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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:PHKA1-BIN1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PHKA1-BIN1
FusionPDB ID: 64924
FusionGDB2.0 ID: 64924
HgeneTgene
Gene symbol

PHKA1

BIN1

Gene ID

5255

274

Gene namephosphorylase kinase regulatory subunit alpha 1bridging integrator 1
SynonymsPHKAAMPH2|AMPHL|CNM2|SH3P9
Cytomap

Xq13.1

2q14.3

Type of geneprotein-codingprotein-coding
Descriptionphosphorylase b kinase regulatory subunit alpha, skeletal muscle isoformphosphorylase kinase alpha M subunitphosphorylase kinase, alpha 1 (muscle), muscle glycogenosismyc box-dependent-interacting protein 1amphiphysin IIamphiphysin-like proteinbox dependant MYC interacting protein 1box-dependent myc-interacting protein 1
Modification date2020031320200322
UniProtAcc.

O00499

Main function of 5'-partner protein: FUNCTION: Is a key player in the control of plasma membrane curvature, membrane shaping and membrane remodeling. Required in muscle cells for the formation of T-tubules, tubular invaginations of the plasma membrane that function in depolarization-contraction coupling (PubMed:24755653). Is a negative regulator of endocytosis (By similarity). Is also involved in the regulation of intracellular vesicles sorting, modulation of BACE1 trafficking and the control of amyloid-beta production (PubMed:27179792). In neuronal circuits, endocytosis regulation may influence the internalization of PHF-tau aggregates (By similarity). May be involved in the regulation of MYC activity and the control cell proliferation (PubMed:8782822). Has actin bundling activity and stabilizes actin filaments against depolymerization in vitro (PubMed:28893863). {ECO:0000250|UniProtKB:O08839, ECO:0000269|PubMed:24755653, ECO:0000269|PubMed:27179792, ECO:0000269|PubMed:28893863, ECO:0000269|PubMed:8782822}.
Ensembl transtripts involved in fusion geneENST idsENST00000339490, ENST00000373539, 
ENST00000373542, ENST00000373545, 
ENST00000541944, 		ENST00000466111, 
ENST00000259238, ENST00000316724, 
ENST00000346226, ENST00000348750, 
ENST00000351659, ENST00000352848, 
ENST00000357970, ENST00000376113, 
ENST00000393040, ENST00000393041, 
ENST00000409400, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 3=488 X 8 X 4=256
# samples 48
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/256*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PHKA1 [Title/Abstract] AND BIN1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PHKA1 [Title/Abstract] AND BIN1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PHKA1(71872394)-BIN1(127819773), # samples:1
Anticipated loss of major functional domain due to fusion event.PHKA1-BIN1 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.
PHKA1-BIN1 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.
PHKA1-BIN1 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.
PHKA1-BIN1 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
TgeneBIN1

