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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:KCNMA1-ECD (FusionGDB2 ID:41485)

Fusion Gene Summary for KCNMA1-ECD

check button Fusion gene summary
Fusion gene informationFusion gene name: KCNMA1-ECD
Fusion gene ID: 41485
HgeneTgene
Gene symbol

KCNMA1

ECD

Gene ID

3778

11319

Gene namepotassium calcium-activated channel subfamily M alpha 1ecdysoneless cell cycle regulator
SynonymsBKTM|CADEDS|IEG16|KCa1.1|LIWAS|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1GCR2|HSGT1|SGT1
Cytomap

10q22.3

10q22.2

Type of geneprotein-codingprotein-coding
Descriptioncalcium-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 HSLOpoprotein ecdysoneless homologecdysoneless homologhuman suppressor of GCR twoprotein SGT1suppressor of GCR2suppressor of S. cerevisiae gcr2
Modification date2020031520200313
UniProtAcc

Q12791

O95905

Ensembl transtripts involved in fusion geneENST00000286627, ENST00000286628, 
ENST00000354353, ENST00000372440, 
ENST00000372443, ENST00000404771, 
ENST00000404857, ENST00000406533, 
ENST00000480683, ENST00000481070, 
ENST00000484507, 		ENST00000372979, 
ENST00000430082, ENST00000454759, 
ENST00000610256, 
Fusion gene scores* DoF score20 X 17 X 10=34003 X 3 X 2=18
# samples 253
** MAII scorelog2(25/3400*10)=-3.76553474636298
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

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

Most frequent breakpointKCNMA1(78943179)-ECD(74923708), # samples:3
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
HgeneKCNMA1

GO:0001666

response to hypoxia

15528406

HgeneKCNMA1

GO:0006813

potassium ion transport

7573516|7877450|11245614|12388065|17706472|18458941

HgeneKCNMA1

GO:0006970

response to osmotic stress

10840032|12388065

HgeneKCNMA1

GO:0030007

cellular potassium ion homeostasis

11245614

HgeneKCNMA1

GO:0034465

response to carbon monoxide

15528406

HgeneKCNMA1

GO:0042391

regulation of membrane potential

7877450|7993625

HgeneKCNMA1

GO:0045794

negative regulation of cell volume

12388065

HgeneKCNMA1

GO:0051592

response to calcium ion

12388065|18458941

HgeneKCNMA1

GO:0060073

micturition

11641143

HgeneKCNMA1

GO:0060083

smooth muscle contraction involved in micturition

11641143

TgeneECD

GO:0045944

positive regulation of transcription by RNA polymerase II

19919181


check buttonFusion gene breakpoints across KCNMA1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ECD (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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
ChimerDB4BRCATCGA-EW-A1OV-01AKCNMA1chr10

78943179

-ECDchr10

74923708

-


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Fusion Gene ORF analysis for KCNMA1-ECD

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-5UTRENST00000286627ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286627ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286627ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286627ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286628ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286628ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286628ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000286628ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000354353ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000354353ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000354353ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000354353ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372440ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372440ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372440ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372440ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372443ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372443ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372443ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000372443ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404771ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404771ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404771ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404771ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404857ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404857ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404857ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000404857ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000406533ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000406533ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000406533ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
5CDS-5UTRENST00000406533ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000480683ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000480683ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000480683ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000480683ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000481070ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000481070ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000481070ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000481070ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000484507ENST00000372979KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000484507ENST00000430082KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000484507ENST00000454759KCNMA1chr10

78943179

-ECDchr10

74923708

-
intron-5UTRENST00000484507ENST00000610256KCNMA1chr10

78943179

-ECDchr10

74923708

-

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 KCNMA1-ECD


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for KCNMA1-ECD


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/:78943179/:74923708)
- 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
KCNMA1

Q12791

ECD

O95905

FUNCTION: Potassium channel activated by both membrane depolarization or increase in cytosolic Ca(2+) that mediates export of K(+) (PubMed:29330545, PubMed:31152168). It is also activated by the concentration of cytosolic Mg(2+). Its activation dampens the excitatory events that elevate the cytosolic Ca(2+) concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity. In smooth muscles, its activation by high level of Ca(2+), caused by ryanodine receptors in the sarcoplasmic reticulum, regulates the membrane potential. In cochlea cells, its number and kinetic properties partly determine the characteristic frequency of each hair cell and thereby helps to establish a tonotopic map. Kinetics of KCNMA1 channels are determined by alternative splicing, phosphorylation status and its combination with modulating beta subunits. Highly sensitive to both iberiotoxin (IbTx) and charybdotoxin (CTX). {ECO:0000269|PubMed:29330545, ECO:0000269|PubMed:31152168}.FUNCTION: Regulator of p53/TP53 stability and function. Inhibits MDM2-mediated degradation of p53/TP53 possibly by cooperating in part with TXNIP (PubMed:16849563, PubMed:23880345). May be involved transcriptional regulation. In vitro has intrinsic transactivation activity enhanced by EP300. May be a transcriptional activator required for the expression of glycolytic genes (PubMed:19919181, PubMed:9928932). Involved in regulation of cell cycle progression. Proposed to disrupt Rb-E2F binding leading to transcriptional activation of E2F proteins (PubMed:19640839). The cell cycle -regulating function may depend on its RUVBL1-mediated association with the R2TP complex (PubMed:26711270). May play a role in regulation of pre-mRNA splicing (PubMed:24722212). {ECO:0000269|PubMed:16849563, ECO:0000269|PubMed:19640839, ECO:0000269|PubMed:19919181, ECO:0000269|PubMed:23880345, ECO:0000269|PubMed:26711270, ECO:0000305|PubMed:24722212, ECO:0000305|PubMed:9928932}.

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 KCNMA1-ECD


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 KCNMA1-ECD


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 KCNMA1-ECD


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 KCNMA1-ECD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource