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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:FARP1_STK24

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: FARP1_STK24
KinaseFusionDB ID: KFG2254
FusionGDB2.0 ID: KFG2254
HgeneTgene
Gene symbol

FARP1

STK24

Gene ID

10160

8428

Gene nameFERM, ARH/RhoGEF and pleckstrin domain protein 1serine/threonine kinase 24
SynonymsCDEP|FARP1-IT1|GLCC1|PLEKHC2|PPP1R75HEL-S-95|MST3|MST3B|STE20|STK3
Cytomap

13q32.2

13q32.2

Type of geneprotein-codingprotein-coding
DescriptionFERM, ARHGEF and pleckstrin domain-containing protein 1FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)FERM, RhoGEF and pleckstrin domain-containing protein 1PH domain-containing family C member 2chondrocyte-derived ezrin-liserine/threonine-protein kinase 24STE20-like kinase 3STE20-like kinase MST3epididymis secretory protein Li 95mammalian STE20-like protein kinase 3serine/threonine kinase 24 (STE20 homolog, yeast)sterile 20-like kinase 3
Modification date2024040720240411
UniProtAcc

Q9Y4F1

Q9Y6E0

Ensembl transtripts involved in fusion geneENST idsENST00000319562, ENST00000376581, 
ENST00000376586, ENST00000595437, 
ENST00000593990, 
ENST00000376547, 
ENST00000481288, ENST00000539966, 
ENST00000397517, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: FARP1 [Title/Abstract] AND STK24 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FARP1(98865667)-STK24(99171727), # samples:1
FARP1(98865667)-STK24(99134575), # samples:1
FARP1(98795746)-STK24(99171727), # 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
TgeneSTK24

GO:0006468

protein phosphorylation

19604147

TgeneSTK24

GO:0034599

cellular response to oxidative stress

22291017

TgeneSTK24

GO:0046777

protein autophosphorylation

17046825|17657516


check buttonKinase Fusion gene breakpoints across FARP1 (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 STK24 (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-Y8-A8RY-11AFARP1chr13

98865667

STK24chr13

99171727

ChimerDB4TCGA-CG-5730-11AFARP1chr13

98865667

STK24chr13

99134575

ChimerDB45357NFARP1chr13

98795746

STK24chr13

99171727



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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)
ENST00000595437ENST00000397517FARP1chr1398865667STK24chr13991717274636474

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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

>ENST00000595437_ENST00000397517_FARP1_chr13_98865667_STK24_chr13_99171727_length(amino acids)=474
MGEIEQRPTPGSRLGAPENSGISTLERGQKPPPTPSGKLVSIKIQMLDDTQEAFEVPNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQ
KVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHS
EKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKV
LFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDSSSEDSDAETDGQAS
GGSDSGDWIFTIREKDPKNLENGALQPSDLDRNKMKDIPKRPFSQCLSTIISPLFAELKEKSQACGGNLGSIEELRGAIYLAEEACPGIS

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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/chr13:98865667/chr13:99171727)
- 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
FARP1

Q9Y4F1

STK24

Q9Y6E0

FUNCTION: Functions as a guanine nucleotide exchange factor for RAC1. May play a role in semaphorin signaling. Plays a role in the assembly and disassembly of dendritic filopodia, the formation of dendritic spines, regulation of dendrite length and ultimately the formation of synapses (By similarity). {ECO:0000250}.FUNCTION: Serine/threonine-protein kinase that acts on both serine and threonine residues and promotes apoptosis in response to stress stimuli and caspase activation. Mediates oxidative-stress-induced cell death by modulating phosphorylation of JNK1-JNK2 (MAPK8 and MAPK9), p38 (MAPK11, MAPK12, MAPK13 and MAPK14) during oxidative stress. Plays a role in a staurosporine-induced caspase-independent apoptotic pathway by regulating the nuclear translocation of AIFM1 and ENDOG and the DNase activity associated with ENDOG. Phosphorylates STK38L on 'Thr-442' and stimulates its kinase activity. In association with STK26 negatively regulates Golgi reorientation in polarized cell migration upon RHO activation (PubMed:27807006). Regulates also cellular migration with alteration of PTPN12 activity and PXN phosphorylation: phosphorylates PTPN12 and inhibits its activity and may regulate PXN phosphorylation through PTPN12. May act as a key regulator of axon regeneration in the optic nerve and radial nerve. {ECO:0000269|PubMed:16314523, ECO:0000269|PubMed:17046825, ECO:0000269|PubMed:19604147, ECO:0000269|PubMed:19782762, ECO:0000269|PubMed:19855390, ECO:0000269|PubMed:27807006}.

