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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:BMPR1B-PDLIM5

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BMPR1B-PDLIM5
FusionPDB ID: 9916
FusionGDB2.0 ID: 9916
HgeneTgene
Gene symbol

BMPR1B

PDLIM5

Gene ID

658

10611

Gene namebone morphogenetic protein receptor type 1BPDZ and LIM domain 5
SynonymsALK-6|ALK6|AMDD|BDA1D|BDA2|CDw293ENH|ENH1|L9|LIM
Cytomap

4q22.3

4q22.3

Type of geneprotein-codingprotein-coding
Descriptionbone morphogenetic protein receptor type-1BBMP type-1B receptorBMPR-1Bactivin receptor-like kinase 6bone morphogenetic protein receptor, type IBserine/threonine receptor kinasePDZ and LIM domain protein 5enigma homologenigma-like LIM domain proteinenigma-like PDZ and LIM domains protein
Modification date2020031320200313
UniProtAcc

O00238

Main function of 5'-partner protein: FUNCTION: On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Receptor for BMP7/OP-1 and GDF5. Positively regulates chondrocyte differentiation through GDF5 interaction. {ECO:0000250|UniProtKB:P36898}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000264568, ENST00000394931, 
ENST00000440890, ENST00000515059, 
ENST00000502683, 		ENST00000359265, 
ENST00000380176, ENST00000504489, 
ENST00000508216, ENST00000512274, 
ENST00000514743, ENST00000542407, 
ENST00000317968, ENST00000318007, 
ENST00000380180, ENST00000437932, 
ENST00000450793, ENST00000538141, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 13 X 6=109215 X 18 X 7=1890
# samples 1721
** MAII scorelog2(17/1092*10)=-2.68336620478215
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/1890*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: BMPR1B [Title/Abstract] AND PDLIM5 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: BMPR1B [Title/Abstract] AND PDLIM5 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BMPR1B(96046272)-PDLIM5(95444875), # samples:2
Anticipated loss of major functional domain due to fusion event.BMPR1B-PDLIM5 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.
BMPR1B-PDLIM5 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.
BMPR1B-PDLIM5 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.
BMPR1B-PDLIM5 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
HgeneBMPR1B

GO:0006468

protein phosphorylation

12065756

HgeneBMPR1B

GO:0030509

BMP signaling pathway

18436533



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/chr4:96046272/chr4:95444875)
- 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 BMPR1B (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 PDLIM5 (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)
ENST00000515059BMPR1Bchr496046272+ENST00000450793PDLIM5chr495444875+14778682831476398
ENST00000515059BMPR1Bchr496046272+ENST00000538141PDLIM5chr495444875+14178682831416378
ENST00000515059BMPR1Bchr496046272+ENST00000380180PDLIM5chr495444875+26118682831476397
ENST00000515059BMPR1Bchr496046272+ENST00000318007PDLIM5chr495444875+25518682831416377
ENST00000515059BMPR1Bchr496046272+ENST00000437932PDLIM5chr495444875+63958682832235650
ENST00000515059BMPR1Bchr496046272+ENST00000317968PDLIM5chr495444875+67198682832562759
ENST00000440890BMPR1Bchr496046272+ENST00000450793PDLIM5chr495444875+1305696211304427
ENST00000440890BMPR1Bchr496046272+ENST00000538141PDLIM5chr495444875+1245696211244407
ENST00000440890BMPR1Bchr496046272+ENST00000380180PDLIM5chr495444875+2439696211304427
ENST00000440890BMPR1Bchr496046272+ENST00000318007PDLIM5chr495444875+2379696211244407
ENST00000440890BMPR1Bchr496046272+ENST00000437932PDLIM5chr495444875+6223696212063680
ENST00000440890BMPR1Bchr496046272+ENST00000317968PDLIM5chr495444875+6547696212390789
ENST00000264568BMPR1Bchr496046272+ENST00000450793PDLIM5chr495444875+13487391541347398
ENST00000264568BMPR1Bchr496046272+ENST00000538141PDLIM5chr495444875+12887391541287378
ENST00000264568BMPR1Bchr496046272+ENST00000380180PDLIM5chr495444875+24827391541347397
ENST00000264568BMPR1Bchr496046272+ENST00000318007PDLIM5chr495444875+24227391541287377
ENST00000264568BMPR1Bchr496046272+ENST00000437932PDLIM5chr495444875+62667391542106650
ENST00000264568BMPR1Bchr496046272+ENST00000317968PDLIM5chr495444875+65907391542433759
ENST00000394931BMPR1Bchr496046272+ENST00000450793PDLIM5chr495444875+1264655701263398
ENST00000394931BMPR1Bchr496046272+ENST00000538141PDLIM5chr495444875+1204655701203378
ENST00000394931BMPR1Bchr496046272+ENST00000380180PDLIM5chr495444875+2398655701263397
ENST00000394931BMPR1Bchr496046272+ENST00000318007PDLIM5chr495444875+2338655701203377
ENST00000394931BMPR1Bchr496046272+ENST00000437932PDLIM5chr495444875+6182655702022650
ENST00000394931BMPR1Bchr496046272+ENST00000317968PDLIM5chr495444875+6506655702349759