GO:0033292

T-tubule organization

24755653

TgeneBIN1

GO:0043065

positive regulation of apoptotic process

16530520

TgeneBIN1

GO:0071156

regulation of cell cycle arrest

10412034



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/chrX:71872394/chr2:127819773)
- 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 PHKA1 (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 BIN1 (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)
ENST00000373542PHKA1chrX71872394-ENST00000376113BIN1chr2127819773-249814051601998612
ENST00000373542PHKA1chrX71872394-ENST00000346226BIN1chr2127819773-278014051602280706
ENST00000373542PHKA1chrX71872394-ENST00000352848BIN1chr2127819773-258814051602088642
ENST00000373542PHKA1chrX71872394-ENST00000393041BIN1chr2127819773-265114051602151663
ENST00000373542PHKA1chrX71872394-ENST00000348750BIN1chr2127819773-245314051601953597
ENST00000373542PHKA1chrX71872394-ENST00000357970BIN1chr2127819773-278314051602283707
ENST00000373542PHKA1chrX71872394-ENST00000259238BIN1chr2127819773-271714051602217685
ENST00000373542PHKA1chrX71872394-ENST00000393040BIN1chr2127819773-267214051602172670
ENST00000373542PHKA1chrX71872394-ENST00000351659BIN1chr2127819773-265114051602151663
ENST00000373542PHKA1chrX71872394-ENST00000316724BIN1chr2127819773-291214051602412750
ENST00000373542PHKA1chrX71872394-ENST00000409400BIN1chr2127819773-253214051602043627
ENST00000373545PHKA1chrX71872394-ENST00000376113BIN1chr2127819773-277716844392277612
ENST00000373545PHKA1chrX71872394-ENST00000346226BIN1chr2127819773-305916844392559706
ENST00000373545PHKA1chrX71872394-ENST00000352848BIN1chr2127819773-286716844392367642
ENST00000373545PHKA1chrX71872394-ENST00000393041BIN1chr2127819773-293016844392430663
ENST00000373545PHKA1chrX71872394-ENST00000348750BIN1chr2127819773-273216844392232597
ENST00000373545PHKA1chrX71872394-ENST00000357970BIN1chr2127819773-306216844392562707
ENST00000373545PHKA1chrX71872394-ENST00000259238BIN1chr2127819773-299616844392496685
ENST00000373545PHKA1chrX71872394-ENST00000393040BIN1chr2127819773-295116844392451670
ENST00000373545PHKA1chrX71872394-ENST00000351659BIN1chr2127819773-293016844392430663
ENST00000373545PHKA1chrX71872394-ENST00000316724BIN1chr2127819773-319116844392691750
ENST00000373545PHKA1chrX71872394-ENST00000409400BIN1chr2127819773-281116844392322627
ENST00000541944PHKA1chrX71872394-ENST00000376113BIN1chr2127819773-263915463012139612
ENST00000541944PHKA1chrX71872394-ENST00000346226BIN1chr2127819773-292115463012421706
ENST00000541944PHKA1chrX71872394-ENST00000352848BIN1chr2127819773-272915463012229642
ENST00000541944PHKA1chrX71872394-ENST00000393041BIN1chr2127819773-279215463012292663
ENST00000541944PHKA1chrX71872394-ENST00000348750BIN1chr2127819773-259415463012094597
ENST00000541944PHKA1chrX71872394-ENST00000357970BIN1chr2127819773-292415463012424707
ENST00000541944PHKA1chrX71872394-ENST00000259238BIN1chr2127819773-285815463012358685
ENST00000541944PHKA1chrX71872394-ENST00000393040BIN1chr2127819773-281315463012313670
ENST00000541944PHKA1chrX71872394-ENST00000351659BIN1chr2127819773-279215463012292663
ENST00000541944PHKA1chrX71872394-ENST00000316724BIN1chr2127819773-305315463012553750
ENST00000541944PHKA1chrX71872394-ENST00000409400BIN1chr2127819773-267315463012184627
ENST00000339490PHKA1chrX71872394-ENST00000376113BIN1chr2127819773-263915463012139612
ENST00000339490PHKA1chrX71872394-ENST00000346226BIN1chr2127819773-292115463012421706
ENST00000339490PHKA1chrX71872394-ENST00000352848BIN1chr2127819773-272915463012229642
ENST00000339490PHKA1chrX71872394-ENST00000393041BIN1chr2127819773-279215463012292663
ENST00000339490PHKA1chrX71872394-ENST00000348750BIN1chr2127819773-259415463012094597
ENST00000339490PHKA1chrX71872394-ENST00000357970BIN1chr2127819773-292415463012424707
ENST00000339490PHKA1chrX71872394-ENST00000259238BIN1chr2127819773-285815463012358685
ENST00000339490PHKA1chrX71872394-ENST00000393040BIN1chr2127819773-281315463012313670
ENST00000339490PHKA1chrX71872394-ENST00000351659BIN1chr2127819773-279215463012292663
ENST00000339490PHKA1chrX71872394-ENST00000316724BIN1chr2127819773-305315463012553750
ENST00000339490PHKA1chrX71872394-ENST00000409400BIN1chr2127819773-267315463012184627
ENST00000373539PHKA1chrX71872394-ENST00000376113BIN1chr2127819773-271616233782216612
ENST00000373539PHKA1chrX71872394-ENST00000346226BIN1chr2127819773-299816233782498706
ENST00000373539PHKA1chrX71872394-ENST00000352848BIN1chr2127819773-280616233782306642
ENST00000373539PHKA1chrX71872394-ENST00000393041BIN1chr2127819773-286916233782369663
ENST00000373539PHKA1chrX71872394-ENST00000348750BIN1chr2127819773-267116233782171597
ENST00000373539PHKA1chrX71872394-ENST00000357970BIN1chr2127819773-300116233782501707
ENST00000373539PHKA1chrX71872394-ENST00000259238BIN1chr2127819773-293516233782435685
ENST00000373539PHKA1chrX71872394-ENST00000393040BIN1chr2127819773-289016233782390670
ENST00000373539PHKA1chrX71872394-ENST00000351659BIN1chr2127819773-286916233782369663
ENST00000373539PHKA1chrX71872394-ENST00000316724BIN1chr2127819773-313016233782630750
ENST00000373539PHKA1chrX71872394-ENST00000409400BIN1chr2127819773-275016233782261627