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
TgeneFARP198865667STK2499171727ENST0000059543701136_28614432DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159
TgeneFARP198865667STK2499171727ENST0000059543701136_28626444DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159


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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 >>>193_FARP1_STK24ENST00000595437ENST00000397517FARP1chr1398865667STK24chr1399171727
MGEIEQRPTPGSRLGAPENSGISTLERGQKPPPTPSGKLVSIKIQMLDDTQEAFEVPNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQ
KVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHS
EKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKV
LFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDSSSEDSDAETDGQAS
GGSDSGDWIFTIREKDPKNLENGALQPSDLDRNKMKDIPKRPFSQCLSTIISPLFAELKEKSQACGGNLGSIEELRGAIYLAEEACPGIS
474
3D view using mol* of 193_FARP1_STK24
PDB file >>>TKFP_347_FARP1_STK24ENST00000595437ENST00000397517FARP1chr1398865667STK24chr1399171727
MGEIEQRPTPGSRLGAPENSGISTLERGQKPPPTPSGKLVSIKIQMLDDTQEAFEVPNLKADPEELFTKLEKIGKGSFGEVFKGIDNRTQ
KVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSPYVTKYYGSYLKDTKLWIIMEYLGGGSALDLLEPGPLDETQIATILREILKGLDYLHS
EKKIHRDIKAANVLLSEHGEVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIKQSAYDSKADIWSLGITAIELARGEPPHSELHPMKV
LFLIPKNNPPTLEGNYSKPLKEFVEACLNKEPSFRPTAKELLKHKFILRNAKKTSYLTELIDRYKRWKAEQSHDDSSSEDSDAETDGQAS
GGSDSGDWIFTIREKDPKNLENGALQPSDLDRNKMKDIPKRPFSQCLSTIISPLFAELKEKSQACGGNLGSIEELRGAIYLAEEACPGIS
474_FARP1_STK24


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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

FARP1_STK24 does not have any known PDB structures.

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pLDDT score distribution

all_data/KinaseFusionDB_T_Results/KinaseFusionDB_T_ViolinPlots/193_FARP1_STK24.png
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.
193_FARP1_STK24.png
all structure sitemap plddt3 193_FARP1_STK24.png
193_FARP1_STK24.png
all structure sitemap plddt4 193_FARP1_STK24.png


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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.

193_FARP1_STK24_ramachandran.png
all structure FARP1-STK24

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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
3'-kinase fusion protein case
all structure FARP1-STK24

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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
193_FARP1_STK24-DOCK_HTVS_1-001Trametinib-6.333019999999999-6.333019999999999-39.3533
193_FARP1_STK24-DOCK_HTVS_1-001Fostamatinib-5.89921-5.96281-48.7977
193_FARP1_STK24-DOCK_HTVS_1-001Fostamatinib-5.89921-5.96281-48.7977
193_FARP1_STK24-DOCK_HTVS_1-001Pexidartinib-5.84596-6.06276-5.92227
193_FARP1_STK24-DOCK_HTVS_1-001Pexidartinib-5.84596-6.06276-5.92227
193_FARP1_STK24-DOCK_HTVS_1-001Larotrectinib-5.7014-5.7014-41.293
193_FARP1_STK24-DOCK_HTVS_1-001Upadacitinib-5.53404-5.53504-33.7278
193_FARP1_STK24-DOCK_HTVS_1-001Tofacitinib-5.53291-5.54441-27.7621
193_FARP1_STK24-DOCK_HTVS_1-001Tofacitinib-5.53291-5.54441-27.7621
193_FARP1_STK24-DOCK_HTVS_1-001Capmatinib-5.50561-5.51121-38.1418
193_FARP1_STK24-DOCK_HTVS_1-001Upadacitinib-5.46148-5.46248-35.7265
193_FARP1_STK24-DOCK_HTVS_1-001Netarsudil-5.4239-5.435-49.2337
193_FARP1_STK24-DOCK_HTVS_1-001Netarsudil-5.4239-5.435-49.2337
193_FARP1_STK24-DOCK_HTVS_1-001Tofacitinib-5.3750800000000005-5.38658-27.3089
193_FARP1_STK24-DOCK_HTVS_1-001Tofacitinib-5.3750800000000005-5.38658-27.3089
193_FARP1_STK24-DOCK_HTVS_1-001Abrocitinib-5.34779-5.35889-34.7382
193_FARP1_STK24-DOCK_HTVS_1-001Abrocitinib-5.34779-5.35889-34.7382
193_FARP1_STK24-DOCK_HTVS_1-001Tucatinib-5.31004-5.68524-48.6199
193_FARP1_STK24-DOCK_HTVS_1-001Axitinib-5.25135-5.25455-38.3329
193_FARP1_STK24-DOCK_HTVS_1-001Nilotinib-5.23581-5.37541-48.8919

