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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:STK10_SNX2

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: STK10_SNX2
KinaseFusionDB ID: KFG6123
FusionGDB2.0 ID: KFG6123
HgeneTgene
Gene symbol

STK10

SNX2

Gene ID

6793

6643

Gene nameserine/threonine kinase 10sorting nexin 2
SynonymsLOK|PRO2729TRG-9
Cytomap

5q35.1

5q23.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase 10lymphocyte-oriented kinasesorting nexin-2CTB-36H16.2transformation-related gene 9 protein
Modification date2024030520240305
UniProtAcc

O94804

Q9Y343

Ensembl transtripts involved in fusion geneENST idsENST00000176763, ENST00000517775, 
ENST00000510372, ENST00000379516, 
ENST00000514949, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: STK10 [Title/Abstract] AND SNX2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)STK10(171614891)-SNX2(122161745), # samples:3
check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneSTK10

GO:0046777

protein autophosphorylation

12639966|18239682

TgeneSNX2

GO:0072673

lamellipodium morphogenesis

20604901


check buttonKinase Fusion gene breakpoints across STK10 (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 SNX2 (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-AB-2875-03ASTK10chr5

171509329

SNX2chr5

122153043

ChimerDB4TCGA-BH-A0HL-01ASTK10chr5

171614891

SNX2chr5

122161745

ChimerDB4TCGA-BH-A0HLSTK10chr5

171614890

SNX2chr5

122161744



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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)
ENST00000176763ENST00000379516STK10chr5171509329SNX2chr51221530433372961

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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

>ENST00000176763_ENST00000379516_STK10_chr5_171509329_SNX2_chr5_122153043_length(amino acids)=961
MERVRGSRRQGWAGQELRGRHKGGGPGDLTGRGRGRARRRLRGSGCSRRGAAQGTLDRGRAAGKGGSGENPERRGVLQLLLLLLAAAEAT
ARARARARAGATAPPAMAFANFRRILRLSTFEKRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEE
LEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVL
MTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDP
PTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVMEEIEDGRDEGEEEDAVDAASTLENHTQNS
SEVSPPSLNADKPLEESPSTPLAPSQSQDSVNEPCSQPSGDRSLQTTSPPVVAPGNENGLAVPVPLRKSRPVSMDARIQVAQEKQVAEQG
GDLSPAANRSQKASQSRPNSSALETLGGEKLANGSLEPPAQAAPGPSKRDSDCSSLCTSESMDYGTNLSTDLSLNKEMGSLSIKDPKLYK
KTLKRTRKFVVDGVEVSITTSKIISEDEKKDEEMRFLRRQELRELRLLQKEEHRNQTQLSNKHELQLEQMHKRFEQEINAKKKFFDTELE
NLERQQKQQVEKMEQDHAVRRREEARRIRLEQDRDYTRFQEQLKLMKKEEALVCHRKELSANTAAFAKSAAMLGNSEDHTALSRALSQLA
EVEEKIDQLHQEQAFADFYMFSELLSDYIRLIAAVKGVFDHRMKCWQKWEDAQITLLKKREAEAKMMVANKPDKIQQAKNEIREWEAKVQ

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

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/chr5:171614891/chr5:122161745)
- 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
STK10

O94804

SNX2

Q9Y343

FUNCTION: Serine/threonine-protein kinase involved in regulation of lymphocyte migration. Phosphorylates MSN, and possibly PLK1. Involved in regulation of lymphocyte migration by mediating phosphorylation of ERM proteins such as MSN. Acts as a negative regulator of MAP3K1/MEKK1. May also act as a cell cycle regulator by acting as a polo kinase kinase: mediates phosphorylation of PLK1 in vitro; however such data require additional evidences in vivo. {ECO:0000269|PubMed:11903060, ECO:0000269|PubMed:12639966, ECO:0000269|PubMed:19255442}.FUNCTION: May be involved in several stages of intracellular trafficking. {ECO:0000250}.

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).
663
PartnerHgeneeneHbpTgeneeneTbpENSTBPexonTotalExonProtein feature lociBPlociTotalLenFeatureNote
HgeneSTK10171509329SNX2122153043ENST00000176763121936_2941969DomainNote=Protein kinase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00159


