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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:PHACTR1-BCL11A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PHACTR1-BCL11A
FusionPDB ID: 64675
FusionGDB2.0 ID: 64675
HgeneTgene
Gene symbol

PHACTR1

BCL11A

Gene ID

221692

53335

Gene namephosphatase and actin regulator 1BAF chromatin remodeling complex subunit BCL11A
SynonymsEIEE70|RPEL|RPEL1|dJ257A7.2BCL11A-L|BCL11A-S|BCL11A-XL|BCL11a-M|CTIP1|DILOS|EVI9|HBFQTL5|ZNF856
Cytomap

6p24.1

2p16.1

Type of geneprotein-codingprotein-coding
Descriptionphosphatase and actin regulator 1RPEL repeat containing 1B-cell lymphoma/leukemia 11AB cell CLL/lymphoma 11AB-cell CLL/lymphoma 11A (zinc finger protein) isoform 2BCL11A B-cell CLL/lymphoma 11A (zinc finger protein) isoform 1BCL11A, BAF complex componentC2H2-type zinc finger proteinCOUP-TF-interacting pro
Modification date2020031320200313
UniProtAcc.

Q9H165

Main function of 5'-partner protein: FUNCTION: Transcription factor associated with the BAF SWI/SNF chromatin remodeling complex (By similarity). Repressor of fetal hemoglobin (HbF) level (PubMed:26375765). Involved in brain development (PubMed:27453576). May play a role in hematopoiesis. Essential factor in lymphopoiesis required for B-cell formation in fetal liver. May function as a modulator of the transcriptional repression activity of ARP1 (By similarity). {ECO:0000250|UniProtKB:Q9QYE3, ECO:0000303|PubMed:26375765, ECO:0000303|PubMed:27453576}.
Ensembl transtripts involved in fusion geneENST idsENST00000332995, ENST00000379348, 
ENST00000379350, ENST00000379329, 
ENST00000379335, ENST00000379345, 
ENST00000457702, ENST00000482982, 
ENST00000335712, ENST00000358510, 
ENST00000477659, ENST00000537768, 
ENST00000356842, ENST00000359629, 
ENST00000538214, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score6 X 8 X 3=14410 X 9 X 3=270
# samples 89
** MAII scorelog2(8/144*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/270*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PHACTR1 [Title/Abstract] AND BCL11A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PHACTR1 [Title/Abstract] AND BCL11A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PHACTR1(12750022)-BCL11A(60679801), # samples:2
Anticipated loss of major functional domain due to fusion event.PHACTR1-BCL11A 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.
PHACTR1-BCL11A 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.
PHACTR1-BCL11A 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.
PHACTR1-BCL11A 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.
PHACTR1-BCL11A seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
PHACTR1-BCL11A seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
TgeneBCL11A

GO:0000122

negative regulation of transcription by RNA polymerase II

19153051



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/chr6:12750022/chr2:60679801)
- 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 PHACTR1 (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 BCL11A (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)
ENST00000379350PHACTR1chr612750022+ENST00000356842BCL11Achr260679801-187937978470130
ENST00000379350PHACTR1chr612750022+ENST00000359629BCL11Achr260679801-187937978470130
ENST00000379350PHACTR1chr612750022+ENST00000538214BCL11Achr260679801-62437978470130
ENST00000379348PHACTR1chr612750022+ENST00000356842BCL11Achr260679801-192742772518148
ENST00000379348PHACTR1chr612750022+ENST00000359629BCL11Achr260679801-192742772518148
ENST00000379348PHACTR1chr612750022+ENST00000538214BCL11Achr260679801-67242772518148
ENST00000332995PHACTR1chr612750022+ENST00000356842BCL11Achr260679801-17502500341113
ENST00000332995PHACTR1chr612750022+ENST00000359629BCL11Achr260679801-17502500341113
ENST00000332995PHACTR1chr612750022+ENST00000538214BCL11Achr260679801-4952500341113

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
ENST00000379350ENST00000356842PHACTR1chr612750022+BCL11Achr260679801-0.143987490.8560125
ENST00000379350ENST00000359629PHACTR1chr612750022+BCL11Achr260679801-0.143987490.8560125
ENST00000379350ENST00000538214PHACTR1chr612750022+BCL11Achr260679801-0.035460120.9645399
ENST00000379348ENST00000356842PHACTR1chr612750022+BCL11Achr260679801-0.1198141350.8801859
ENST00000379348ENST00000359629PHACTR1chr612750022+BCL11Achr260679801-0.1198141350.8801859
ENST00000379348ENST00000538214PHACTR1chr612750022+BCL11Achr260679801-0.048233130.9517669
ENST00000332995ENST00000356842PHACTR1chr612750022+BCL11Achr260679801-0.073758280.9262417
ENST00000332995ENST00000359629PHACTR1chr612750022+BCL11Achr260679801-0.073758280.9262417
ENST00000332995ENST00000538214PHACTR1chr612750022+BCL11Achr260679801-0.0407105130.95928955

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 PHACTR1-BCL11A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PHACTR1chr612750022BCL11Achr26067980125079SDTPYLAEARISFNLGAGSSHTPIRR
PHACTR1chr612750022BCL11Achr26067980137996SDTPYLAEARISFNLGAGSSHTPIRR
PHACTR1chr612750022BCL11Achr260679801427114SDTPYLAEARISFNLGAGSSHTPIRR

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Potential FusionNeoAntigen Information of PHACTR1-BCL11A 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.
PHACTR1-BCL11A_12750022_60679801.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)
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:04ARISFNLGA0.99950.92817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:05ARISFNLGA0.99940.9777817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:02AEARISFNL0.99570.6211615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B13:01AEARISFNL0.99390.8016615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B44:03AEARISFNL0.99370.9709615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B39:06ARISFNLGA0.98670.8034817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B45:01AEARISFNL0.9840.8479615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B47:01AEARISFNL0.97110.5773615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B41:01AEARISFNL0.4550.9215615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B39:13AEARISFNL0.42330.959615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:01AEARISFNL0.14260.6847615
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:22YLAEARISFNL0.99980.7198415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:60YLAEARISFNL0.99950.6856415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:24YLAEARISFNL0.99950.6741415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:67YLAEARISFNL0.99950.6741415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:30YLAEARISFNL0.99950.6741415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:11YLAEARISFNL0.99950.6938415
PHACTR1-BCL11Achr612750022chr260679801250HLA-B45:01AEARISFNLGA0.99930.8853617
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:27YLAEARISFNL0.99910.6689415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:04YLAEARISFNL0.99910.6454415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:16YLAEARISFNL0.99860.5065415
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:02AEARISFNLGA0.99810.7412617
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:19YLAEARISFNL0.99690.5041415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:29YLAEARISFNL0.99630.6829415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:35YLAEARISFNL0.99530.7125415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:20YLAEARISFNL0.98690.6766415
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:01AEARISFNLGA0.89890.7322617
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:14ARISFNLGA0.99950.94817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B40:06AEARISFNL0.99940.6721615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B73:01ARISFNLGA0.99790.7605817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:03ARISFNLGA0.96280.9807817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B39:08AEARISFNL0.520.9281615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B73:01EARISFNLGA0.91740.6619717
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:05YLAEARISFNL0.99970.6288415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:07YLAEARISFNL0.99950.6928415
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:01YLAEARISFNL0.99950.6741415
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:09ARISFNLGA0.99960.977817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:10ARISFNLGA0.99960.9623817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:08ARISFNLGA0.99940.9615817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B27:06ARISFNLGA0.99940.9189817
PHACTR1-BCL11Achr612750022chr260679801250HLA-B40:04AEARISFNL0.99920.6456615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B44:07AEARISFNL0.99370.9709615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B44:13AEARISFNL0.99370.9709615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B44:26AEARISFNL0.99370.9709615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B41:03AEARISFNL0.60680.6513615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B39:02AEARISFNL0.44450.958615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:04AEARISFNL0.14260.6847615
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:05AEARISFNL0.14260.6847615
PHACTR1-BCL11Achr612750022chr260679801250HLA-A02:14YLAEARISFNL0.99940.731415
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:05AEARISFNLGA0.89890.7322617
PHACTR1-BCL11Achr612750022chr260679801250HLA-B50:04AEARISFNLGA0.89890.7322617

