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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:SUDS3_CDK4

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: SUDS3_CDK4
KinaseFusionDB ID: KFG6310
FusionGDB2.0 ID: KFG6310
HgeneTgene
Gene symbol

SUDS3

CDK4

Gene ID

64426

1019

Gene nameSDS3 homolog, SIN3A corepressor complex componentcyclin dependent kinase 4
SynonymsSAP45|SDS3CMM3|PSK-J3
Cytomap

12q24.23

12q14.1

Type of geneprotein-codingprotein-coding
Descriptionsin3 histone deacetylase corepressor complex component SDS345 kDa Sin3-associated polypeptidesin3A-associated protein, 45kDasuppressor of defective silencing 3 protein homologcyclin-dependent kinase 4cell division protein kinase 4
Modification date2024030520240416
UniProtAcc

Q9H7L9

P11802

Ensembl transtripts involved in fusion geneENST idsENST00000397564, ENST00000543473, 
ENST00000541280, 		ENST00000257904, 
ENST00000312990, ENST00000540325, 
ENST00000551888, ENST00000549606, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: SUDS3 [Title/Abstract] AND CDK4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SUDS3(118829087)-CDK4(58145519), # 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
HgeneSUDS3

GO:0006338

chromatin remodeling

21239494

TgeneCDK4

GO:0000082

G1/S transition of mitotic cell cycle

19237565

TgeneCDK4

GO:0006468

protein phosphorylation

8114739

TgeneCDK4

GO:0010971

positive regulation of G2/M transition of mitotic cell cycle

19124461

TgeneCDK4

GO:0051726

regulation of cell cycle

19124461


check buttonKinase Fusion gene breakpoints across SUDS3 (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 CDK4 (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
ChimerDB4TCGA-06-5856-01ASUDS3chr12

118829087

CDK4chr12

58145519



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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/:118829087/:58145519)
- 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
SUDS3

Q9H7L9

CDK4

P11802

FUNCTION: Regulatory protein which represses transcription and augments histone deacetylase activity of HDAC1. May have a potential role in tumor suppressor pathways through regulation of apoptosis. May function in the assembly and/or enzymatic activity of the mSin3A corepressor complex or in mediating interactions between the complex and other regulatory complexes. {ECO:0000269|PubMed:12724404, ECO:0000269|PubMed:21239494}.FUNCTION: Ser/Thr-kinase component of cyclin D-CDK4 (DC) complexes that phosphorylate and inhibit members of the retinoblastoma (RB) protein family including RB1 and regulate the cell-cycle during G(1)/S transition. Phosphorylation of RB1 allows dissociation of the transcription factor E2F from the RB/E2F complexes and the subsequent transcription of E2F target genes which are responsible for the progression through the G(1) phase. Hypophosphorylates RB1 in early G(1) phase. Cyclin D-CDK4 complexes are major integrators of various mitogenenic and antimitogenic signals. Also phosphorylates SMAD3 in a cell-cycle-dependent manner and represses its transcriptional activity. Component of the ternary complex, cyclin D/CDK4/CDKN1B, required for nuclear translocation and activity of the cyclin D-CDK4 complex. {ECO:0000269|PubMed:15241418, ECO:0000269|PubMed:18827403, ECO:0000269|PubMed:9003781}.

