATCTACTGCCG

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

Top

Information of the samples that have these potential fusion neoantigens of ATP6V1C1-PML

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
UCECATP6V1C1-PMLchr8104054635ENST00000395862chr1574315168ENST00000268058TCGA-FI-A2F9

Top

Potential target of CAR-T therapy development for ATP6V1C1-PML

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

Top

Related Drugs to ATP6V1C1-PML

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to ATP6V1C1-PML

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
TgenePMLC0023487Acute Promyelocytic Leukemia21CTD_human;ORPHANET
TgenePMLC0014518Toxic Epidermal Necrolysis1CTD_human
TgenePMLC0017636Glioblastoma1CTD_human
TgenePMLC0019207Hepatoma, Morris1CTD_human
TgenePMLC0019208Hepatoma, Novikoff1CTD_human
TgenePMLC0023904Liver Neoplasms, Experimental1CTD_human
TgenePMLC0027627Neoplasm Metastasis1CTD_human
TgenePMLC0029401Osteitis Deformans1CTD_human
TgenePMLC0033578Prostatic Neoplasms1CTD_human
TgenePMLC0036341Schizophrenia1CTD_human
TgenePMLC0038325Stevens-Johnson Syndrome1CTD_human
TgenePMLC0085183Neoplasms, Second Primary1CTD_human
TgenePMLC0086404Experimental Hepatoma1CTD_human
TgenePMLC0086696Neoplasms, Therapy-Associated1CTD_human
TgenePMLC0334588Giant Cell Glioblastoma1CTD_human
TgenePMLC0376358Malignant neoplasm of prostate1CTD_human
TgenePMLC0877578Treatment related secondary malignancy1CTD_human
TgenePMLC1274933Drug-Induced Stevens Johnson Syndrome1CTD_human
TgenePMLC1621958Glioblastoma Multiforme1CTD_human
TgenePMLC3658301Mycoplasma-Induced Stevens-Johnson Syndrome1CTD_human
TgenePMLC3658302Stevens-Johnson Syndrome Toxic Epidermal Necrolysis Spectrum1CTD_human