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Kinase-Substrate Information of FARP1_STK24


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
STK24Q9Y6E0humanPRKAA1Q13131T183sDGEFLRtsCGsPNyPkinase
STK24Q9Y6E0humanPPP1R14CQ8TAE6T73RHQQGKVtVkYDRKEPP1_inhibitor
STK24Q9Y6E0humanTAOK1Q7L7X3T440RNREHFAtIRtAsLV
STK24Q9Y6E0humanSIK2Q9H0K1T175kSGELLAtWCGSPPYPkinase
STK24Q9Y6E0humanRAB8AP61006T72AGQERFRtITTAyyRRas
STK24Q9Y6E0humanSTK24Q9Y6E0T190DtQIkRNtFVGtPFWPkinase
STK24Q9Y6E0humanSIK1P57059T182kSGEPLStWCGSPPYPkinase
STK24Q9Y6E0humanSIK3Q9Y2K2T221TPGQLLKtWCGSPPYPkinase
STK24Q9Y6E0humanSTK38LQ9Y2H1T442DWVFLNytyKRFEGLPkinase_C
STK24Q9Y6E0humanPRKAA2P54646T172sDGEFLRtsCGsPNyPkinase


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
STK24IDDescription0.00e+00
STK24GO:1901985positive regulation of protein acetylation1.01e-04
STK24GO:1901983regulation of protein acetylation2.52e-04
STK24GO:0046777protein autophosphorylation3.31e-04
STK24GO:1903943regulation of hepatocyte apoptotic process1.12e-03
STK24GO:1903432regulation of TORC1 signaling1.12e-03
STK24GO:0038202TORC1 signaling1.13e-03
STK24GO:0006473protein acetylation1.14e-03
STK24GO:0010506regulation of autophagy1.14e-03
STK24GO:0042752regulation of circadian rhythm1.14e-03
STK24GO:0071380cellular response to prostaglandin E stimulus1.14e-03
STK24GO:2000758positive regulation of peptidyl-lysine acetylation1.14e-03
STK24GO:0055089fatty acid homeostasis1.18e-03
STK24GO:0071379cellular response to prostaglandin stimulus1.30e-03
STK24GO:0090043regulation of tubulin deacetylation1.30e-03
STK24GO:0097284hepatocyte apoptotic process1.30e-03
STK24GO:0032006regulation of TOR signaling1.30e-03
STK24GO:0043543protein acylation1.30e-03
STK24GO:0045821positive regulation of glycolytic process1.34e-03
STK24GO:0090042tubulin deacetylation1.38e-03
STK24GO:0034695response to prostaglandin E1.38e-03
STK24GO:0070507regulation of microtubule cytoskeleton organization1.38e-03
STK24GO:0031929TOR signaling1.47e-03
STK24GO:2000756regulation of peptidyl-lysine acetylation1.65e-03
STK24GO:0009267cellular response to starvation1.65e-03
STK24GO:0006109regulation of carbohydrate metabolic process1.84e-03
STK24GO:0034063stress granule assembly1.86e-03
STK24GO:0034694response to prostaglandin1.91e-03
STK24GO:0007623circadian rhythm1.99e-03
STK24GO:0032869cellular response to insulin stimulus1.99e-03
STK24GO:0034389lipid droplet organization1.99e-03
STK24GO:0090311regulation of protein deacetylation1.99e-03
STK24GO:0042594response to starvation2.22e-03
STK24GO:0031669cellular response to nutrient levels3.27e-03
STK24GO:1904262negative regulation of TORC1 signaling3.29e-03
STK24GO:0032886regulation of microtubule-based process3.34e-03
STK24GO:0042149cellular response to glucose starvation3.51e-03
STK24GO:0032868response to insulin3.57e-03
STK24GO:0006110regulation of glycolytic process3.60e-03
STK24GO:0031668cellular response to extracellular stimulus3.85e-03
STK24GO:0006476protein deacetylation4.24e-03
STK24GO:0048511rhythmic process4.24e-03
STK24GO:0006695cholesterol biosynthetic process4.24e-03
STK24GO:1902653secondary alcohol biosynthetic process4.24e-03
STK24GO:0071375cellular response to peptide hormone stimulus4.37e-03
STK24GO:0043470regulation of carbohydrate catabolic process4.37e-03
STK24GO:0070050neuron cellular homeostasis4.37e-03
STK24GO:1904036negative regulation of epithelial cell apoptotic process4.41e-03
STK24GO:0016126sterol biosynthetic process4.59e-03
STK24GO:0035601protein deacylation4.59e-03

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Related Drugs to FARP1_STK24


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 FARP1-STK24 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 FARP1_STK24


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