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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:PANK4-RGS6

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PANK4-RGS6
FusionPDB ID: 62561
FusionGDB2.0 ID: 62561
HgeneTgene
Gene symbol

PANK4

RGS6

Gene ID

55229

9628

Gene namepantothenate kinase 4 (inactive)regulator of G protein signaling 6
Synonyms-GAP|HA117|S914
Cytomap

1p36.32

14q24.2

Type of geneprotein-codingprotein-coding
Description4'-phosphopantetheine phosphataseinactive pantothenic acid kinase 4pantothenic acid kinase 4regulator of G-protein signaling 6regulator of G-protein signalling 6
Modification date2020031520200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000378466, ENST00000435556, 
ENST00000491212, 
ENST00000434263, 
ENST00000553690, ENST00000554782, 
ENST00000343854, ENST00000355512, 
ENST00000402788, ENST00000404301, 
ENST00000406236, ENST00000407322, 
ENST00000553525, ENST00000553530, 
ENST00000555571, ENST00000556437, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score5 X 8 X 6=24011 X 10 X 6=660
# samples 713
** MAII scorelog2(7/240*10)=-1.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/660*10)=-2.34395440121736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PANK4 [Title/Abstract] AND RGS6 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PANK4 [Title/Abstract] AND RGS6 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PANK4(2442777)-RGS6(72818803), # samples:2
Anticipated loss of major functional domain due to fusion event.PANK4-RGS6 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.
PANK4-RGS6 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.
PANK4-RGS6 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.
PANK4-RGS6 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
TgeneRGS6

GO:0043547

positive regulation of GTPase activity

10521509



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/chr1:2442777/chr14:72818803)
- 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 PANK4 (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 RGS6 (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)
ENST00000378466PANK4chr12442777-ENST00000553525RGS6chr1472818803+324418461332341073
ENST00000378466PANK4chr12442777-ENST00000555571RGS6chr1472818803+318118461331801056
ENST00000378466PANK4chr12442777-ENST00000553530RGS6chr1472818803+466018461331801055
ENST00000378466PANK4chr12442777-ENST00000556437RGS6chr1472818803+336018461332341073
ENST00000378466PANK4chr12442777-ENST00000355512RGS6chr1472818803+332618461331441043
ENST00000378466PANK4chr12442777-ENST00000406236RGS6chr1472818803+323818461331891058
ENST00000378466PANK4chr12442777-ENST00000404301RGS6chr1472818803+325918461332041063
ENST00000378466PANK4chr12442777-ENST00000407322RGS6chr1472818803+325918461331951060
ENST00000378466PANK4chr12442777-ENST00000402788RGS6chr1472818803+318118461331801056
ENST00000378466PANK4chr12442777-ENST00000343854RGS6chr1472818803+312418461331231037
ENST00000435556PANK4chr12442777-ENST00000553525RGS6chr1472818803+31231725931131034
ENST00000435556PANK4chr12442777-ENST00000555571RGS6chr1472818803+30601725930591016
ENST00000435556PANK4chr12442777-ENST00000553530RGS6chr1472818803+45391725930591016
ENST00000435556PANK4chr12442777-ENST00000556437RGS6chr1472818803+32391725931131034
ENST00000435556PANK4chr12442777-ENST00000355512RGS6chr1472818803+32051725930231004
ENST00000435556PANK4chr12442777-ENST00000406236RGS6chr1472818803+31171725930681019
ENST00000435556PANK4chr12442777-ENST00000404301RGS6chr1472818803+31381725930831024
ENST00000435556PANK4chr12442777-ENST00000407322RGS6chr1472818803+31381725930741021
ENST00000435556PANK4chr12442777-ENST00000402788RGS6chr1472818803+30601725930591016
ENST00000435556PANK4chr12442777-ENST00000343854RGS6chr1472818803+3003172593002997

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
ENST00000378466ENST00000553525PANK4chr12442777-RGS6chr1472818803+0.0020241380.9979759
ENST00000378466ENST00000555571PANK4chr12442777-RGS6chr1472818803+0.0019507760.99804926
ENST00000378466ENST00000553530PANK4chr12442777-RGS6chr1472818803+0.0008921870.9991078
ENST00000378466ENST00000556437PANK4chr12442777-RGS6chr1472818803+0.0017826970.9982173
ENST00000378466ENST00000355512PANK4chr12442777-RGS6chr1472818803+0.0022076980.99779236
ENST00000378466ENST00000406236PANK4chr12442777-RGS6chr1472818803+0.0022980770.99770194
ENST00000378466ENST00000404301PANK4chr12442777-RGS6chr1472818803+0.0026071860.9973928
ENST00000378466ENST00000407322PANK4chr12442777-RGS6chr1472818803+0.0016072230.99839276
ENST00000378466ENST00000402788PANK4chr12442777-RGS6chr1472818803+0.0019507760.99804926
ENST00000378466ENST00000343854PANK4chr12442777-RGS6chr1472818803+0.0014789950.99852103
ENST00000435556ENST00000553525PANK4chr12442777-RGS6chr1472818803+0.001535190.9984648
ENST00000435556ENST00000555571PANK4chr12442777-RGS6chr1472818803+0.0024810070.997519
ENST00000435556ENST00000553530PANK4chr12442777-RGS6chr1472818803+0.0012342120.9987658
ENST00000435556ENST00000556437PANK4chr12442777-RGS6chr1472818803+0.0013507670.9986493
ENST00000435556ENST00000355512PANK4chr12442777-RGS6chr1472818803+0.0019414250.9980585
ENST00000435556ENST00000406236PANK4chr12442777-RGS6chr1472818803+0.0020545220.9979455
ENST00000435556ENST00000404301PANK4chr12442777-RGS6chr1472818803+0.0025001550.9974999
ENST00000435556ENST00000407322PANK4chr12442777-RGS6chr1472818803+0.001882790.9981172
ENST00000435556ENST00000402788PANK4chr12442777-RGS6chr1472818803+0.0024810070.997519
ENST00000435556ENST00000343854PANK4chr12442777-RGS6chr1472818803+0.0017115810.99828845

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 PANK4-RGS6

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PANK4chr12442777RGS6chr14728188031725572LVDSYSEWLQRLKIEDIITKMQDDKT
PANK4chr12442777RGS6chr14728188031846611LVDSYSEWLQRLKIEDIITKMQDDKT

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Potential FusionNeoAntigen Information of PANK4-RGS6 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.
PANK4-RGS6_2442777_72818803.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)
PANK4-RGS6chr12442777chr14728188031846HLA-B44:03SEWLQRLKI0.99080.9233514
PANK4-RGS6chr12442777chr14728188031846HLA-B13:01SEWLQRLKI0.97410.8426514
PANK4-RGS6chr12442777chr14728188031846HLA-B45:01SEWLQRLKI0.97060.8404514
PANK4-RGS6chr12442777chr14728188031846HLA-B41:01SEWLQRLKI0.43470.8324514
PANK4-RGS6chr12442777chr14728188031846HLA-B39:13SEWLQRLKI0.11380.8522514
PANK4-RGS6chr12442777chr14728188031846HLA-B50:01SEWLQRLKI0.09230.6467514
PANK4-RGS6chr12442777chr14728188031846HLA-B52:01SEWLQRLKI0.03720.9046514
PANK4-RGS6chr12442777chr14728188031846HLA-A30:08RLKIEDIITK0.9920.73271020
PANK4-RGS6chr12442777chr14728188031846HLA-A74:09RLKIEDIITK0.84260.56741020
PANK4-RGS6chr12442777chr14728188031846HLA-A74:11RLKIEDIITK0.84260.56741020
PANK4-RGS6chr12442777chr14728188031846HLA-A74:03RLKIEDIITK0.84260.56741020
PANK4-RGS6chr12442777chr14728188031846HLA-B27:05QRLKIEDIITK0.99990.8156920
PANK4-RGS6chr12442777chr14728188031846HLA-B40:06SEWLQRLKI0.99830.5152514
PANK4-RGS6chr12442777chr14728188031846HLA-B39:08SEWLQRLKI0.25560.733514
PANK4-RGS6chr12442777chr14728188031846HLA-B51:07SEWLQRLKI0.02930.765514
PANK4-RGS6chr12442777chr14728188031846HLA-B27:14QRLKIEDIITK0.99980.7245920
PANK4-RGS6chr12442777chr14728188031846HLA-B27:03QRLKIEDIITK0.99610.8337920
PANK4-RGS6chr12442777chr14728188031846HLA-B27:09QRLKIEDII0.9980.7921918
PANK4-RGS6chr12442777chr14728188031846HLA-B44:26SEWLQRLKI0.99080.9233514
PANK4-RGS6chr12442777chr14728188031846HLA-B44:07SEWLQRLKI0.99080.9233514
PANK4-RGS6chr12442777chr14728188031846HLA-B44:13SEWLQRLKI0.99080.9233514
PANK4-RGS6chr12442777chr14728188031846HLA-B40:04SEWLQRLKI0.99060.6336514
PANK4-RGS6chr12442777chr14728188031846HLA-B18:03SEWLQRLKI0.74240.8937514
PANK4-RGS6chr12442777chr14728188031846HLA-B39:02SEWLQRLKI0.09840.8522514
PANK4-RGS6chr12442777chr14728188031846HLA-B50:05SEWLQRLKI0.09230.6467514
PANK4-RGS6chr12442777chr14728188031846HLA-B50:04SEWLQRLKI0.09230.6467514
PANK4-RGS6chr12442777chr14728188031846HLA-A30:01RLKIEDIITK0.99280.85211020
PANK4-RGS6chr12442777chr14728188031846HLA-A74:01RLKIEDIITK0.84260.56741020
PANK4-RGS6chr12442777chr14728188031846HLA-B27:10QRLKIEDIITK0.99990.8097920
PANK4-RGS6chr12442777chr14728188031846HLA-B27:08QRLKIEDIITK0.99990.6825920

