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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:CASK_BCDIN3D

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: CASK_BCDIN3D
KinaseFusionDB ID: KFG922
FusionGDB2.0 ID: KFG922
HgeneTgene
Gene symbol

CASK

BCDIN3D

Gene ID

8573

144233

Gene namecalcium/calmodulin dependent serine protein kinaseBCDIN3 domain containing RNA methyltransferase
SynonymsCAGH39|CAMGUK|CMG|FGS4|LIN2|MICPCH|MRXSNA|TNRC8|hCASK-
Cytomap

Xp11.4

12q13.12

Type of geneprotein-codingprotein-coding
Descriptionperipheral plasma membrane protein CASKcalcium/calmodulin-dependent serin protein kinasecalcium/calmodulin-dependent serine protein kinase (MAGUK family)calcium/calmodulin-dependent serine protein kinase membrane-associated guanylate kinaseprotein linRNA 5'-monophosphate methyltransferaseBCDIN3 domain containing RNA methyltransfeaseBCDIN3 domain-containing proteinpre-miRNA 5'-monophosphate methyltransferaseprobable methyltransferase BCDIN3D
Modification date2024041120240305
UniProtAcc

P07498

Q7Z5W3

Ensembl transtripts involved in fusion geneENST idsENST00000318588, ENST00000361962, 
ENST00000378154, ENST00000378158, 
ENST00000378163, ENST00000378166, 
ENST00000421587, ENST00000442742, 
ENST00000472704, 		ENST00000333924, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: CASK [Title/Abstract] AND BCDIN3D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CASK(41533081)-BCDIN3D(50231088), # samples:1
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCASK

GO:0010839

negative regulation of keratinocyte proliferation

18664494

TgeneBCDIN3D

GO:0001510

RNA methylation

33664453

TgeneBCDIN3D

GO:0030488

tRNA methylation

28119416|31919512

TgeneBCDIN3D

GO:0031054

pre-miRNA processing

33664453

TgeneBCDIN3D

GO:2000632

negative regulation of pre-miRNA processing

23063121


check buttonKinase Fusion gene breakpoints across CASK (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonKinase Fusion gene breakpoints across BCDIN3D (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.


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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
ChiTaRS5.0BF342823CASKchrX

41533081

BCDIN3Dchr12

50231088



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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)

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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

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/:41533081/:50231088)
- 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
CASK

P07498

BCDIN3D

Q7Z5W3

FUNCTION: Kappa-casein stabilizes micelle formation, preventing casein precipitation in milk.FUNCTION: O-methyltransferase that specifically monomethylates 5'-monophosphate of cytoplasmic histidyl tRNA (tRNA(His)), acting as a capping enzyme by protecting tRNA(His) from cleavage by DICER1 (PubMed:28119416, PubMed:31329584, PubMed:31919512). Also able, with less efficiently, to methylate the 5' monophosphate of a subset of pre-miRNAs, acting as a negative regulator of miRNA processing (PubMed:23063121, PubMed:28119416). The 5' monophosphate of pre-miRNAs is recognized by DICER1 and is required for pre-miRNAs processing: methylation at this position reduces the processing of pre-miRNAs by DICER1 (PubMed:23063121). Was also reported to mediate dimethylation of pre-miR-145; however dimethylation cannot be reproduced by another group which observes a monomethylation of pre-miR-145 (PubMed:23063121, PubMed:28119416). {ECO:0000269|PubMed:23063121, ECO:0000269|PubMed:28119416, ECO:0000269|PubMed:31329584, ECO:0000269|PubMed:31919512}.

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).
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote


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


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Kinase-Substrate Information of CASK_BCDIN3D


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
CASKO14936humanCASKO14936S151PHCVLLAsKENsAPVPkinase
CASKO14936humanNRXN1P58400-1S425VKEKQPssAKsSNKNSyndecan
CASKO14936humanNRXN1P58400-1S424VVKEKQPssAKsSNKSyndecan
CASKO14936humanCASKO14936S155LLAsKENsAPVKLGGPkinase
CASKO14936humanNRXN1P58400-1S428KQPssAKsSNKNKKNSyndecan


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
CASKIDDescription0.00e+00
CASKGO:0007269neurotransmitter secretion3.41e-03
CASKGO:0099643signal release from synapse3.41e-03
CASKGO:0001505regulation of neurotransmitter levels3.53e-03
CASKGO:0006836neurotransmitter transport3.53e-03
CASKGO:0023061signal release1.13e-02
CASKGO:0050804modulation of chemical synaptic transmission1.13e-02
CASKGO:0099177regulation of trans-synaptic signaling1.13e-02
CASKGO:0097104postsynaptic membrane assembly1.36e-02
CASKGO:0098598learned vocalization behavior or vocal learning1.36e-02
CASKGO:0046710GDP metabolic process1.36e-02
CASKGO:0031223auditory behavior1.36e-02
CASKGO:0007638mechanosensory behavior1.38e-02
CASKGO:0090280positive regulation of calcium ion import1.38e-02
CASKGO:0007158neuron cell-cell adhesion1.38e-02
CASKGO:0071625vocalization behavior1.38e-02
CASKGO:0009135purine nucleoside diphosphate metabolic process1.38e-02
CASKGO:0009179purine ribonucleoside diphosphate metabolic process1.38e-02
CASKGO:0090128regulation of synapse maturation1.38e-02
CASKGO:0097107postsynaptic density assembly1.38e-02
CASKGO:0010839negative regulation of keratinocyte proliferation1.43e-02
CASKGO:0046037GMP metabolic process1.43e-02
CASKGO:0098698postsynaptic specialization assembly1.43e-02
CASKGO:0009185ribonucleoside diphosphate metabolic process1.43e-02
CASKGO:0010996response to auditory stimulus1.43e-02
CASKGO:1904861excitatory synapse assembly1.43e-02
CASKGO:2000463positive regulation of excitatory postsynaptic potential1.43e-02
CASKGO:0090279regulation of calcium ion import1.43e-02
CASKGO:0060074synapse maturation1.43e-02
CASKGO:0051968positive regulation of synaptic transmissio3.71e-03
CASKGO:0097106postsynaptic density organization1.43e-02
CASKGO:0001941postsynaptic membrane organization1.43e-02
CASKGO:0099068postsynapse assembly1.43e-02
CASKGO:0001953negative regulation of cell-matrix adhesion1.43e-02
CASKGO:0009167purine ribonucleoside monophosphate metabolic process1.43e-02
CASKGO:0009126purine nucleoside monophosphate metabolic process1.45e-02
CASKGO:0099084postsynaptic specialization organization1.45e-02
CASKGO:2000300regulation of synaptic vesicle exocytosis1.45e-02
CASKGO:0010837regulation of keratinocyte proliferation1.49e-02
CASKGO:0070509calcium ion import1.49e-02
CASKGO:0098815modulation of excitatory postsynaptic potential1.49e-02
CASKGO:0050885neuromuscular process controlling balance1.51e-02
CASKGO:0035176social behavior1.51e-02
CASKGO:0051703biological process involved in intraspecies interaction between organisms1.53e-02
CASKGO:0043113receptor clustering1.56e-02
CASKGO:0009161ribonucleoside monophosphate metabolic process1.56e-02
CASKGO:0043616keratinocyte proliferation1.56e-02
CASKGO:0071709membrane assembly1.56e-02
CASKGO:0051965positive regulation of synapse assembly1.59e-02
CASKGO:0044091membrane biogenesis1.59e-02

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Related Drugs to CASK_BCDIN3D


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 CASK-BCDIN3D 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 CASK_BCDIN3D


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