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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:STK39_PARVA

Kinase Fusion Protein Summary

check button Kinase Fusion gene summary
Kinase Fusion partner gene informationKinase Fusion gene name: STK39_PARVA
KinaseFusionDB ID: KFG6231
FusionGDB2.0 ID: KFG6231
HgeneTgene
Gene symbol

STK39

PARVA

Gene ID

27347

55742

Gene nameserine/threonine kinase 39parvin alpha
SynonymsDCHT|PASK|SPAKCH-ILKBP|MXRA2
Cytomap

2q24.3

11p15.3

Type of geneprotein-codingprotein-coding
DescriptionSTE20/SPS1-related proline-alanine-rich protein kinaseSTE20/SPS1 homologSte20-like protein kinaseproline-alanine-rich STE20-related kinaseserine threonine kinase 39 (STE20/SPS1 homolog, yeast)serine/threonine-protein kinase 39small intestine SPAK-lialpha-parvinactopaxincalponin-like integrin-linked kinase-binding proteinmatrix-remodeling-associated protein 2
Modification date2024041120240411
UniProtAcc

Q9UEW8

Q9NVD7

Ensembl transtripts involved in fusion geneENST idsENST00000355999, ENST00000487143, 
ENST00000526746, ENST00000538608, 
ENST00000334956, ENST00000539723, 
ENST00000550549, 
Context (manual curation of fusion genes in KinaseFusionDB)

PubMed: STK39 [Title/Abstract] AND PARVA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)STK39(169103738)-PARVA(12495292), # 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
HgeneSTK39

GO:0006884

cell volume homeostasis

36318922

HgeneSTK39

GO:0007165

signal transduction

24393035

HgeneSTK39

GO:0018105

peptidyl-serine phosphorylation

24393035

HgeneSTK39

GO:0018107

peptidyl-threonine phosphorylation

24393035

HgeneSTK39

GO:0035556

intracellular signal transduction

24393035

HgeneSTK39

GO:0070294

renal sodium ion absorption

18270262

HgeneSTK39

GO:0071474

cellular hyperosmotic response

36318922

HgeneSTK39

GO:0071476

cellular hypotonic response

24393035

HgeneSTK39

GO:1901017

negative regulation of potassium ion transmembrane transporter activity

24393035

HgeneSTK39

GO:1901380

negative regulation of potassium ion transmembrane transport

24393035

HgeneSTK39

GO:1905408

negative regulation of creatine transmembrane transporter activity

25531585

HgeneSTK39

GO:2000650

negative regulation of sodium ion transmembrane transporter activity

25531585


check buttonKinase Fusion gene breakpoints across STK39 (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 PARVA (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-QK-A6IG-01ASTK39chr2

169103738

PARVAchr11

12495292



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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/:169103738/:12495292)
- 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
STK39

Q9UEW8

PARVA

Q9NVD7

FUNCTION: Effector serine/threonine-protein kinase component of the WNK-SPAK/OSR1 kinase cascade, which is involved in various processes, such as ion transport, response to hypertonic stress and blood pressure (PubMed:16669787, PubMed:18270262, PubMed:21321328, PubMed:34289367). Specifically recognizes and binds proteins with a RFXV motif (PubMed:16669787, PubMed:21321328). Acts downstream of WNK kinases (WNK1, WNK2, WNK3 or WNK4): following activation by WNK kinases, catalyzes phosphorylation of ion cotransporters, such as SLC12A1/NKCC2, SLC12A2/NKCC1, SLC12A3/NCC, SLC12A5/KCC2 or SLC12A6/KCC3, regulating their activity (PubMed:21321328). Mediates regulatory volume increase in response to hyperosmotic stress by catalyzing phosphorylation of ion cotransporters SLC12A1/NKCC2, SLC12A2/NKCC1 and SLC12A6/KCC3 downstream of WNK1 and WNK3 kinases (PubMed:12740379, PubMed:16669787, PubMed:21321328). Phosphorylation of Na-K-Cl cotransporters SLC12A2/NKCC1 and SLC12A2/NKCC1 promote their activation and ion influx; simultaneously, phosphorylation of K-Cl cotransporters SLC12A5/KCC2 and SLC12A6/KCC3 inhibit their activity, blocking ion efflux (PubMed:16669787, PubMed:19665974, PubMed:21321328). Acts as a regulator of NaCl reabsorption in the distal nephron by mediating phosphorylation and activation of the thiazide-sensitive Na-Cl cotransporter SLC12A3/NCC in distal convoluted tubule cells of kidney downstream of WNK4 (PubMed:18270262). Mediates the inhibition of SLC4A4, SLC26A6 as well as CFTR activities (By similarity). Phosphorylates RELT (By similarity). {ECO:0000250|UniProtKB:Q9Z1W9, ECO:0000269|PubMed:12740379, ECO:0000269|PubMed:16669787, ECO:0000269|PubMed:18270262, ECO:0000269|PubMed:19665974, ECO:0000269|PubMed:21321328, ECO:0000269|PubMed:34289367}.FUNCTION: Plays a role in sarcomere organization and in smooth muscle cell contraction. Required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. Plays a role in sprouting angiogenesis and is required for normal adhesion of vascular smooth muscle cells to endothelial cells during blood vessel development (By similarity). Plays a role in the reorganization of the actin cytoskeleton, formation of lamellipodia and ciliogenesis. Plays a role in the establishment of cell polarity, cell adhesion, cell spreading, and directed cell migration. {ECO:0000250, ECO:0000269|PubMed:11134073, ECO:0000269|PubMed:11331308, ECO:0000269|PubMed:15284246, ECO:0000269|PubMed:20393563}.

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 STK39_PARVA


check button Phosphorylation target of the kinase
(phosphosite, 03-17-2024)
KinaseKinase UniProt AccKinase speciesSubstrateSubstrate UniProt AccSubstrate phosphorylated residuesSubstrate phosphorylated sites (+/-7AA)Domain
STK39Q9UEW8humanSLC12A1Q13621T105LQtFGHNtMDAVPKIAA_permease_N
STK39Q9UEW8humanSLC4A4Q9Y6R1S65ERIsENysDKsDIEN
STK39Q9UEW8humanSLC12A2P55011T207YYDtHTNtyYLRtFGAA_permease_N
STK39Q9UEW8humanSLC12A2P55011T203HQHYYYDtHTNtyYLAA_permease_N
STK39Q9UEW8humanSLC12A6Q9UHW9T1048YQEKVHMtWTKDKYMSLC12
STK39Q9UEW8humanSLC12A1Q13621T95AYDsHTNtYYLQtFGAA_permease_N
STK39Q9UEW8humanSLC12A6Q9UHW9S96IEDLSQNsITGEHSQ
STK39Q9UEW8humanSLC12A1Q13621T100TNtYYLQtFGHNtMDAA_permease_N
STK39Q9UEW8humanSLC12A3P55017T60MRtFGYNtIDVVPtYAA_permease_N
STK39Q9UEW8humanSLC12A3P55017T46SSHPSHLtHSStFCMAA_permease_N
STK39Q9UEW8humanSLC12A3P55017T55SStFCMRtFGYNtIDAA_permease_N
STK39Q9UEW8humanSNAI1O95863T203QGHVRtHtGEkPFSC
STK39Q9UEW8humanSLC12A2P55011T212TNtyYLRtFGHNtMDAA_permease_N


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
STK39IDDescription0.00e+00
STK39GO:0055064chloride ion homeostasis2.10e-09
STK39GO:0055081monoatomic anion homeostasis2.10e-09
STK39GO:0055075potassium ion homeostasis7.89e-09
STK39GO:0006884cell volume homeostasis7.89e-09
STK39GO:0098656monoatomic anion transmembrane transport7.89e-09
STK39GO:0015698inorganic anion transport1.25e-08
STK39GO:0006820monoatomic anion transport1.25e-08
STK39GO:1990573potassium ion import across plasma membrane1.43e-08
STK39GO:1902476chloride transmembrane transport4.46e-07
STK39GO:0006821chloride transport6.73e-07
STK39GO:0098661inorganic anion transmembrane transport7.39e-07
STK39GO:0098659inorganic cation import across plasma membrane7.49e-07
STK39GO:0099587inorganic ion import across plasma membrane7.49e-07
STK39GO:0035725sodium ion transmembrane transport2.09e-06
STK39GO:0008361regulation of cell size2.27e-06
STK39GO:0098739import across plasma membrane3.52e-06
STK39GO:0071805potassium ion transmembrane transport3.64e-06
STK39GO:0055078sodium ion homeostasis3.70e-06
STK39GO:0006813potassium ion transport4.96e-06
STK39GO:0006814sodium ion transport5.28e-06
STK39GO:0032535regulation of cellular component size2.49e-05
STK39GO:0072488ammonium transmembrane transport6.23e-05
STK39GO:0006970response to osmotic stress2.90e-03
STK39GO:0010232vascular transport3.08e-03
STK39GO:0150104transport across blood-brain barrier3.08e-03
STK39GO:0071241cellular response to inorganic substance2.02e-02
STK39GO:0003018vascular process in circulatory system2.40e-02
STK39GO:0030002intracellular monoatomic anion homeostasis2.40e-02
STK39GO:0030644intracellular chloride ion homeostasis2.40e-02
STK39GO:0042368vitamin D biosynthetic process2.40e-02
STK39GO:0060536cartilage morphogenesis2.40e-02
STK39GO:0061314Notch signaling involved in heart development2.40e-02
STK39GO:0071476cellular hypotonic response2.40e-02
STK39GO:1904464regulation of matrix metallopeptidase secretion2.40e-02
STK39GO:1990773matrix metallopeptidase secretion2.40e-02
STK39GO:0030656regulation of vitamin metabolic process2.40e-02
STK39GO:0060707trophoblast giant cell differentiation2.40e-02
STK39GO:0006971hypotonic response2.40e-02
STK39GO:0035865cellular response to potassium ion2.40e-02
STK39GO:0042362fat-soluble vitamin biosynthetic process2.40e-02
STK39GO:0070294renal sodium ion absorption2.40e-02
STK39GO:0061043regulation of vascular wound healing2.40e-02
STK39GO:0071472cellular response to salt stress2.40e-02
STK39GO:0098814spontaneous synaptic transmission2.40e-02
STK39GO:0062012regulation of small molecule metabolic process2.40e-02
STK39GO:0003198epithelial to mesenchymal transition involved in endocardial cushion formation2.40e-02
STK39GO:0030007intracellular potassium ion homeostasis2.40e-02
STK39GO:0036376sodium ion export across plasma membrane2.40e-02
STK39GO:0043518negative regulation of DNA damage respons4.76e-03

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Related Drugs to STK39_PARVA


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 STK39-PARVA 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 STK39_PARVA


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