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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:MAST2-TM4SF1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MAST2-TM4SF1
FusionPDB ID: 51840
FusionGDB2.0 ID: 51840
HgeneTgene
Gene symbol

MAST2

TM4SF1

Gene ID

23139

4071

Gene namemicrotubule associated serine/threonine kinase 2transmembrane 4 L six family member 1
SynonymsMAST205|MTSSKH-L6|L6|M3S1|TAAL6
Cytomap

1p34.1

3q25.1

Type of geneprotein-codingprotein-coding
Descriptionmicrotubule-associated serine/threonine-protein kinase 2microtubule associated testis specific serine/threonine protein kinasetransmembrane 4 L6 family member 1membrane component, chromosome 3, surface marker 1transmembrane 4 superfamily member 1tumor-associated antigen L6
Modification date2020031320200313
UniProtAcc

Q6P0Q8

Main function of 5'-partner protein: FUNCTION: Appears to link the dystrophin/utrophin network with microtubule filaments via the syntrophins. Phosphorylation of DMD or UTRN may modulate their affinities for associated proteins. Functions in a multi-protein complex in spermatid maturation. Regulates lipopolysaccharide-induced IL-12 synthesis in macrophages by forming a complex with TRAF6, resulting in the inhibition of TRAF6 NF-kappa-B activation (By similarity). {ECO:0000250}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000361297, ENST00000372009, 
ENST00000477968, 
ENST00000472441, 
ENST00000305366, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score25 X 15 X 13=487510 X 6 X 5=300
# samples 2810
** MAII scorelog2(28/4875*10)=-4.12190348657937
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/300*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MAST2 [Title/Abstract] AND TM4SF1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MAST2 [Title/Abstract] AND TM4SF1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MAST2(46295253)-TM4SF1(149093556), # samples:2
Anticipated loss of major functional domain due to fusion event.MAST2-TM4SF1 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.
MAST2-TM4SF1 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


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/chr1:46295253/chr3:149093556)
- 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 MAST2 (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 TM4SF1 (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)
ENST00000372009MAST2chr146295253+ENST00000305366TM4SF1chr3149093556-20277512831182299
ENST00000361297MAST2chr146295253+ENST00000305366TM4SF1chr3149093556-20277512831182299

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
ENST00000372009ENST00000305366MAST2chr146295253+TM4SF1chr3149093556-0.1047597750.89524025
ENST00000361297ENST00000305366MAST2chr146295253+TM4SF1chr3149093556-0.1047597750.89524025

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 MAST2-TM4SF1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
MAST2chr146295253TM4SF1chr3149093556751156SLGQSAPSLTAGLMLLPAFVFIGLEQ

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Potential FusionNeoAntigen Information of MAST2-TM4SF1 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.
MAST2-TM4SF1_46295253_149093556.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)
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:13GLMLLPAFV0.98890.50021120
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:22SLTAGLMLL0.97360.5599716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:04GLMLLPAFV0.94680.74811120
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:67SLTAGLMLL0.93160.5139716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:30SLTAGLMLL0.93160.5139716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:24SLTAGLMLL0.93160.5139716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:11SLTAGLMLL0.93160.5413716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:16SLTAGLMLL0.92910.5221716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:60SLTAGLMLL0.92870.5044716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:21SLTAGLMLL0.92380.6539716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:27SLTAGLMLL0.9130.687716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:38SLTAGLMLL0.90310.7787716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:35SLTAGLMLL0.90220.5491716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:04SLTAGLMLL0.89940.6876716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:13SLTAGLMLL0.89750.7902716
MAST2-TM4SF1chr146295253chr3149093556751HLA-B35:03APSLTAGLM0.88310.7687514
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:17SLTAGLMLL0.87120.6498716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:17GLMLLPAFV0.8610.68581120
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:29SLTAGLMLL0.84240.5239716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:20SLTAGLMLL0.82180.5161716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:19SLTAGLMLL0.77350.5934716
MAST2-TM4SF1chr146295253chr3149093556751HLA-B35:04APSLTAGLM0.58490.9527514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B35:02APSLTAGLM0.58490.9527514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B81:01APSLTAGLM0.04010.6001514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B82:01APSLTAGLM0.03630.6058514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B81:01APSLTAGLML0.71860.5477515
MAST2-TM4SF1chr146295253chr3149093556751HLA-B82:01APSLTAGLML0.52210.5955515
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:05SLTAGLMLL0.96810.5429716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:01SLTAGLMLL0.93160.5139716
MAST2-TM4SF1chr146295253chr3149093556751HLA-B35:12APSLTAGLM0.58490.9527514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B39:10APSLTAGLM0.41850.9272514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B42:01APSLTAGLM0.1080.6571514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B42:01APSLTAGLML0.67770.6587515
MAST2-TM4SF1chr146295253chr3149093556751HLA-C01:17SAPSLTAGLML0.99560.9533415
MAST2-TM4SF1chr146295253chr3149093556751HLA-C01:30SAPSLTAGLML0.99370.9585415
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:03SLTAGLMLL0.96490.7359716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:14SLTAGLMLL0.92720.6258716
MAST2-TM4SF1chr146295253chr3149093556751HLA-A02:06SLTAGLMLL0.92380.6539716
MAST2-TM4SF1chr146295253chr3149093556751HLA-B35:09APSLTAGLM0.58490.9527514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B55:04APSLTAGLM0.50740.5375514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B67:01APSLTAGLM0.46140.8901514
MAST2-TM4SF1chr146295253chr3149093556751HLA-B40:21SLTAGLMLL0.03930.5873716
MAST2-TM4SF1chr146295253chr3149093556751HLA-B82:02APSLTAGLM0.03630.6058514
MAST2-TM4SF1chr146295253chr3149093556751HLA-C01:02SAPSLTAGLM0.95840.9483414
MAST2-TM4SF1chr146295253chr3149093556751HLA-B67:01APSLTAGLML0.70120.8812515
MAST2-TM4SF1chr146295253chr3149093556751HLA-B82:02APSLTAGLML0.52210.5955515
MAST2-TM4SF1chr146295253chr3149093556751HLA-C01:03SAPSLTAGLML0.99750.9488415
MAST2-TM4SF1chr146295253chr3149093556751HLA-C01:02SAPSLTAGLML0.99580.9518415