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Potential FusionNeoAntigen Information of PANK4-RGS6 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.
PANK4-RGS6_2442777_72818803.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)
PANK4-RGS6chr12442777chr14728188031846DRB1-0415RLKIEDIITKMQDDK1025
PANK4-RGS6chr12442777chr14728188031846DRB1-0436RLKIEDIITKMQDDK1025
PANK4-RGS6chr12442777chr14728188031846DRB1-0437RLKIEDIITKMQDDK1025
PANK4-RGS6chr12442777chr14728188031846DRB1-0442RLKIEDIITKMQDDK1025
PANK4-RGS6chr12442777chr14728188031846DRB1-0453RLKIEDIITKMQDDK1025
PANK4-RGS6chr12442777chr14728188031846DRB1-0458RLKIEDIITKMQDDK1025

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Fusion breakpoint peptide structures of PANK4-RGS6

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
2250EWLQRLKIEDIITKPANK4RGS6chr12442777chr14728188031846

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PANK4-RGS6

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-B14:023BVN2250EWLQRLKIEDIITK-7.9962-8.1096
HLA-B14:023BVN2250EWLQRLKIEDIITK-5.70842-6.74372
HLA-B52:013W392250EWLQRLKIEDIITK-6.83737-6.95077
HLA-B52:013W392250EWLQRLKIEDIITK-4.4836-5.5189
HLA-A11:014UQ22250EWLQRLKIEDIITK-10.0067-10.1201
HLA-A11:014UQ22250EWLQRLKIEDIITK-9.03915-10.0745
HLA-A24:025HGA2250EWLQRLKIEDIITK-6.56204-6.67544
HLA-A24:025HGA2250EWLQRLKIEDIITK-5.42271-6.45801
HLA-B44:053DX82250EWLQRLKIEDIITK-7.85648-8.89178
HLA-B44:053DX82250EWLQRLKIEDIITK-5.3978-5.5112
HLA-A02:016TDR2250EWLQRLKIEDIITK-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PANK4-RGS6

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
PANK4-RGS6chr12442777chr14728188031020RLKIEDIITKAGATTAAAGATTGAAGACATCATTACAAAG
PANK4-RGS6chr12442777chr1472818803514SEWLQRLKIAGCGAGTGGCTTCAGAGATTAAAGATT
PANK4-RGS6chr12442777chr1472818803918QRLKIEDIICAGAGATTAAAGATTGAAGACATCATT
PANK4-RGS6chr12442777chr1472818803920QRLKIEDIITKCAGAGATTAAAGATTGAAGACATCATTACAAAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PANK4-RGS6chr12442777chr14728188031025RLKIEDIITKMQDDKAGATTAAAGATTGAAGACATCATTACAAAGATGCAAGATGACAAG

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Information of the samples that have these potential fusion neoantigens of PANK4-RGS6

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
LUSCPANK4-RGS6chr12442777ENST00000378466chr1472818803ENST00000343854TCGA-94-8491-01A

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Potential target of CAR-T therapy development for PANK4-RGS6

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 PANK4-RGS6

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 PANK4-RGS6

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