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Center for Computational Systems Medicine
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Kinase Fusion Gene Summary

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Kinase Fusion Gene Sample Information

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Kinase Fusion ORF Analysis

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Kinase Fusion Amino Acid Sequences

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Multiple Sequence Alignment of All Fusion Protein Isoforms

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Kinase Fusion Protein Functional Features

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Kinase Fusion Protein Structures

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Comparison of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

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pLDDT Scores and Difference Analysis of pLDDT Scores Between the Active Sites (Best) and Non-Active Sites.

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Ramachandran Plot of Kinase Fusion Protein Structure

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Potential Active Site Information

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Virtual Screening Results

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Kinase-Substrate Information

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Related Drugs with This Kinase Fusion Protein

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Related Disease with This Kinase Fusion Protein

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Clinical Trials of the Found Drugs/Small Molecules

Kinase Fusion Gene:BMPR1B_PDLIM5

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: BMPR1B_PDLIM5
KinaseFusionDB ID: KFG661
FusionGDB2.0 ID: KFG661
HgeneTgene
Gene symbol

BMPR1B

PDLIM5

Gene ID

658

10611

Gene namebone morphogenetic protein receptor type 1BPDZ and LIM domain 5
SynonymsALK-6|ALK6|AMD3|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 date2024041320240407
UniProtAcc

O00238

Q96HC4

Ensembl transtripts involved in fusion geneENST idsENST00000264568, ENST00000394931, 
ENST00000440890, ENST00000515059, 
ENST00000502683, 
ENST00000359265, 
ENST00000380176, ENST00000504489, 
ENST00000508216, ENST00000512274, 
ENST00000514743, ENST00000542407, 
ENST00000317968, ENST00000318007, 
ENST00000380180, ENST00000437932, 
ENST00000450793, ENST00000538141, 
Context (manual curation of fusion genes in KinaseFusionDB)

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

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BMPR1B(96046272)-PDLIM5(95444875), # samples:2
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:0030509

BMP signaling pathway

12065756|18184661|18436533


check buttonKinase Fusion 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 buttonKinase Fusion 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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Kinase Fusion Gene Sample Information

check buttonKinase Fusion gene information.
check button Kinase Fusion gene information from four resources (ChiTars 5.0, ChimerDB 4.0, COSMIC, and CCLE)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceSampleHgeneHchrHbpTgeneTchrTbp
ChimerDB4TCGA-A7-A26J-01ABMPR1Bchr4

96046272

PDLIM5chr4

95444875

ChimerDB4TCGA-AO-A12C-01ABMPR1Bchr4

95679219

PDLIM5chr4

95494502

ChimerDB4TCGA-HC-A4ZV-01ABMPR1Bchr4

95679219

PDLIM5chr4

95444875

ChimerDB4TCGA-A7-A26J-01ABMPR1Bchr4

95917285

PDLIM5chr4

95561427

ChimerDB4TCGA-EJ-7330-01ABMPR1Bchr4

95679219

PDLIM5chr4

95561427



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Kinase Fusion ORF Analysis


check buttonKinase Fusion information from ORFfinder translation from full-length transcript sequence from KinaseFusionDB.
HenstTenstHgeneHchrHbpTgeneTchrTbpSeq length
(transcript)
Seq length
(amino acids)
ENST00000515059ENST00000450793BMPR1Bchr496046272PDLIM5chr4954448751477398

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Kinase Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from KinaseFusionDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>Henst_Tenst_Hgene_Hchr_Hbp_Tgene_Tchr_Tbp_length(fusion AA)_AAseq