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
ENST00000373542ENST00000376113PHKA1chrX71872394-BIN1chr2127819773-0.001475550.9985245
ENST00000373542ENST00000346226PHKA1chrX71872394-BIN1chr2127819773-0.0020711450.99792886
ENST00000373542ENST00000352848PHKA1chrX71872394-BIN1chr2127819773-0.0017045840.99829537
ENST00000373542ENST00000393041PHKA1chrX71872394-BIN1chr2127819773-0.0021269310.99787307
ENST00000373542ENST00000348750PHKA1chrX71872394-BIN1chr2127819773-0.0015270120.998473
ENST00000373542ENST00000357970PHKA1chrX71872394-BIN1chr2127819773-0.0020992130.9979007
ENST00000373542ENST00000259238PHKA1chrX71872394-BIN1chr2127819773-0.0021058050.9978942
ENST00000373542ENST00000393040PHKA1chrX71872394-BIN1chr2127819773-0.0023560310.997644
ENST00000373542ENST00000351659PHKA1chrX71872394-BIN1chr2127819773-0.0021269310.99787307
ENST00000373542ENST00000316724PHKA1chrX71872394-BIN1chr2127819773-0.0021082140.99789184
ENST00000373542ENST00000409400PHKA1chrX71872394-BIN1chr2127819773-0.0016632520.9983367
ENST00000373545ENST00000376113PHKA1chrX71872394-BIN1chr2127819773-0.0015983220.9984017
ENST00000373545ENST00000346226PHKA1chrX71872394-BIN1chr2127819773-0.0020477170.9979522
ENST00000373545ENST00000352848PHKA1chrX71872394-BIN1chr2127819773-0.0017727880.9982272
ENST00000373545ENST00000393041PHKA1chrX71872394-BIN1chr2127819773-0.0021626420.99783736
ENST00000373545ENST00000348750PHKA1chrX71872394-BIN1chr2127819773-0.0016475960.9983524
ENST00000373545ENST00000357970PHKA1chrX71872394-BIN1chr2127819773-0.002132550.99786747
ENST00000373545ENST00000259238PHKA1chrX71872394-BIN1chr2127819773-0.0021614170.99783856
ENST00000373545ENST00000393040PHKA1chrX71872394-BIN1chr2127819773-0.0023330360.99766695
ENST00000373545ENST00000351659PHKA1chrX71872394-BIN1chr2127819773-0.0021626420.99783736
ENST00000373545ENST00000316724PHKA1chrX71872394-BIN1chr2127819773-0.0020746030.9979254
ENST00000373545ENST00000409400PHKA1chrX71872394-BIN1chr2127819773-0.0017306470.9982693
ENST00000541944ENST00000376113PHKA1chrX71872394-BIN1chr2127819773-0.0015860390.9984139
ENST00000541944ENST00000346226PHKA1chrX71872394-BIN1chr2127819773-0.0020724440.99792755
ENST00000541944ENST00000352848PHKA1chrX71872394-BIN1chr2127819773-0.0018064210.99819356
ENST00000541944ENST00000393041PHKA1chrX71872394-BIN1chr2127819773-0.0022222130.99777776
ENST00000541944ENST00000348750PHKA1chrX71872394-BIN1chr2127819773-0.0016239320.998376