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 >>>257_STK10_SNX2ENST00000176763ENST00000379516STK10chr5171509329SNX2chr5122153043
MERVRGSRRQGWAGQELRGRHKGGGPGDLTGRGRGRARRRLRGSGCSRRGAAQGTLDRGRAAGKGGSGENPERRGVLQLLLLLLAAAEAT
ARARARARAGATAPPAMAFANFRRILRLSTFEKRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEE
LEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVL
MTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDP
PTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVMEEIEDGRDEGEEEDAVDAASTLENHTQNS
SEVSPPSLNADKPLEESPSTPLAPSQSQDSVNEPCSQPSGDRSLQTTSPPVVAPGNENGLAVPVPLRKSRPVSMDARIQVAQEKQVAEQG
GDLSPAANRSQKASQSRPNSSALETLGGEKLANGSLEPPAQAAPGPSKRDSDCSSLCTSESMDYGTNLSTDLSLNKEMGSLSIKDPKLYK
KTLKRTRKFVVDGVEVSITTSKIISEDEKKDEEMRFLRRQELRELRLLQKEEHRNQTQLSNKHELQLEQMHKRFEQEINAKKKFFDTELE
NLERQQKQQVEKMEQDHAVRRREEARRIRLEQDRDYTRFQEQLKLMKKEEALVCHRKELSANTAAFAKSAAMLGNSEDHTALSRALSQLA
EVEEKIDQLHQEQAFADFYMFSELLSDYIRLIAAVKGVFDHRMKCWQKWEDAQITLLKKREAEAKMMVANKPDKIQQAKNEIREWEAKVQ
961
3D view using mol* of 257_STK10_SNX2
PDB file >>>HKFP_377_STK10_SNX2ENST00000176763ENST00000379516STK10chr5171509329SNX2chr5122153043
MERVRGSRRQGWAGQELRGRHKGGGPGDLTGRGRGRARRRLRGSGCSRRGAAQGTLDRGRAAGKGGSGENPERRGVLQLLLLLLAAAEAT
ARARARARAGATAPPAMAFANFRRILRLSTFEKRKSREYEHVRRDLDPNEVWEIVGELGDGAFGKVYKAKNKETGALAAAKVIETKSEEE
LEDYIVEIEILATCDHPYIVKLLGAYYHDGKLWIMIEFCPGGAVDAIMLELDRGLTEPQIQVVCRQMLEALNFLHSKRIIHRDLKAGNVL
MTLEGDIRLADFGVSAKNLKTLQKRDSFIGTPYWMAPEVVMCETMKDTPYDYKADIWSLGITLIEMAQIEPPHHELNPMRVLLKIAKSDP
PTLLTPSKWSVEFRDFLKIALDKNPETRPSAAQLLEHPFVSSITSNKALRELVAEAKAEVMEEIEDGRDEGEEEDAVDAASTLENHTQNS
SEVSPPSLNADKPLEESPSTPLAPSQSQDSVNEPCSQPSGDRSLQTTSPPVVAPGNENGLAVPVPLRKSRPVSMDARIQVAQEKQVAEQG
GDLSPAANRSQKASQSRPNSSALETLGGEKLANGSLEPPAQAAPGPSKRDSDCSSLCTSESMDYGTNLSTDLSLNKEMGSLSIKDPKLYK
KTLKRTRKFVVDGVEVSITTSKIISEDEKKDEEMRFLRRQELRELRLLQKEEHRNQTQLSNKHELQLEQMHKRFEQEINAKKKFFDTELE
NLERQQKQQVEKMEQDHAVRRREEARRIRLEQDRDYTRFQEQLKLMKKEEALVCHRKELSANTAAFAKSAAMLGNSEDHTALSRALSQLA
EVEEKIDQLHQEQAFADFYMFSELLSDYIRLIAAVKGVFDHRMKCWQKWEDAQITLLKKREAEAKMMVANKPDKIQQAKNEIREWEAKVQ
961_STK10_SNX2


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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

STK10_SNX2 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.
257_STK10_SNX2.png
all structure sitemap plddt 257_STK10_SNX2.png
257_STK10_SNX2.png
all structure sitemap plddt2 257_STK10_SNX2.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.

257_STK10_SNX2_ramachandran.png
all structure STK10-SNX2

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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 STK10-SNX2
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
257_STK10_SNX2-DOCK_HTVS_1-001Lapatinib-6.9249600000000004-7.01376-39.9452
257_STK10_SNX2-DOCK_HTVS_1-001Lapatinib-6.75201-6.84081-38.6337
257_STK10_SNX2-DOCK_HTVS_1-001Ponatinib-6.58863-6.79523-40.9093
257_STK10_SNX2-DOCK_HTVS_1-001Ponatinib-6.58863-6.79523-40.9093
257_STK10_SNX2-DOCK_HTVS_1-001Ponatinib-6.58863-6.79523-40.9093
257_STK10_SNX2-DOCK_HTVS_1-001Upadacitinib-6.564960000000001-6.5659600000000005-29.4436
257_STK10_SNX2-DOCK_HTVS_1-001Netarsudil-6.45158-6.462680000000001-42.1469
257_STK10_SNX2-DOCK_HTVS_1-001Netarsudil-6.45158-6.462680000000001-42.1469
257_STK10_SNX2-DOCK_HTVS_1-001Pacritinib-6.26082-6.2659199999999995-44.4561
257_STK10_SNX2-DOCK_HTVS_1-001Pexidartinib-6.23682-6.45362-31.2789
257_STK10_SNX2-DOCK_HTVS_1-001Pexidartinib-6.23682-6.45362-31.2789
257_STK10_SNX2-DOCK_HTVS_1-001Tepotinib-6.19219-6.19329-53.7964
257_STK10_SNX2-DOCK_HTVS_1-001Upadacitinib-5.95908-5.9600800000000005-25.447
257_STK10_SNX2-DOCK_HTVS_1-001Upadacitinib-5.94602-5.947019999999999-27.5244
257_STK10_SNX2-DOCK_HTVS_1-001Gilteritinib-5.945069999999999-5.97147-51.0447
257_STK10_SNX2-DOCK_HTVS_1-001Gilteritinib-5.945069999999999-5.97147-51.0447
257_STK10_SNX2-DOCK_HTVS_1-001Pralsetinib-5.78596-5.87746-55.9459
257_STK10_SNX2-DOCK_HTVS_1-001Ponatinib-5.730919999999999-6.48562-44.9637
257_STK10_SNX2-DOCK_HTVS_1-001Ponatinib-5.730919999999999-6.48562-44.9637
257_STK10_SNX2-DOCK_HTVS_1-001Ponatinib-5.730919999999999-6.48562-44.9637

