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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:COL6A2-FUS

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: COL6A2-FUS
FusionPDB ID: 18435
FusionGDB2.0 ID: 18435
HgeneTgene
Gene symbol

COL6A2

FUS

Gene ID

1292

2521

Gene namecollagen type VI alpha 2 chainFUS RNA binding protein
SynonymsBTHLM1|PP3610|UCMD1ALS6|ETM4|FUS1|HNRNPP2|POMP75|TLS
Cytomap

21q22.3

16p11.2

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-2(VI) chaincollagen VI, alpha-2 polypeptidecollagen, type VI, alpha 2epididymis secretory sperm binding proteinhuman mRNA for collagen VI alpha-2 C-terminal globular domainRNA-binding protein FUS75 kDa DNA-pairing proteinfus-like proteinfused in sarcomafusion gene in myxoid liposarcomaheterogeneous nuclear ribonucleoprotein P2oncogene FUSoncogene TLStranslocated in liposarcoma protein
Modification date2020032820200329
UniProtAcc

P12110

Main function of 5'-partner protein: FUNCTION: Collagen VI acts as a cell-binding protein.

P35637

Main function of 5'-partner protein: FUNCTION: DNA/RNA-binding protein that plays a role in various cellular processes such as transcription regulation, RNA splicing, RNA transport, DNA repair and damage response (PubMed:27731383). Binds to nascent pre-mRNAs and acts as a molecular mediator between RNA polymerase II and U1 small nuclear ribonucleoprotein thereby coupling transcription and splicing (PubMed:26124092). Binds also its own pre-mRNA and autoregulates its expression; this autoregulation mechanism is mediated by non-sense-mediated decay (PubMed:24204307). Plays a role in DNA repair mechanisms by promoting D-loop formation and homologous recombination during DNA double-strand break repair (PubMed:10567410). In neuronal cells, plays crucial roles in dendritic spine formation and stability, RNA transport, mRNA stability and synaptic homeostasis (By similarity). {ECO:0000250|UniProtKB:P56959, ECO:0000269|PubMed:10567410, ECO:0000269|PubMed:24204307, ECO:0000269|PubMed:26124092, ECO:0000269|PubMed:27731383}.
Ensembl transtripts involved in fusion geneENST idsENST00000300527, ENST00000310645, 
ENST00000357838, ENST00000397763, 
ENST00000409416, ENST00000460886, 
ENST00000474990, ENST00000254108, 
ENST00000380244, ENST00000568685, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 8=93620 X 13 X 10=2600
# samples 1322
** MAII scorelog2(13/936*10)=-2.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(22/2600*10)=-3.56293619439116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: COL6A2 [Title/Abstract] AND FUS [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: COL6A2 [Title/Abstract] AND FUS [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)COL6A2(47546455)-FUS(31199645), # samples:2
Anticipated loss of major functional domain due to fusion event.COL6A2-FUS 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.
COL6A2-FUS 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.
COL6A2-FUS 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.
COL6A2-FUS 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
TgeneFUS

GO:0006355

regulation of transcription, DNA-templated

26124092

TgeneFUS

GO:0006357

regulation of transcription by RNA polymerase II

25453086

TgeneFUS

GO:0008380

RNA splicing

26124092

TgeneFUS

GO:0043484

regulation of RNA splicing

25453086|27731383

TgeneFUS

GO:0048255

mRNA stabilization

27378374

TgeneFUS

GO:0051260

protein homooligomerization

25453086

TgeneFUS

GO:1905168

positive regulation of double-strand break repair via homologous recombination

10567410



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/chr21:47546455/chr16:31199645)
- 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 COL6A2 (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 FUS (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)
ENST00000300527COL6A2chr2147546455+ENST00000254108FUSchr1631199645+371525651733461109
ENST00000300527COL6A2chr2147546455+ENST00000380244FUSchr1631199645+351125651733461109
ENST00000300527COL6A2chr2147546455+ENST00000568685FUSchr1631199645+348725651733491110
ENST00000310645COL6A2chr2147546455+ENST00000254108FUSchr1631199645+369325438233241080
ENST00000310645COL6A2chr2147546455+ENST00000380244FUSchr1631199645+348925438233241080
ENST00000310645COL6A2chr2147546455+ENST00000568685FUSchr1631199645+346525438233271081
ENST00000357838COL6A2chr2147546455+ENST00000254108FUSchr1631199645+369325438233241080
ENST00000357838COL6A2chr2147546455+ENST00000380244FUSchr1631199645+348925438233241080
ENST00000357838COL6A2chr2147546455+ENST00000568685FUSchr1631199645+346525438233271081
ENST00000409416COL6A2chr2147546455+ENST00000254108FUSchr1631199645+36742524033051101
ENST00000409416COL6A2chr2147546455+ENST00000380244FUSchr1631199645+34702524033051101
ENST00000409416COL6A2chr2147546455+ENST00000568685FUSchr1631199645+34462524033081102
ENST00000397763COL6A2chr2147546455+ENST00000254108FUSchr1631199645+363824882732691080
ENST00000397763COL6A2chr2147546455+ENST00000380244FUSchr1631199645+343424882732691080
ENST00000397763COL6A2chr2147546455+ENST00000568685FUSchr1631199645+341024882732721081