>ENST00000515059_ENST00000450793_BMPR1B_chr4_96046272_PDLIM5_chr4_95444875_length(amino acids)=398
MLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICSTDGYCFTMIEEDDSGLPVVTSGCLGLEGSDFQCRDTPIPHQR
RSIECCTERNECNKDLHPTLPPLKNRDFVDGPIHHRALLISVTVCSLLLVLIILFCYFRYKRQETRPRYSIGLEQDETYIPPGESLRDLI
EQSQSSGSGSGLPLLLKDGGKAAQANVRIGDVVLSIDGINAQGMTHLEAQNKIKGCTGSLNMTLQRASAAPKPEPVPVQKPTVTSVCSET
SQELAEGQRRGSQGDSKQQNGPVPRKIPPRKHIVERYTEFYHVPTHSDASKKRLIEDTEDWRPRTGTTQSRSFRILAQITGTEHLKESEA

--------------------------------------------------------------

Multiple Sequence Alignment of All Fusion Protein Isoforms



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Kinase Fusion Protein Functional Features


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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BMPR1B

O00238

PDLIM5

Q96HC4

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}.FUNCTION: May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a role in the regulation of cardiomyocyte expansion. Isoforms lacking the LIM domains may negatively modulate the scaffolding activity of isoform 1. Overexpression promotes the development of heart hypertrophy. Contributes to the regulation of dendritic spine morphogenesis in neurons. May be required to restrain postsynaptic growth of excitatory synapses. Isoform 1, but not isoform 2, expression favors spine thinning and elongation. {ECO:0000250|UniProtKB:Q62920}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.

check button - Retained domain in the 5'-partner of fusion protein (protein functional feature from UniProt).
225
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote
HgeneBMPR1B96046272PDLIM595444875ENST00000515059611174_2031533DomainNote=GS;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00585


check button - Retained domain in the 3'-partner of fusion protein (protein functional feature from UniProt).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


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Kinase Fusion Protein Structures

check button CIF files of the predicted kinase fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Kinase Fusion protein CIF link (fusion AA seq ID in KinaseFusionDB)HenstTenstHgeneHchrHbpTgeneTchrTbpAA seqLen(AA seq)
PDB file >>>HKFP_58_BMPR1B_PDLIM5ENST00000515059ENST00000450793BMPR1Bchr496046272PDLIM5chr495444875
MLLRSAGKLNVGTKKEDGESTAPTPRPKVLRCKCHHHCPEDSVNNICSTDGYCFTMIEEDDSGLPVVTSGCLGLEGSDFQCRDTPIPHQR
RSIECCTERNECNKDLHPTLPPLKNRDFVDGPIHHRALLISVTVCSLLLVLIILFCYFRYKRQETRPRYSIGLEQDETYIPPGESLRDLI
EQSQSSGSGSGLPLLLKDGGKAAQANVRIGDVVLSIDGINAQGMTHLEAQNKIKGCTGSLNMTLQRASAAPKPEPVPVQKPTVTSVCSET
SQELAEGQRRGSQGDSKQQNGPVPRKIPPRKHIVERYTEFYHVPTHSDASKKRLIEDTEDWRPRTGTTQSRSFRILAQITGTEHLKESEA
398_BMPR1B_PDLIM5
3D view using mol* of HKFP_58_BMPR1B_PDLIM5


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Comparison of Fusion Protein Isoforms

check button Superimpose the 3D Structures Among All Fusion Protein Isoforms
* Download the pdb file and open it from the molstar online viewer.

check button Comparison of the Secondary Structures of Fusion Protein Isoforms

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Comparison of Fusion Protein Sequences/Structures with Known Sequences/Structures from PDB

BMPR1B_PDLIM5 does not have any known PDB structures.

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pLDDT score distribution

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
* The blue color at the bottom marks the best active site residues.


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Potential Active Site Information


check button The potential binding sites of these fusion proteins were identified using SiteMap, a module of the Schrodinger suite.
Kinase Fusion AA seq ID in KinaseFusionDBSite scoreSizeDscoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues

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Ramachandran Plot of Kinase Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

HKFP_58_BMPR1B_PDLIM5_ramachandran.png
all structure BMPR1B-PDLIM5

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Virtual Screening Results


check button Distribution of the average docking score across all approved kinase inhibitors.
Distribution of the number of occurrence across all approved kinase inhibitors.
5'-kinase fusion protein case
all structure BMPR1B-PDLIM5
3'-kinase fusion protein case

