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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:CACNA1C-MNAT1 (FusionGDB2 ID:12308)

Fusion Gene Summary for CACNA1C-MNAT1

check button Fusion gene summary
Fusion gene informationFusion gene name: CACNA1C-MNAT1
Fusion gene ID: 12308
HgeneTgene
Gene symbol

CACNA1C

MNAT1

Gene ID

775

4331

Gene namecalcium voltage-gated channel subunit alpha1 CMNAT1 component of CDK activating kinase
SynonymsCACH2|CACN2|CACNL1A1|CCHL1A1|CaV1.2|LQT8|TS|TS. LQT8CAP35|MAT1|RNF66|TFB3
Cytomap

12p13.33

14q23.1

Type of geneprotein-codingprotein-coding
Descriptionvoltage-dependent L-type calcium channel subunit alpha-1CDHPR, alpha-1 subunitcalcium channel, L type, alpha-1 polypeptide, isoform 1, cardiac musclecalcium channel, cardic dihydropyridine-sensitive, alpha-1 subunitcalcium channel, voltage-dependent, CDK-activating kinase assembly factor MAT1CDK7/cyclin-H assembly factorMNAT CDK-activating kinase assembly factor 1MNAT1, CDK activating kinase assembly factorRING finger protein 66RING finger protein MAT1cyclin G1 interacting proteinmenage a trois
Modification date2020031520200313
UniProtAcc

Q13936

P51948

Ensembl transtripts involved in fusion geneENST00000327702, ENST00000335762, 
ENST00000344100, ENST00000347598, 
ENST00000399591, ENST00000399595, 
ENST00000399597, ENST00000399601, 
ENST00000399603, ENST00000399606, 
ENST00000399617, ENST00000399621, 
ENST00000399629, ENST00000399634, 
ENST00000399637, ENST00000399638, 
ENST00000399641, ENST00000399644, 
ENST00000399649, ENST00000399655, 
ENST00000402845, ENST00000406454, 
ENST00000480911, ENST00000491104, 
ENST00000261245, ENST00000539616, 
ENST00000555545, 
Fusion gene scores* DoF score19 X 16 X 8=243214 X 14 X 7=1372
# samples 1919
** MAII scorelog2(19/2432*10)=-3.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1372*10)=-2.85220915784186
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CACNA1C [Title/Abstract] AND MNAT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCACNA1C(2162778)-MNAT1(61346430), # 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
HgeneCACNA1C

GO:0007204

positive regulation of cytosolic calcium ion concentration

12130699

HgeneCACNA1C

GO:0061577

calcium ion transmembrane transport via high voltage-gated calcium channel

15454078

HgeneCACNA1C

GO:0070588

calcium ion transmembrane transport

15454078

TgeneMNAT1

GO:0006357

regulation of transcription by RNA polymerase II

10801852

TgeneMNAT1

GO:0006366

transcription by RNA polymerase II

9852112

TgeneMNAT1

GO:0045944

positive regulation of transcription by RNA polymerase II

8692841

TgeneMNAT1

GO:1905775

negative regulation of DNA helicase activity

11445587


check buttonFusion gene breakpoints across CACNA1C (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 MNAT1 (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
ChiTaRS5.0N/ADA692923CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+


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Fusion Gene ORF analysis for CACNA1C-MNAT1

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-intronENST00000327702ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000327702ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000327702ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000335762ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000335762ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000335762ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000344100ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000344100ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000344100ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000347598ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000347598ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000347598ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399591ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399591ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399591ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399595ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399595ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399595ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399597ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399597ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399597ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399601ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399601ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399601ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399603ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399603ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399603ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399606ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399606ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399606ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399617ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399617ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399617ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399621ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399621ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399621ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399629ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399629ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399629ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399634ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399634ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399634ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399637ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399637ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399637ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399638ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399638ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399638ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399641ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399641ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399641ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399644ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399644ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399644ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399649ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399649ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399649ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399655ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399655ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000399655ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000402845ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000402845ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000402845ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000406454ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000406454ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000406454ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000480911ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000480911ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
5CDS-intronENST00000480911ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
intron-intronENST00000491104ENST00000261245CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
intron-intronENST00000491104ENST00000539616CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+
intron-intronENST00000491104ENST00000555545CACNA1Cchr12

