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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:BCAS3-MARCH10

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BCAS3-MARCH10
FusionPDB ID: 9219
FusionGDB2.0 ID: 9219
HgeneTgene
Gene symbol

BCAS3

MARCH10

Gene ID

54828

162333

Gene nameBCAS3 microtubule associated cell migration factormembrane associated ring-CH-type finger 10
SynonymsGAOB1|MAABMARCH-X|MARCH10|RNF190
Cytomap

17q23.2

17q23.2

Type of geneprotein-codingprotein-coding
Descriptionbreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1probable E3 ubiquitin-protein ligase MARCH10RING-type E3 ubiquitin transferase MARCH10membrane associated ring finger 10membrane-associated RING finger protein 10membrane-associated RING-CH protein Xmembrane-associated ring finger (C3HC4) 10, E3 ubiq
Modification date2020031320200313
UniProtAcc

Q9H6U6

Main function of 5'-partner protein: FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000390652, ENST00000407086, 
ENST00000408905, ENST00000585744, 
ENST00000588462, ENST00000588874, 
ENST00000589222, ENST00000585812, 
ENST00000582358, ENST00000311269, 
ENST00000456609, ENST00000544856, 
ENST00000583600, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score53 X 35 X 17=3153510 X 6 X 6=360
# samples 619
** MAII scorelog2(61/31535*10)=-5.69200088030826
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/360*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: BCAS3 [Title/Abstract] AND MARCH10 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: BCAS3 [Title/Abstract] AND MARCH10 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BCAS3(59024713)-MARCH10(60837367), # samples:4
Anticipated loss of major functional domain due to fusion event.BCAS3-MARCH10 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.
BCAS3-MARCH10 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
HgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

HgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

HgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058



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/chr17:59024713/chr17:60837367)
- 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 BCAS3 (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 MARCH10 (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)
ENST00000589222BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-389512896835051145
ENST00000589222BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-389412896835051145
ENST00000589222BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-400812896836191183
ENST00000589222BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-403812896834781136
ENST00000407086BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-387512694834851145
ENST00000407086BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-387412694834851145
ENST00000407086BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-398812694835991183
ENST00000407086BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-401812694834581136
ENST00000390652BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-385812523134681145
ENST00000390652BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-385712523134681145
ENST00000390652BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-397112523135821183
ENST00000390652BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-400112523134411136
ENST00000408905BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-38271221034371145
ENST00000408905BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-38261221034371145
ENST00000408905BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-39401221035511183
ENST00000408905BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-39701221034101136
ENST00000588462BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-38271221034371145
ENST00000588462BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-38261221034371145
ENST00000588462BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-39401221035511183
ENST00000588462BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-39701221034101136
ENST00000585744BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-3243637132853946
ENST00000585744BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-3242637132853946
ENST00000585744BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-3356637132967984
ENST00000585744BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-3386637132826937
ENST00000588874BCAS3chr1759024713+ENST00000456609MARCH10chr1760837367-33287221882938916
ENST00000588874BCAS3chr1759024713+ENST00000311269MARCH10chr1760837367-33277221882938916
ENST00000588874BCAS3chr1759024713+ENST00000583600MARCH10chr1760837367-34417221883052954
ENST00000588874BCAS3chr1759024713+ENST00000544856MARCH10chr1760837367-34717221882911907

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
ENST00000589222ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.0007153330.9992847
ENST00000589222ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0007223970.99927765
ENST00000589222ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.0004431940.99955684
ENST00000589222ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.0004243120.9995757
ENST00000407086ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.0007071020.99929285
ENST00000407086ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0007141450.9992859
ENST00000407086ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.0004399480.99956006
ENST00000407086ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.0004176990.99958235
ENST00000390652ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.0006788480.9993212
ENST00000390652ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0006853590.99931467
ENST00000390652ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.0004237130.9995763
ENST00000390652ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.0004019870.9995981
ENST00000408905ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.0006655730.9993344
ENST00000408905ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0006721480.9993279
ENST00000408905ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.0004125070.9995875
ENST00000408905ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.0003874480.9996126
ENST00000588462ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.0006655730.9993344
ENST00000588462ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0006721480.9993279
ENST00000588462ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.0004125070.9995875
ENST00000588462ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.0003874480.9996126
ENST00000585744ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.0018087810.9981912
ENST00000585744ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0018295770.9981704
ENST00000585744ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.0014366020.99856347
ENST00000585744ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.0013403330.9986596
ENST00000588874ENST00000456609BCAS3chr1759024713+MARCH10chr1760837367-0.001527430.9984725
ENST00000588874ENST00000311269BCAS3chr1759024713+MARCH10chr1760837367-0.0015440260.998456
ENST00000588874ENST00000583600BCAS3chr1759024713+MARCH10chr1760837367-0.001230970.998769
ENST00000588874ENST00000544856BCAS3chr1759024713+MARCH10chr1760837367-0.00113830.9988617

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 BCAS3-MARCH10

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
BCAS3chr1759024713MARCH10chr17608373671221407HLYTLHRGETEAKSSSEEDALTEPRS
BCAS3chr1759024713MARCH10chr17608373671252407HLYTLHRGETEAKSSSEEDALTEPRS
BCAS3chr1759024713MARCH10chr17608373671269407HLYTLHRGETEAKSSSEEDALTEPRS
BCAS3chr1759024713MARCH10chr17608373671289407HLYTLHRGETEAKSSSEEDALTEPRS
BCAS3chr1759024713MARCH10chr1760837367637208HLYTLHRGETEAKSSSEEDALTEPRS
BCAS3chr1759024713MARCH10chr1760837367722178HLYTLHRGETEAKSSSEEDALTEPRS

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Potential FusionNeoAntigen Information of BCAS3-MARCH10 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.
BCAS3-MARCH10_59024713_60837367.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)
BCAS3-MARCH10chr1759024713chr17608373671252HLA-B50:02GETEAKSSS0.61870.6475716

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Potential FusionNeoAntigen Information of BCAS3-MARCH10 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 BCAS3-MARCH10

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
7859RGETEAKSSSEEDABCAS3MARCH10chr1759024713chr17608373671252

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BCAS3-MARCH10

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-B14:023BVN7859RGETEAKSSSEEDA-7.15543-7.26883
HLA-B14:023BVN7859RGETEAKSSSEEDA-4.77435-5.80965
HLA-B52:013W397859RGETEAKSSSEEDA-6.80875-6.92215
HLA-B52:013W397859RGETEAKSSSEEDA-4.20386-5.23916
HLA-A11:014UQ27859RGETEAKSSSEEDA-7.5194-8.5547
HLA-A11:014UQ27859RGETEAKSSSEEDA-6.9601-7.0735
HLA-A24:025HGA7859RGETEAKSSSEEDA-7.52403-7.63743
HLA-A24:025HGA7859RGETEAKSSSEEDA-5.82433-6.85963
HLA-B27:056PYJ7859RGETEAKSSSEEDA-3.28285-4.31815
HLA-B44:053DX87859RGETEAKSSSEEDA-5.91172-6.94702
HLA-B44:053DX87859RGETEAKSSSEEDA-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of BCAS3-MARCH10

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
BCAS3-MARCH10chr1759024713chr1760837367716GETEAKSSSGGAGAAACTGAAGCCAAAAGTTCTAGT

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 BCAS3-MARCH10

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
LUSCBCAS3-MARCH10chr1759024713ENST00000390652chr1760837367ENST00000311269TCGA-63-7023-01A

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Potential target of CAR-T therapy development for BCAS3-MARCH10

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 BCAS3-MARCH10

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 BCAS3-MARCH10

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