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Kinase-Substrate Information of STK10_SNX2


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
STK10O94804humanRDXP35241T564AGRDKyKtLRQIRQGERM_C
STK10O94804humanEZRP15311T567QGRDkyKtLRQIRQGERM_C
STK10O94804humanPLK1P53350T210YDGERKktLCGtPNyPkinase
STK10O94804humanMSNP26038T558LGRDKyKtLRQIRQGERM_C


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
STK10IDDescription0.00e+00
STK10GO:1902946protein localization to early endosome1.25e-07
STK10GO:1905668positive regulation of protein localization to endosome1.25e-07
STK10GO:1905666regulation of protein localization to endosome1.25e-07
STK10GO:1903651positive regulation of cytoplasmic transport1.49e-07
STK10GO:2000641regulation of early endosome to late endosome transport2.54e-07
STK10GO:0036010protein localization to endosome6.39e-07
STK10GO:0045732positive regulation of protein catabolic process7.22e-07
STK10GO:1902115regulation of organelle assembly7.22e-07
STK10GO:1903649regulation of cytoplasmic transport7.22e-07
STK10GO:0045022early endosome to late endosome transport1.73e-06
STK10GO:0061028establishment of endothelial barrier2.01e-06
STK10GO:0098927vesicle-mediated transport between endosomal compartments2.01e-06
STK10GO:0042176regulation of protein catabolic process3.85e-06
STK10GO:0001885endothelial cell development3.89e-06
STK10GO:1903829positive regulation of protein localization9.79e-06
STK10GO:0045446endothelial cell differentiation2.53e-05
STK10GO:0008360regulation of cell shape3.43e-05
STK10GO:0003158endothelium development3.46e-05
STK10GO:0072697protein localization to cell cortex3.58e-05
STK10GO:0016482cytosolic transport6.43e-05
STK10GO:0032388positive regulation of intracellular transport8.26e-05
STK10GO:0002064epithelial cell development9.52e-05
STK10GO:0022604regulation of cell morphogenesis1.40e-04
STK10GO:0032386regulation of intracellular transport3.38e-04
STK10GO:0010737protein kinase A signaling3.47e-04
STK10GO:1990778protein localization to cell periphery3.61e-04
STK10GO:0032535regulation of cellular component size4.01e-04
STK10GO:0140694non-membrane-bounded organelle assembly5.18e-04
STK10GO:0022406membrane docking1.77e-03
STK10GO:1904375regulation of protein localization to cell periphery3.80e-03
STK10GO:0030010establishment of cell polarity4.77e-03
STK10GO:0051017actin filament bundle assembly4.92e-03
STK10GO:0061572actin filament bundle organization5.01e-03
STK10GO:0008361regulation of cell size6.24e-03
STK10GO:0007051spindle organization7.07e-03
STK10GO:0007163establishment or maintenance of cell polarity8.75e-03
STK10GO:0072659protein localization to plasma membrane1.37e-02
STK10GO:1901990regulation of mitotic cell cycle phase transition1.84e-02
STK10GO:0030953astral microtubule organization1.84e-02
STK10GO:0051081nuclear membrane disassembly1.84e-02
STK10GO:0051660establishment of centrosome localization1.84e-02
STK10GO:0071803positive regulation of podosome assembly1.84e-02
STK10GO:0010639negative regulation of organelle organization1.84e-02
STK10GO:0030397membrane disassembly1.94e-02
STK10GO:0034111negative regulation of homotypic cell-cell adhesion1.97e-02
STK10GO:0071394cellular response to testosterone stimulus1.97e-02
STK10GO:0032530regulation of microvillus organization1.97e-02
STK10GO:0032536regulation of cell projection size1.97e-02
STK10GO:0070486leukocyte aggregation1.97e-02

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Related Drugs to STK10_SNX2


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 STK10-SNX2 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 STK10_SNX2


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