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
ENST00000515059ENST00000450793BMPR1Bchr496046272+PDLIM5chr495444875+0.0032909410.996709
ENST00000515059ENST00000538141BMPR1Bchr496046272+PDLIM5chr495444875+0.0060141590.99398583
ENST00000515059ENST00000380180BMPR1Bchr496046272+PDLIM5chr495444875+0.0008921690.9991078
ENST00000515059ENST00000318007BMPR1Bchr496046272+PDLIM5chr495444875+0.0005785350.9994215
ENST00000515059ENST00000437932BMPR1Bchr496046272+PDLIM5chr495444875+0.0001843410.99981564
ENST00000515059ENST00000317968BMPR1Bchr496046272+PDLIM5chr495444875+0.0001431220.9998568
ENST00000440890ENST00000450793BMPR1Bchr496046272+PDLIM5chr495444875+0.0059488610.99405116
ENST00000440890ENST00000538141BMPR1Bchr496046272+PDLIM5chr495444875+0.0121434070.9878566
ENST00000440890ENST00000380180BMPR1Bchr496046272+PDLIM5chr495444875+0.001222640.99877733
ENST00000440890ENST00000318007BMPR1Bchr496046272+PDLIM5chr495444875+0.0009433380.99905664
ENST00000440890ENST00000437932BMPR1Bchr496046272+PDLIM5chr495444875+0.0010674560.99893254
ENST00000440890ENST00000317968BMPR1Bchr496046272+PDLIM5chr495444875+0.0008428780.9991571
ENST00000264568ENST00000450793BMPR1Bchr496046272+PDLIM5chr495444875+0.0029526250.99704736
ENST00000264568ENST00000538141BMPR1Bchr496046272+PDLIM5chr495444875+0.0048796280.99512035
ENST00000264568ENST00000380180BMPR1Bchr496046272+PDLIM5chr495444875+0.0007448610.9992551
ENST00000264568ENST00000318007BMPR1Bchr496046272+PDLIM5chr495444875+0.0004556650.9995443
ENST00000264568ENST00000437932BMPR1Bchr496046272+PDLIM5chr495444875+0.0001854840.99981457
ENST00000264568ENST00000317968BMPR1Bchr496046272+PDLIM5chr495444875+0.000136640.9998634
ENST00000394931ENST00000450793BMPR1Bchr496046272+PDLIM5chr495444875+0.00277160.99722844
ENST00000394931ENST00000538141BMPR1Bchr496046272+PDLIM5chr495444875+0.0048042890.9951957
ENST00000394931ENST00000380180BMPR1Bchr496046272+PDLIM5chr495444875+0.0006995570.9993005
ENST00000394931ENST00000318007BMPR1Bchr496046272+PDLIM5chr495444875+0.0004378780.9995621
ENST00000394931ENST00000437932BMPR1Bchr496046272+PDLIM5chr495444875+0.0001812620.99981874
ENST00000394931ENST00000317968BMPR1Bchr496046272+PDLIM5chr495444875+0.0001325420.99986744