2162778

+MNAT1chr14

61346430

+

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 CACNA1C-MNAT1


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)
CACNA1Cchr122162777+MNAT1chr1461346431+0.0680861850.9319138
CACNA1Cchr122162777+MNAT1chr1461346431+0.0680861850.9319138

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.
genomic feature of top 1%

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Fusion Protein Features for CACNA1C-MNAT1


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/:2162778/:61346430)
- 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
CACNA1C

Q13936

MNAT1

P51948

FUNCTION: Pore-forming, alpha-1C subunit of the voltage-gated calcium channel that gives rise to L-type calcium currents (PubMed:8392192, PubMed:7737988, PubMed:9087614, PubMed:9013606, PubMed:9607315, PubMed:12176756, PubMed:17071743, PubMed:11741969, PubMed:8099908, PubMed:12181424, PubMed:29078335, PubMed:29742403, PubMed:16299511, PubMed:20953164, PubMed:15454078, PubMed:15863612, PubMed:17224476, PubMed:24728418, PubMed:26253506, PubMed:27218670, PubMed:23677916). Mediates influx of calcium ions into the cytoplasm, and thereby triggers calcium release from the sarcoplasm (By similarity). Plays an important role in excitation-contraction coupling in the heart. Required for normal heart development and normal regulation of heart rhythm (PubMed:15454078, PubMed:15863612, PubMed:17224476, PubMed:24728418, PubMed:26253506). Required for normal contraction of smooth muscle cells in blood vessels and in the intestine. Essential for normal blood pressure regulation via its role in the contraction of arterial smooth muscle cells (PubMed:28119464). Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group (Probable). {ECO:0000250|UniProtKB:P15381, ECO:0000269|PubMed:11741969, ECO:0000269|PubMed:12176756, ECO:0000269|PubMed:12181424, ECO:0000269|PubMed:15454078, ECO:0000269|PubMed:15863612, ECO:0000269|PubMed:16299511, ECO:0000269|PubMed:17071743, ECO:0000269|PubMed:17224476, ECO:0000269|PubMed:20953164, ECO:0000269|PubMed:23677916, ECO:0000269|PubMed:24728418, ECO:0000269|PubMed:26253506, ECO:0000269|PubMed:27218670, ECO:0000269|PubMed:28119464, ECO:0000269|PubMed:29078335, ECO:0000269|PubMed:29742403, ECO:0000269|PubMed:7737988, ECO:0000269|PubMed:8099908, ECO:0000269|PubMed:8392192, ECO:0000269|PubMed:9013606, ECO:0000269|PubMed:9087614, ECO:0000269|PubMed:9607315, ECO:0000305}.; FUNCTION: (Microbial infection) Acts as a receptor for Influenzavirus (PubMed:29779930). May play a critical role in allowing virus entry when sialylated and expressed on lung tissues (PubMed:29779930). {ECO:0000269|PubMed:29779930}.FUNCTION: Stabilizes the cyclin H-CDK7 complex to form a functional CDK-activating kinase (CAK) enzymatic complex. CAK activates the cyclin-associated kinases CDK1, CDK2, CDK4 and CDK6 by threonine phosphorylation. CAK complexed to the core-TFIIH basal transcription factor activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter and elongation of the transcripts. Involved in cell cycle control and in RNA transcription by RNA polymerase II. {ECO:0000269|PubMed:10024882}.

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 CACNA1C-MNAT1


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 CACNA1C-MNAT1


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 CACNA1C-MNAT1


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 CACNA1C-MNAT1


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