ENST00000541944ENST00000357970PHKA1chrX71872394-BIN1chr2127819773-0.0021786550.99782133
ENST00000541944ENST00000259238PHKA1chrX71872394-BIN1chr2127819773-0.0021692780.9978307
ENST00000541944ENST00000393040PHKA1chrX71872394-BIN1chr2127819773-0.0023675490.9976324
ENST00000541944ENST00000351659PHKA1chrX71872394-BIN1chr2127819773-0.0022222130.99777776
ENST00000541944ENST00000316724PHKA1chrX71872394-BIN1chr2127819773-0.0021061550.99789387
ENST00000541944ENST00000409400PHKA1chrX71872394-BIN1chr2127819773-0.0017616110.9982383
ENST00000339490ENST00000376113PHKA1chrX71872394-BIN1chr2127819773-0.0015860390.9984139
ENST00000339490ENST00000346226PHKA1chrX71872394-BIN1chr2127819773-0.0020724440.99792755
ENST00000339490ENST00000352848PHKA1chrX71872394-BIN1chr2127819773-0.0018064210.99819356
ENST00000339490ENST00000393041PHKA1chrX71872394-BIN1chr2127819773-0.0022222130.99777776
ENST00000339490ENST00000348750PHKA1chrX71872394-BIN1chr2127819773-0.0016239320.998376
ENST00000339490ENST00000357970PHKA1chrX71872394-BIN1chr2127819773-0.0021786550.99782133
ENST00000339490ENST00000259238PHKA1chrX71872394-BIN1chr2127819773-0.0021692780.9978307
ENST00000339490ENST00000393040PHKA1chrX71872394-BIN1chr2127819773-0.0023675490.9976324
ENST00000339490ENST00000351659PHKA1chrX71872394-BIN1chr2127819773-0.0022222130.99777776
ENST00000339490ENST00000316724PHKA1chrX71872394-BIN1chr2127819773-0.0021061550.99789387
ENST00000339490ENST00000409400PHKA1chrX71872394-BIN1chr2127819773-0.0017616110.9982383
ENST00000373539ENST00000376113PHKA1chrX71872394-BIN1chr2127819773-0.0015813740.99841857
ENST00000373539ENST00000346226PHKA1chrX71872394-BIN1chr2127819773-0.0020217050.99797827
ENST00000373539ENST00000352848PHKA1chrX71872394-BIN1chr2127819773-0.0017674530.99823254
ENST00000373539ENST00000393041PHKA1chrX71872394-BIN1chr2127819773-0.0021356980.9978643
ENST00000373539ENST00000348750PHKA1chrX71872394-BIN1chr2127819773-0.0016308310.99836916
ENST00000373539ENST00000357970PHKA1chrX71872394-BIN1chr2127819773-0.0021160190.997884
ENST00000373539ENST00000259238PHKA1chrX71872394-BIN1chr2127819773-0.0021411830.9978588
ENST00000373539ENST00000393040PHKA1chrX71872394-BIN1chr2127819773-0.0023259970.99767405
ENST00000373539ENST00000351659PHKA1chrX71872394-BIN1chr2127819773-0.0021356980.9978643
ENST00000373539ENST00000316724PHKA1chrX71872394-BIN1chr2127819773-0.0020550870.9979449
ENST00000373539ENST00000409400PHKA1chrX71872394-BIN1chr2127819773-0.0017344950.99826556