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 SUDS3_CDK4


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
CDK4P11802humanRB1P06400S780strPPtLsPIPHIPrRb_C
CDK4P11802humanTFEBP19484S467KASsRRssFsMEEGDDUF3371
CDK4P11802humanRBL2Q08999T401SKALRIStPLtGVRY
CDK4P11802humanTFEBP19484T331RVHGLPttsPsGMNMDUF3371
CDK4P11802humanFOXM1Q08050T510EDSSQsPtPRPKKSy
CDK4P11802humanCDC25AP30304S40ASAAGGLsPVTNLTV
CDK4P11802humanFOXO1Q12778S249EGGkSGksPrRrAAs
CDK4P11802humanTP73O15350T86AASASPYtPEHAASV
CDK4P11802humanDNMT1P26358S127VGMADANsPPKPLsk
CDK4P11802humanMEF2DQ14814S98KGFNGCDsPEPDGEDHJURP_C
CDK4P11802humanFOXM1Q08050T611ETLPISstPSkSVLP
CDK4P11802humanTSC2P49815S1452LPSssPRsPsGLrPr
CDK4P11802humanFOXM1Q08050S508sWEDSSQsPtPRPKK
CDK4P11802humanEGLN2Q96KS0S130EDGGDAPsPsKRPWA
CDK4P11802humanTCF3P15923S245PMLGGGSsPLPLPPG
CDK4P11802humanWDR77Q9BQA1S264CVTGLVFsPHSVPFL
CDK4P11802humanVCPP55072S664LkANLRksPVAkDVD
CDK4P11802humanDNMT1P26358S954TFNIKLSsPVkRPRkBAH
CDK4P11802humanTFEBP19484S211LVGVTSSsCPADLTQ
CDK4P11802humanRB1P06400T356DsFEtQRtPRksNLD
CDK4P11802humanFOXM1Q08050S522KSySGLRsPtRCVSE
CDK4P11802humanRB1P06400T826LPtPtkMtPRsRILVRb_C
CDK4P11802humanTCF3P15923S139LNsPGPLsPsGMKGT
CDK4P11802humanRBL2Q08999S672tLyDRySsPPAsTtR
CDK4P11802humanFLCNQ8NFG4S571HLMSTVRsPTASESR
CDK4P11802humanRB1P06400S795sPykFPssPLrIPGGRb_C
CDK4P11802humanRUNX3Q13761S356SSSGGDRsPTRMLASRunxI
CDK4P11802humanCELF1Q92879S302TSSGSsPsSSSSNSV
CDK4P11802humanRB1P06400T252PINGsPRtPRRGQNR
CDK4P11802humanRBL1P28749S975HIKQQPGsPRRIsQQRb_C
CDK4P11802humanRBL1P28749T369KRSFAPstPLtGRRY
CDK4P11802humanKAT2AQ92830T272LNYWKLEtPAQFRQRPCAF_N
CDK4P11802humanGATA4P43694S105AYTPPPVsPRFsFPGGATA-N
CDK4P11802humanRB1P06400S788PIPHIPrsPykFPssRb_C
CDK4P11802humanFOXM1Q08050T627tPEsWRLtPPAKVGG
CDK4P11802humanCDKN1AP38936S98GGRRPGTsPALLQGT
CDK4P11802humanRB1P06400S249AVIPINGsPRtPRRG
CDK4P11802humanSMAD3P84022T179PQSNIPEtPPPGYLS
CDK4P11802humanRBL2Q08999S1035NMDAPPLsPyPFVRt
CDK4P11802humanSMAD3P84022S213NLsPNPMsPAHNNLD
CDK4P11802humanRB1P06400S612MyLsPVRsPKKKGsT
CDK4P11802humanFLCNQ8NFG4S73GAsVEsssPGPKKSD
CDK4P11802humanFOXM1Q08050S704IDVPKPGsPEPQVSG
CDK4P11802humanTFEBP19484S142AGNsAPNsPMAMLHIMITF_TFEB_C_3_N
CDK4P11802humanRUNX2Q13950S465MVPGGDRsPSRMLPPRunxI
CDK4P11802humanRBL1P28749S640RRDMQPLsPIsVHER
CDK4P11802humanPELP1Q8IZL8S477ADALKLRsPRGsPDGNUC202
CDK4P11802humanCDKN1AP38936S130sGEQAEGsPGGPGDs
CDK4P11802humanFOXM1Q08050S489PPLEEWPsPAPSFkE
CDK4P11802humanSMAD3P84022S208DAGsPNLsPNPMsPA
CDK4P11802humanBRCA1P38398S632LVVSRNLsPPNCTEL
CDK4P11802humanTFEBP19484S114HIsPAQGsPkPPPAAMITF_TFEB_C_3_N
CDK4P11802humanSMAD3P84022S204NHSMDAGsPNLsPNP
CDK4P11802humanFOXM1Q08050S4____MKTsPRRPLIL
CDK4P11802humanKAT2AQ92830S372EEIYGANsPIWESGF
CDK4P11802humanTFE3P19532S246PTGSAPNsPMALLTIMITF_TFEB_C_3_N
CDK4P11802humanFLNAP21333S2152tRRRRAPsVANVGsHFilamin
CDK4P11802humanRB1P06400T373VNVIPPHtPVRTVMNRB_A
CDK4P11802humanSOD2P04179S106SIFWTNLsPNGGGEPSod_Fe_N
CDK4P11802humanRPRMQ9NS64S98LVKDRRPsKEVEAVV
CDK4P11802humanMDM4O15151S314TECKKFNsPSKRYCFzf-RanBP
CDK4P11802humanFOXM1Q08050T600EVGGPFKtPIkETLP
CDK4P11802humanTP53P04637R249CMGGMNRrPILTIITP53
CDK4P11802humanRBL1P28749S964MMDAPPLsPFPHIKQRb_C
CDK4P11802humanVCPP55072T509kFLkFGMtPskGVLF
CDK4P11802humanTOB2Q14106S254PAPQSQLsPNAKEFVPAM2
CDK4P11802humanRB1P06400S608tAADMyLsPVRsPKK
CDK4P11802humanRB1P06400S807PGGNIyIsPLksPykRb_C
CDK4P11802humanFLNAP21333S1459kCsGPGLsPGMVRANFilamin
CDK4P11802humanSMAD3P84022T8MSSILPFtPPIVkRL
CDK4P11802humanFOXM1Q08050T620SkSVLPRtPEsWRLt
CDK4P11802humanWDR77Q9BQA1S306FVRDATWsPLNHSLL
CDK4P11802humanSPOPO43791S6__MSRVPsPPPPAEM
CDK4P11802humanRASSF1Q9NS23-2S203TsVRRRtsFYLPKDARA
CDK4P11802humanTSC2P49815S1217MSLENPLsPFSSDIN
CDK4P11802humanRB1P06400S811IyIsPLksPykIsEGRb_C
CDK4P11802humanWDR77Q9BQA1T5___MRkEtPPPLVPP
CDK4P11802humanFOXM1Q08050S451LLFGEGFsPLLPVQT
CDK4P11802humanMEF2DQ14814S110GEDsLEQsPLLEDKyHJURP_C
CDK4P11802humanFLCNQ8NFG4S62NSRMRAHsPAEGAsV
CDK4P11802humanFOXM1Q08050S35SEEEPKRsPAQQEsN