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
ENST00000300527ENST00000254108COL6A2chr2147546455+FUSchr1631199645+0.0009070590.99909294
ENST00000300527ENST00000380244COL6A2chr2147546455+FUSchr1631199645+0.0010069050.9989931
ENST00000300527ENST00000568685COL6A2chr2147546455+FUSchr1631199645+0.0009591990.9990408
ENST00000310645ENST00000254108COL6A2chr2147546455+FUSchr1631199645+0.0009018910.9990982
ENST00000310645ENST00000380244COL6A2chr2147546455+FUSchr1631199645+0.0010058270.9989942
ENST00000310645ENST00000568685COL6A2chr2147546455+FUSchr1631199645+0.0009542040.9990458
ENST00000357838ENST00000254108COL6A2chr2147546455+FUSchr1631199645+0.0009018910.9990982
ENST00000357838ENST00000380244COL6A2chr2147546455+FUSchr1631199645+0.0010058270.9989942
ENST00000357838ENST00000568685COL6A2chr2147546455+FUSchr1631199645+0.0009542040.9990458
ENST00000409416ENST00000254108COL6A2chr2147546455+FUSchr1631199645+0.0008801130.99911994
ENST00000409416ENST00000380244COL6A2chr2147546455+FUSchr1631199645+0.0009765310.99902344
ENST00000409416ENST00000568685COL6A2chr2147546455+FUSchr1631199645+0.0009396930.99906033
ENST00000397763ENST00000254108COL6A2chr2147546455+FUSchr1631199645+0.0008456270.9991543
ENST00000397763ENST00000380244COL6A2chr2147546455+FUSchr1631199645+0.0009390970.9990609
ENST00000397763ENST00000568685COL6A2chr2147546455+FUSchr1631199645+0.0009068480.9990932

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 COL6A2-FUS

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
COL6A2chr2147546455FUSchr16311996452488359DPGNRGPDGYPGEAGSPGERGDQGGK
COL6A2chr2147546455FUSchr16311996452488935ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452488936ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452488936TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452488937TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452524380DPGNRGPDGYPGEAGSPGERGDQGGK
COL6A2chr2147546455FUSchr16311996452524956ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452524957ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452524957TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452524958TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452543359DPGNRGPDGYPGEAGSPGERGDQGGK
COL6A2chr2147546455FUSchr16311996452543935ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452543936ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452543936TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452543937TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452565388DPGNRGPDGYPGEAGSPGERGDQGGK
COL6A2chr2147546455FUSchr16311996452565964ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452565965ATRRADFNRGGGNGRGGRGRGGPMGR
COL6A2chr2147546455FUSchr16311996452565965TRRADFNRGGGNGRGGRGRGGPMGRG
COL6A2chr2147546455FUSchr16311996452565966TRRADFNRGGGNGRGGRGRGGPMGRG

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Potential FusionNeoAntigen Information of COL6A2-FUS 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.
COL6A2-FUS_47546455_31199645.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)
COL6A2-FUSchr2147546455chr16311996452565HLA-A33:01DFNRGGGNGR0.98150.7089414
COL6A2-FUSchr2147546455chr16311996452565HLA-A33:05DFNRGGGNGR0.98150.7089414

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Potential FusionNeoAntigen Information of COL6A2-FUS 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 COL6A2-FUS

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
6351NRGGGNGRGGRGRGCOL6A2FUSchr2147546455chr16311996452565

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of COL6A2-FUS

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-B14:023BVN6351NRGGGNGRGGRGRG-6.72408-7.75938
HLA-B14:023BVN6351NRGGGNGRGGRGRG-6.47075-6.58415
HLA-B52:013W396351NRGGGNGRGGRGRG-7.14093-7.25433
HLA-B52:013W396351NRGGGNGRGGRGRG-4.59991-5.63521
HLA-A24:025HGA6351NRGGGNGRGGRGRG-8.73176-8.84516
HLA-A24:025HGA6351NRGGGNGRGGRGRG-5.2601-6.2954
HLA-B44:053DX86351NRGGGNGRGGRGRG-5.60406-5.71746
HLA-B44:053DX86351NRGGGNGRGGRGRG-4.79709-5.83239

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Vaccine Design for the FusionNeoAntigens of COL6A2-FUS

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
COL6A2-FUSchr2147546455chr1631199645414DFNRGGGNGRTGTGCCCAGACCTTCCCTGCCAAACAGGCC

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 COL6A2-FUS

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
PRADCOL6A2-FUSchr2147546455ENST00000300527chr1631199645ENST00000254108TCGA-FC-7961

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Potential target of CAR-T therapy development for COL6A2-FUS

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 COL6A2-FUS

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 COL6A2-FUS

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
TgeneFUSC1842675AMYOTROPHIC LATERAL SCLEROSIS 6 (disorder)5UNIPROT
TgeneFUSC3468114Juvenile amyotrophic lateral sclerosis5ORPHANET
TgeneFUSC0002736Amyotrophic Lateral Sclerosis2CTD_human;ORPHANET
TgeneFUSC0206634Liposarcoma, Myxoid2CTD_human;ORPHANET
TgeneFUSC0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
TgeneFUSC0497327Dementia1GENOMICS_ENGLAND
TgeneFUSC0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
TgeneFUSC3539195TREMOR, HEREDITARY ESSENTIAL, 41CTD_human;UNIPROT
TgeneFUSC3888102Frontotemporal Dementia With Motor Neuron Disease1ORPHANET