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 BMPR1B-PDLIM5

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
BMPR1Bchr496046272PDLIM5chr495444875655193EQSQSSGSGSGLPLLLKDGGKAAQAN
BMPR1Bchr496046272PDLIM5chr495444875696223EQSQSSGSGSGLPLLLKDGGKAAQAN
BMPR1Bchr496046272PDLIM5chr495444875739193EQSQSSGSGSGLPLLLKDGGKAAQAN
BMPR1Bchr496046272PDLIM5chr495444875868193EQSQSSGSGSGLPLLLKDGGKAAQAN

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Potential FusionNeoAntigen Information of BMPR1B-PDLIM5 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.
BMPR1B-PDLIM5_96046272_95444875.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)
BMPR1B-PDLIM5chr496046272chr495444875739HLA-C15:06SGSGLPLLL0.9960.971716
BMPR1B-PDLIM5chr496046272chr495444875739HLA-C02:06SGSGLPLLL0.51610.9807716
BMPR1B-PDLIM5chr496046272chr495444875739HLA-C15:05SGSGLPLLL0.99610.98716
BMPR1B-PDLIM5chr496046272chr495444875739HLA-C15:02SGSGLPLLL0.99480.9699716
BMPR1B-PDLIM5chr496046272chr495444875739HLA-C17:01SGSGLPLLL0.66960.9893716
BMPR1B-PDLIM5chr496046272chr495444875739HLA-B07:13SGSGLPLLL0.15080.8314716

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Potential FusionNeoAntigen Information of BMPR1B-PDLIM5 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 BMPR1B-PDLIM5

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
3125GSGSGLPLLLKDGGBMPR1BPDLIM5chr496046272chr495444875739

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BMPR1B-PDLIM5

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-B14:023BVN3125GSGSGLPLLLKDGG-7.15543-7.26883
HLA-B14:023BVN3125GSGSGLPLLLKDGG-4.77435-5.80965
HLA-B52:013W393125GSGSGLPLLLKDGG-6.80875-6.92215
HLA-B52:013W393125GSGSGLPLLLKDGG-4.20386-5.23916
HLA-A11:014UQ23125GSGSGLPLLLKDGG-7.5194-8.5547
HLA-A11:014UQ23125GSGSGLPLLLKDGG-6.9601-7.0735
HLA-A24:025HGA3125GSGSGLPLLLKDGG-7.52403-7.63743
HLA-A24:025HGA3125GSGSGLPLLLKDGG-5.82433-6.85963
HLA-B27:056PYJ3125GSGSGLPLLLKDGG-3.28285-4.31815
HLA-B44:053DX83125GSGSGLPLLLKDGG-5.91172-6.94702
HLA-B44:053DX83125GSGSGLPLLLKDGG-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of BMPR1B-PDLIM5

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
BMPR1B-PDLIM5chr496046272chr495444875716SGSGLPLLLTCAGGCCTCCCTCTGCTGCTAAAAGAT

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 BMPR1B-PDLIM5

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
BRCABMPR1B-PDLIM5chr496046272ENST00000264568chr495444875ENST00000317968TCGA-A7-A26J-01A

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Potential target of CAR-T therapy development for BMPR1B-PDLIM5

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
HgeneBMPR1Bchr4:96046272chr4:95444875ENST00000264568+611127_148195503.0TransmembraneHelical
HgeneBMPR1Bchr4:96046272chr4:95444875ENST00000394931+510127_148195503.0TransmembraneHelical
HgeneBMPR1Bchr4:96046272chr4:95444875ENST00000440890+611127_148225533.0TransmembraneHelical
HgeneBMPR1Bchr4:96046272chr4:95444875ENST00000515059+813127_148195503.0TransmembraneHelical

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 BMPR1B-PDLIM5

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 BMPR1B-PDLIM5

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