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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:CALM2-STK39 (FusionGDB2 ID:HG805TG27347)

Fusion Gene Summary for CALM2-STK39

check button Fusion gene summary
Fusion gene informationFusion gene name: CALM2-STK39
Fusion gene ID: hg805tg27347
HgeneTgene
Gene symbol

CALM2

STK39

Gene ID

805

27347

Gene namecalmodulin 2serine/threonine kinase 39
SynonymsCALM|CALML2|CAM1|CAM3|CAMC|CAMII|CAMIII|LQT15|PHKD|PHKD2|caMDCHT|PASK|SPAK
Cytomap('CALM2')('STK39')

2p21

2q24.3

Type of geneprotein-codingprotein-coding
Descriptioncalmodulin-2Calmodulin-1Calmodulin-3LP7057 proteincalmodulin 2 (phosphorylase kinase, delta)phosphorylase kinase deltaphosphorylase kinase subunit deltaprepro-calmodulin 2STE20/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-li
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000272298, ENST00000409563, 
ENST00000484408, 
Fusion gene scores* DoF score17 X 13 X 4=88414 X 9 X 10=1260
# samples 1714
** MAII scorelog2(17/884*10)=-2.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/1260*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CALM2 [Title/Abstract] AND STK39 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCALM2(47403579)-STK39(168931741), # samples:1
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneCALM2

GO:0010880

regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum

20226167

HgeneCALM2

GO:0032516

positive regulation of phosphoprotein phosphatase activity

8631777

HgeneCALM2

GO:0035307

positive regulation of protein dephosphorylation

8631777

HgeneCALM2

GO:0051343

positive regulation of cyclic-nucleotide phosphodiesterase activity

8631777

HgeneCALM2

GO:0051592

response to calcium ion

7607248

HgeneCALM2

GO:0060315

negative regulation of ryanodine-sensitive calcium-release channel activity

26164367

HgeneCALM2

GO:0060316

positive regulation of ryanodine-sensitive calcium-release channel activity

20226167

TgeneSTK39

GO:0018105

peptidyl-serine phosphorylation

24393035

TgeneSTK39

GO:0018107

peptidyl-threonine phosphorylation

24393035

TgeneSTK39

GO:0023014

signal transduction by protein phosphorylation

24393035

TgeneSTK39

GO:0035556

intracellular signal transduction

24393035

TgeneSTK39

GO:1901017

negative regulation of potassium ion transmembrane transporter activity

24393035

TgeneSTK39

GO:1901380

negative regulation of potassium ion transmembrane transport

24393035

TgeneSTK39

GO:1905408

negative regulation of creatine transmembrane transporter activity

25531585

TgeneSTK39

GO:2000650

negative regulation of sodium ion transmembrane transporter activity

25531585



check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4Non-Cancer231NCALM2chr2

47403579

-STK39chr2

168931741

-


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Fusion Gene ORF analysis for CALM2-STK39

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5CDS-5UTRENST00000272298ENST00000355999CALM2chr2

47403579

-STK39chr2

168931741

-
5CDS-5UTRENST00000272298ENST00000487143CALM2chr2

47403579

-STK39chr2

168931741

-
5UTR-5UTRENST00000409563ENST00000355999CALM2chr2

47403579

-STK39chr2

168931741

-
5UTR-5UTRENST00000409563ENST00000487143CALM2chr2

47403579

-STK39chr2

168931741

-
intron-5UTRENST00000484408ENST00000355999CALM2chr2

47403579

-STK39chr2

168931741

-
intron-5UTRENST00000484408ENST00000487143CALM2chr2

47403579

-STK39chr2

168931741

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for CALM2-STK39


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for CALM2-STK39


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/:47403579/:168931741)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {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.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for CALM2-STK39


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for CALM2-STK39


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for CALM2-STK39


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for CALM2-STK39


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCALM2C4015695LONG QT SYNDROME 156CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCALM2C0011570Mental Depression5PSYGENET
HgeneCALM2C0011581Depressive disorder5PSYGENET
HgeneCALM2C0005586Bipolar Disorder2PSYGENET
HgeneCALM2C0035828Romano-Ward Syndrome2ORPHANET
HgeneCALM2C0006868Cannabis Abuse1CTD_human
HgeneCALM2C0006870Cannabis Dependence1CTD_human
HgeneCALM2C0009171Cocaine Abuse1CTD_human
HgeneCALM2C0018614Hashish Abuse1CTD_human
HgeneCALM2C0024809Marijuana Abuse1CTD_human
HgeneCALM2C0031391Phencyclidine Abuse1CTD_human
HgeneCALM2C0236735Cannabis-Related Disorder1CTD_human
HgeneCALM2C0236736Cocaine-Related Disorders1CTD_human
HgeneCALM2C0236742Phencyclidine-Related Disorders1CTD_human
HgeneCALM2C0588008Severe depression1PSYGENET
HgeneCALM2C0600427Cocaine Dependence1CTD_human
HgeneCALM2C1142166Brugada Syndrome (disorder)1ORPHANET
HgeneCALM2C1631597VENTRICULAR TACHYCARDIA, CATECHOLAMINERGIC POLYMORPHIC, 1 (disorder)1ORPHANET
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0152013Adenocarcinoma of lung (disorder)1CTD_human