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check button Drug information from DrugBank of the top 20 interacting small molecules.
* The detailed information of individual kinase inhibitors are available in the download page.
Fusion gene name infoDrugDocking scoreGlide g scoreGlide energy
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Lapatinib-6.10702-6.1958199999999986-53.2204
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Larotrectinib-6.0678800000000015-6.0678800000000015-43.2334
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Entrectinib-5.99234-6.05704-50.0456
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Entrectinib-5.99234-6.05704-50.0456
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Entrectinib-5.8404-5.9051-49.6393
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nintedanib-5.7812-6.2612-57.7212
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nintedanib-5.7812-6.2612-57.7212
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nintedanib-5.7812-6.2612-57.7212
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nintedanib-5.7812-6.2612-57.7212
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nintedanib-5.7812-6.2612-57.7212
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Fostamatinib-5.7453400000000014-5.80894-46.5596
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Fostamatinib-5.7453400000000014-5.80894-46.5596
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nilotinib-5.71146-6.636260000000001-53.5249
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Nilotinib-5.71146-6.636260000000001-53.5249
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Mobocertinib-5.67506-5.68276-54.6319
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Belumosudil-5.57871-5.58641-48.0723
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Pazopanib-5.56454-5.57144-42.1722
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Pazopanib-5.56454-5.57144-42.1722
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Baricitinib-5.4842900000000006-5.4842900000000006-37.1582
HKFP_58_BMPR1B_PDLIM5-out-DOCK_HTVS_1-001Lapatinib-5.46814-5.55694-54.1544
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Mobocertinib-6.66241-6.67011-49.2216
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Belumosudil-6.03059-6.03829-46.483000000000004
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Erdafitinib-5.90171-5.90191-43.1495
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Gefitinib-5.68772-6.10272-38.2193
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Gefitinib-5.68772-6.10272-38.2193
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Entrectinib-5.61494-5.67964-47.9385
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Entrectinib-5.61494-5.67964-47.9385
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Baricitinib-5.5677900000000005-5.5677900000000005-37.9339
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Entrectinib-5.546869999999999-5.6115699999999995-47.7536
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Neratinib-5.43273-5.6186300000000005-54.566
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Cabozantinib-5.42625-5.47125-44.8923
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Cabozantinib-5.42625-5.47125-44.8923
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Lapatinib-5.42481-5.51361-55.2065
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Axitinib-5.33553-5.33873-39.0593
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Lapatinib-5.323919999999999-5.412719999999999-58.2398
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Midostaurin-5.3232-5.3232-38.3644
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Tepotinib-5.29204-5.29314-46.6324
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Sorafenib-5.28519-5.29729-44.1714
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Sorafenib-5.28519-5.29729-44.1714
327_BMPR1B_PDLIM5-DOCK_HTVS_1-001Netarsudil-5.23389-5.2449900000000005-44.9312

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Kinase-Substrate Information of BMPR1B_PDLIM5


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
BMPR1BO00238humanSMAD1Q15797S465HNPIssVs_______
BMPR1BO00238humanSMAD2Q15796S467sVRCssMs_______
BMPR1BO00238humanSMAD1Q15797S462GsPHNPIssVs____
BMPR1BO00238humanSMAD2Q15796S465sPsVRCssMs_____
BMPR1BO00238humanSMAD1Q15797S463sPHNPIssVs_____
BMPR1BO00238humanSMAD2Q15796S464GsPsVRCssMs____


check button Biological Network Integration of This Kinase and Substrates
(GeneMANIA website)