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Potential FusionNeoAntigen Information of PHACTR1-BCL11A 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.
PHACTR1-BCL11A_12750022_60679801.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)
PHACTR1-BCL11Achr612750022chr260679801250DRB1-1179DTPYLAEARISFNLG116
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0201EARISFNLGAGSSHT722
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0201AEARISFNLGAGSSH621
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0204EARISFNLGAGSSHT722
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0204AEARISFNLGAGSSH621
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0214EARISFNLGAGSSHT722
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0214AEARISFNLGAGSSH621
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0224EARISFNLGAGSSHT722
PHACTR1-BCL11Achr612750022chr260679801250DRB3-0224AEARISFNLGAGSSH621

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Fusion breakpoint peptide structures of PHACTR1-BCL11A

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
135AEARISFNLGAGSSPHACTR1BCL11Achr612750022chr260679801250

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PHACTR1-BCL11A

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-B14:023BVN135AEARISFNLGAGSS-6.9015-7.0162
HLA-B14:023BVN135AEARISFNLGAGSS-6.88733-7.92393
HLA-B52:013W39135AEARISFNLGAGSS-6.20276-6.31746
HLA-B52:013W39135AEARISFNLGAGSS-3.23728-4.27388
HLA-A24:025HGA135AEARISFNLGAGSS-6.25402-7.29062
HLA-A24:025HGA135AEARISFNLGAGSS-5.4385-5.5532
HLA-B44:053DX8135AEARISFNLGAGSS-6.77944-6.89414
HLA-B44:053DX8135AEARISFNLGAGSS-5.78397-6.82057
HLA-A02:016TDR135AEARISFNLGAGSS-2.00985-3.04645

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Vaccine Design for the FusionNeoAntigens of PHACTR1-BCL11A

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
PHACTR1-BCL11Achr612750022chr260679801415YLAEARISFNLCCAGGATCTCCTTTAACCTGGGGGCAGGTTCTT
PHACTR1-BCL11Achr612750022chr260679801615AEARISFNLTCTCCTTTAACCTGGGGGCAGGTTCTT
PHACTR1-BCL11Achr612750022chr260679801617AEARISFNLGATCTCCTTTAACCTGGGGGCAGGTTCTTCACACA
PHACTR1-BCL11Achr612750022chr260679801717EARISFNLGACCTTTAACCTGGGGGCAGGTTCTTCACACA
PHACTR1-BCL11Achr612750022chr260679801817ARISFNLGATTAACCTGGGGGCAGGTTCTTCACACA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PHACTR1-BCL11Achr612750022chr260679801116DTPYLAEARISFNLGTCGCAGAGGCCAGGATCTCCTTTAACCTGGGGGCAGGTTCTTCAC
PHACTR1-BCL11Achr612750022chr260679801621AEARISFNLGAGSSHTCTCCTTTAACCTGGGGGCAGGTTCTTCACACACCCCCATTCGGC
PHACTR1-BCL11Achr612750022chr260679801722EARISFNLGAGSSHTCCTTTAACCTGGGGGCAGGTTCTTCACACACCCCCATTCGGCGTA

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Information of the samples that have these potential fusion neoantigens of PHACTR1-BCL11A

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
LUADPHACTR1-BCL11Achr612750022ENST00000332995chr260679801ENST00000356842TCGA-44-7670-01A

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Potential target of CAR-T therapy development for PHACTR1-BCL11A

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 PHACTR1-BCL11A

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 PHACTR1-BCL11A

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