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
CDK4IDDescription0.00e+00
CDK4GO:0031667response to nutrient levels1.70e-05
CDK4GO:2000377regulation of reactive oxygen species metabolic process1.84e-04
CDK4GO:2000134negative regulation of G1/S transition of mitotic cell cycle1.95e-04
CDK4GO:0045786negative regulation of cell cycle1.95e-04
CDK4GO:1902807negative regulation of cell cycle G1/S phase transition1.95e-04
CDK4GO:0009267cellular response to starvation1.95e-04
CDK4GO:0008630intrinsic apoptotic signaling pathway in response to DNA damage2.11e-04
CDK4GO:1901991negative regulation of mitotic cell cycle phase transition2.11e-04
CDK4GO:0097193intrinsic apoptotic signaling pathway2.11e-04
CDK4GO:0010948negative regulation of cell cycle process2.11e-04
CDK4GO:0044772mitotic cell cycle phase transition2.11e-04
CDK4GO:0051216cartilage development2.28e-04
CDK4GO:0002062chondrocyte differentiation2.42e-04
CDK4GO:0070482response to oxygen levels2.46e-04
CDK4GO:0042594response to starvation2.46e-04
CDK4GO:0009895negative regulation of catabolic process2.47e-04
CDK4GO:1901990regulation of mitotic cell cycle phase transition2.60e-04
CDK4GO:0072593reactive oxygen species metabolic process3.09e-04
CDK4GO:0045599negative regulation of fat cell differentiation3.40e-04
CDK4GO:0006978DNA damage respons4.28e-06
CDK4GO:0045930negative regulation of mitotic cell cycle3.40e-04
CDK4GO:0042772DNA damage respons5.08e-06
CDK4GO:0000082G1/S transition of mitotic cell cycle3.40e-04
CDK4GO:0055093response to hyperoxia3.61e-04
CDK4GO:0045598regulation of fat cell differentiation3.61e-04
CDK4GO:0044839cell cycle G2/M phase transition4.66e-04
CDK4GO:0030330DNA damage respons8.75e-06
CDK4GO:0044843cell cycle G1/S phase transition4.79e-04
CDK4GO:0006606protein import into nucleus4.79e-04
CDK4GO:0031668cellular response to extracellular stimulus4.79e-04
CDK4GO:0060537muscle tissue development4.79e-04
CDK4GO:0061448connective tissue development4.91e-04
CDK4GO:0051170import into nucleus5.05e-04
CDK4GO:1901987regulation of cell cycle phase transition6.15e-04
CDK4GO:0072331signal transduction by p53 class mediator6.18e-04
CDK4GO:0036296response to increased oxygen levels6.20e-04
CDK4GO:0010660regulation of muscle cell apoptotic process6.20e-04
CDK4GO:0034504protein localization to nucleus6.75e-04
CDK4GO:2000045regulation of G1/S transition of mitotic cell cycle6.94e-04
CDK4GO:0050673epithelial cell proliferation7.37e-04
CDK4GO:0010657muscle cell apoptotic process7.40e-04
CDK4GO:0030308negative regulation of cell growth7.40e-04
CDK4GO:0042770signal transduction in response to DNA damage7.40e-04
CDK4GO:0007264small GTPase mediated signal transduction7.73e-04
CDK4GO:1904705regulation of vascular associated smooth muscle cell proliferation7.73e-04
CDK4GO:0016049cell growth8.07e-04
CDK4GO:1990874vascular associated smooth muscle cell proliferation8.07e-04
CDK4GO:0062012regulation of small molecule metabolic process8.69e-04
CDK4GO:0007265Ras protein signal transduction9.11e-04

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Related Drugs to SUDS3_CDK4


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 SUDS3-CDK4 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 SUDS3_CDK4


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