check button Enriched GO biological processes of the phosphorylation target genes of the kinase
KinaseGOIDGO termP.adjust
BMPR1BIDDescription0.00e+00
BMPR1BGO:0031053primary miRNA processing1.68e-04
BMPR1BGO:0035196miRNA processing4.21e-04
BMPR1BGO:0009880embryonic pattern specification4.21e-04
BMPR1BGO:0001707mesoderm formation4.21e-04
BMPR1BGO:0048332mesoderm morphogenesis4.21e-04
BMPR1BGO:0060395SMAD protein signal transduction4.21e-04
BMPR1BGO:0070918regulatory ncRNA processing4.21e-04
BMPR1BGO:0001657ureteric bud development4.21e-04
BMPR1BGO:0072163mesonephric epithelium development4.21e-04
BMPR1BGO:0072164mesonephric tubule development4.21e-04
BMPR1BGO:0001823mesonephros development4.21e-04
BMPR1BGO:0001704formation of primary germ layer5.97e-04
BMPR1BGO:0007498mesoderm development6.23e-04
BMPR1BGO:0072073kidney epithelium development7.04e-04
BMPR1BGO:0030509BMP signaling pathway7.81e-04
BMPR1BGO:0035265organ growth7.81e-04
BMPR1BGO:0071772response to BMP7.81e-04
BMPR1BGO:0071773cellular response to BMP stimulus7.81e-04
BMPR1BGO:0007369gastrulation8.96e-04
BMPR1BGO:0007179transforming growth factor beta receptor signaling pathway1.15e-03
BMPR1BGO:0045165cell fate commitment1.64e-03
BMPR1BGO:0071560cellular response to transforming growth factor beta stimulus1.64e-03
BMPR1BGO:0071559response to transforming growth factor beta1.64e-03
BMPR1BGO:0001822kidney development1.81e-03
BMPR1BGO:0072001renal system development1.85e-03
BMPR1BGO:0007178transmembrane receptor protein serine/threonine kinase signaling pathway2.84e-03
BMPR1BGO:0034470ncRNA processing3.14e-03
BMPR1BGO:0007389pattern specification process3.55e-03
BMPR1BGO:0007440foregut morphogenesis5.55e-03
BMPR1BGO:0048340paraxial mesoderm morphogenesis5.55e-03
BMPR1BGO:0071895odontoblast differentiation5.90e-03
BMPR1BGO:0009950dorsal/ventral axis specification6.24e-03
BMPR1BGO:0048368lateral mesoderm development7.56e-03
BMPR1BGO:0001710mesodermal cell fate commitment8.08e-03
BMPR1BGO:1901522positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus8.08e-03
BMPR1BGO:0048339paraxial mesoderm development8.32e-03
BMPR1BGO:0003184pulmonary valve morphogenesis8.32e-03
BMPR1BGO:0060039pericardium development8.32e-03
BMPR1BGO:0038092nodal signaling pathway8.53e-03
BMPR1BGO:0023019signal transduction involved in regulation of gene expression9.15e-03
BMPR1BGO:0003177pulmonary valve development9.33e-03
BMPR1BGO:0062009secondary palate development1.03e-02
BMPR1BGO:0032925regulation of activin receptor signaling pathway1.03e-02
BMPR1BGO:0030325adrenal gland development1.03e-02
BMPR1BGO:1903672positive regulation of sprouting angiogenesis1.03e-02
BMPR1BGO:0070723response to cholesterol1.08e-02
BMPR1BGO:0060795cell fate commitment involved in formation of primary germ layer1.11e-02
BMPR1BGO:0061036positive regulation of cartilage development1.11e-02
BMPR1BGO:0048333mesodermal cell differentiation1.15e-02

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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

check button Distribution of the number of studies mentioning BMPR1B-PDLIM5 and kinase inhibitors the PubMed Abstract (04-01-2024)

Fusion gene - drug pair 1Fusion gene - drug pair 2PMIDPublication dateDOIStudy title

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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 Related diseases from the literature mentioned this fusion gene and drug.
(PubMed, 04-01-2024)
MeSH IDMeSH term

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource


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Clinical Trials of the Found Drugs/Small Molecules


check button Statistics of the Clinical Trials of the Found Kinase Inibitors from clinicaltrials.gov (06-17-2024)

check button Clinical Trials from clinicaltrials.gov (06-17-2024)

Fusion GeneKinase InhibitorNCT IDStudy StatusPhasesDisease# EnrolmentDate