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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:MTA3-KCNMA1 (FusionGDB2 ID:HG57504TG3778)

Fusion Gene Summary for MTA3-KCNMA1

check button Fusion gene summary
Fusion gene informationFusion gene name: MTA3-KCNMA1
Fusion gene ID: hg57504tg3778
HgeneTgene
Gene symbol

MTA3

KCNMA1

Gene ID

57504

3778

Gene namemetastasis associated 1 family member 3potassium calcium-activated channel subfamily M alpha 1
Synonyms-BKTM|CADEDS|IEG16|KCa1.1|LIWAS|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1
Cytomap('MTA3')('KCNMA1')

2p21

10q22.3

Type of geneprotein-codingprotein-coding
Descriptionmetastasis-associated protein MTA3metastasis associated gene family, member 3calcium-activated potassium channel subunit alpha-1uncharacterized proteinBK channel alpha subunitBKCA alpha subunitbig potassium channel alpha subunitcalcium-activated potassium channel, subfamily M subunit alpha-1k(VCA)alphamaxi-K channel HSLOpo
Modification date2020031320200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000405094, ENST00000405592, 
ENST00000406652, ENST00000406911, 
ENST00000407270, ENST00000472767, 
Fusion gene scores* DoF score10 X 10 X 3=30018 X 17 X 8=2448
# samples 1121
** MAII scorelog2(11/300*10)=-1.44745897697122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/2448*10)=-3.54314232502653
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MTA3 [Title/Abstract] AND KCNMA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMTA3(42952029)-KCNMA1(78762955), # 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
TgeneKCNMA1

GO:0001666

response to hypoxia

15528406

TgeneKCNMA1

GO:0006813

potassium ion transport

7573516|7877450|11245614|12388065|17706472|18458941

TgeneKCNMA1

GO:0006970

response to osmotic stress

10840032|12388065

TgeneKCNMA1

GO:0030007

cellular potassium ion homeostasis

11245614

TgeneKCNMA1

GO:0034465

response to carbon monoxide

15528406

TgeneKCNMA1

GO:0042391

regulation of membrane potential

7877450|7993625

TgeneKCNMA1

GO:0045794

negative regulation of cell volume

12388065

TgeneKCNMA1

GO:0051592

response to calcium ion

12388065|18458941

TgeneKCNMA1

GO:0060073

micturition

11641143

TgeneKCNMA1

GO:0060083

smooth muscle contraction involved in micturition

11641143



check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChiTaRS5.0N/AM85843MTA3chr2

42952029

+KCNMA1chr10

78762955

-


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Fusion Gene ORF analysis for MTA3-KCNMA1

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
intron-intronENST00000405094ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405094ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000405592ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406652ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000406911ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000407270ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000286627MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000286628MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000354353MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000372440MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000372443MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000404771MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000404857MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000406533MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000480683MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000481070MTA3chr2

42952029

+KCNMA1chr10

78762955

-
intron-intronENST00000472767ENST00000484507MTA3chr2

42952029

+KCNMA1chr10

78762955

-

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 MTA3-KCNMA1


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 MTA3-KCNMA1


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/:42952029/:78762955)
- 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 MTA3-KCNMA1


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 MTA3-KCNMA1


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 MTA3-KCNMA1


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 MTA3-KCNMA1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC1836173Generalized Epilepsy and Paroxysmal Dyskinesia3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0005944Metabolic Bone Disorder1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0018273Growth Disorders1CTD_human
TgeneC0019284Diaphragmatic Hernia1CTD_human
TgeneC0020542Pulmonary Hypertension1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0028756Obesity, Morbid1CTD_human
TgeneC0029453Osteopenia1CTD_human
TgeneC0038220Status Epilepticus1CTD_human
TgeneC0043094Weight Gain1CTD_human
TgeneC0270823Petit mal status1CTD_human
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0311335Grand Mal Status Epilepticus1CTD_human
TgeneC0393734Complex Partial Status Epilepticus1CTD_human
TgeneC0410916Neonatal Death1CTD_human
TgeneC0701826Perinatal death1CTD_human
TgeneC0751522Status Epilepticus, Subclinical1CTD_human
TgeneC0751523Non-Convulsive Status Epilepticus1CTD_human
TgeneC0751524Simple Partial Status Epilepticus1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC4539985CEREBELLAR ATROPHY, DEVELOPMENTAL DELAY, AND SEIZURES1GENOMICS_ENGLAND