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Potential FusionNeoAntigen Information of MAST2-TM4SF1 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 MAST2-TM4SF1

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
6999PSLTAGLMLLPAFVMAST2TM4SF1chr146295253chr3149093556751

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MAST2-TM4SF1

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-B14:023BVN6999PSLTAGLMLLPAFV-7.54146-7.65486
HLA-B14:023BVN6999PSLTAGLMLLPAFV-5.05101-6.08631
HLA-B52:013W396999PSLTAGLMLLPAFV-7.48565-7.59905
HLA-B52:013W396999PSLTAGLMLLPAFV-5.61839-6.65369
HLA-A11:014UQ26999PSLTAGLMLLPAFV-5.36758-5.48098
HLA-A11:014UQ26999PSLTAGLMLLPAFV-2.41377-3.44907
HLA-A24:025HGA6999PSLTAGLMLLPAFV-8.3266-8.44
HLA-A24:025HGA6999PSLTAGLMLLPAFV-5.24481-6.28011
HLA-B44:053DX86999PSLTAGLMLLPAFV-4.07996-5.11526
HLA-B44:053DX86999PSLTAGLMLLPAFV-3.86967-3.98307

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Vaccine Design for the FusionNeoAntigens of MAST2-TM4SF1

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
MAST2-TM4SF1chr146295253chr31490935561120GLMLLPAFVGGCCTGATGCTCCTGCCAGCATTTGTC
MAST2-TM4SF1chr146295253chr3149093556414SAPSLTAGLMTCTGCACCTTCTCTTACTGCTGGCCTGATG
MAST2-TM4SF1chr146295253chr3149093556415SAPSLTAGLMLTCTGCACCTTCTCTTACTGCTGGCCTGATGCTC
MAST2-TM4SF1chr146295253chr3149093556514APSLTAGLMGCACCTTCTCTTACTGCTGGCCTGATG
MAST2-TM4SF1chr146295253chr3149093556515APSLTAGLMLGCACCTTCTCTTACTGCTGGCCTGATGCTC
MAST2-TM4SF1chr146295253chr3149093556716SLTAGLMLLTCTCTTACTGCTGGCCTGATGCTCCTG

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 MAST2-TM4SF1

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
LIHCMAST2-TM4SF1chr146295253ENST00000361297chr3149093556ENST00000305366TCGA-BC-A217-01A

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Potential target of CAR-T therapy development for MAST2-TM4SF1

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
TgeneTM4SF1chr1:46295253chr3:149093556ENST0000030536605162_1820203.0TransmembraneHelical
TgeneTM4SF1chr1:46295253chr3:149093556ENST000003053660594_1140203.0TransmembraneHelical

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 MAST2-TM4SF1

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 MAST2-TM4SF1

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