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 PHKA1-BIN1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PHKA1chrX71872394BIN1chr21278197731405415GQSLYILGSLMAELNQNLNDVLVGLE
PHKA1chrX71872394BIN1chr21278197731546415GQSLYILGSLMAELNQNLNDVLVGLE
PHKA1chrX71872394BIN1chr21278197731623415GQSLYILGSLMAELNQNLNDVLVGLE
PHKA1chrX71872394BIN1chr21278197731684415GQSLYILGSLMAELNQNLNDVLVGLE

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Potential FusionNeoAntigen Information of PHKA1-BIN1 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.
PHKA1-BIN1_71872394_127819773.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)
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:21LMAELNQNL0.99660.5018918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:27LMAELNQNL0.99650.5183918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:04LMAELNQNL0.99570.6448918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:13LMAELNQNL0.99550.6337918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:22ILGSLMAEL0.99340.5565514
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:13ILGSLMAEL0.98640.7406514
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:27ILGSLMAEL0.98380.6073514
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:11ILGSLMAEL0.98120.5166514
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:38ILGSLMAEL0.96390.6091514
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:04ILGSLMAEL0.96240.6205514
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:17ILGSLMAEL0.95030.5411514
PHKA1-BIN1chrX71872394chr21278197731546HLA-B13:01LMAELNQNL0.10940.9362918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:22SLMAELNQNL0.9980.5945818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:11SLMAELNQNL0.99550.5482818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:24SLMAELNQNL0.99540.5265818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:67SLMAELNQNL0.99540.5265818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:30SLMAELNQNL0.99540.5265818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:27SLMAELNQNL0.99530.6604818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:60SLMAELNQNL0.99510.5141818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:13SLMAELNQNL0.99480.7552818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:16SLMAELNQNL0.99380.5092818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:04SLMAELNQNL0.99170.6948818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:38SLMAELNQNL0.98690.7152818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:35SLMAELNQNL0.95980.5448818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:19SLMAELNQNL0.95750.5217818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:29SLMAELNQNL0.92020.5326818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:20SLMAELNQNL0.87890.5285818
PHKA1-BIN1chrX71872394chr21278197731546HLA-C08:15MAELNQNL10.96721018
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:05LMAELNQNL0.99840.5508918
PHKA1-BIN1chrX71872394chr21278197731546HLA-C01:17LMAELNQNL0.97120.9083918
PHKA1-BIN1chrX71872394chr21278197731546HLA-C01:30LMAELNQNL0.87080.9083918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:05SLMAELNQNL0.99710.5944818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:01SLMAELNQNL0.99540.5265818
PHKA1-BIN1chrX71872394chr21278197731546HLA-C08:02MAELNQNL10.96721018
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:03LMAELNQNL0.99830.5951918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:06LMAELNQNL0.99660.5018918
PHKA1-BIN1chrX71872394chr21278197731546HLA-C01:03LMAELNQNL0.99550.9012918
PHKA1-BIN1chrX71872394chr21278197731546HLA-B15:73LMAELNQNL0.98240.9595918
PHKA1-BIN1chrX71872394chr21278197731546HLA-C01:02LMAELNQNL0.97870.9055918
PHKA1-BIN1chrX71872394chr21278197731546HLA-B15:30LMAELNQNL0.94730.9361918
PHKA1-BIN1chrX71872394chr21278197731546HLA-C07:04LMAELNQNL0.8520.8846918
PHKA1-BIN1chrX71872394chr21278197731546HLA-C17:01LMAELNQNL0.68890.8092918
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:03SLMAELNQNL0.99710.745818
PHKA1-BIN1chrX71872394chr21278197731546HLA-A02:14SLMAELNQNL0.99290.6007818
PHKA1-BIN1chrX71872394chr21278197731546HLA-B41:03AELNQNLNDVL0.95350.55491122

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Potential FusionNeoAntigen Information of PHKA1-BIN1 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 PHKA1-BIN1

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
5032LGSLMAELNQNLNDPHKA1BIN1chrX71872394chr21278197731546

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PHKA1-BIN1

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-B14:023BVN5032LGSLMAELNQNLND-7.9962-8.1096
HLA-B14:023BVN5032LGSLMAELNQNLND-5.70842-6.74372
HLA-B52:013W395032LGSLMAELNQNLND-6.83737-6.95077
HLA-B52:013W395032LGSLMAELNQNLND-4.4836-5.5189
HLA-A11:014UQ25032LGSLMAELNQNLND-10.0067-10.1201
HLA-A11:014UQ25032LGSLMAELNQNLND-9.03915-10.0745
HLA-A24:025HGA5032LGSLMAELNQNLND-6.56204-6.67544
HLA-A24:025HGA5032LGSLMAELNQNLND-5.42271-6.45801
HLA-B44:053DX85032LGSLMAELNQNLND-7.85648-8.89178
HLA-B44:053DX85032LGSLMAELNQNLND-5.3978-5.5112
HLA-A02:016TDR5032LGSLMAELNQNLND-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PHKA1-BIN1

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
PHKA1-BIN1chrX71872394chr21278197731018MAELNQNLATGGCAGAGCTCAACCAGAACCTC
PHKA1-BIN1chrX71872394chr21278197731122AELNQNLNDVLGCAGAGCTCAACCAGAACCTCAATGATGTGCTG
PHKA1-BIN1chrX71872394chr2127819773514ILGSLMAELATTTTAGGAAGCTTGATGGCAGAGCTC
PHKA1-BIN1chrX71872394chr2127819773818SLMAELNQNLAGCTTGATGGCAGAGCTCAACCAGAACCTC
PHKA1-BIN1chrX71872394chr2127819773918LMAELNQNLTTGATGGCAGAGCTCAACCAGAACCTC

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 PHKA1-BIN1

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
SARCPHKA1-BIN1chrX71872394ENST00000339490chr2127819773ENST00000259238TCGA-DX-A23R-01A

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Potential target of CAR-T therapy development for PHKA1-BIN1

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 PHKA1-BIN1

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 PHKA1-BIN1

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