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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:TENM3-ATP2C1 (FusionGDB2 ID:89438)

Fusion Gene Summary for TENM3-ATP2C1

check button Fusion gene summary
Fusion gene informationFusion gene name: TENM3-ATP2C1
Fusion gene ID: 89438
HgeneTgene
Gene symbol

TENM3

ATP2C1

Gene ID

55714

27032

Gene nameteneurin transmembrane protein 3ATPase secretory pathway Ca2+ transporting 1
SynonymsMCOPCB9|MCOPS15|ODZ3|TEN3|TNM3|Ten-m3|ten-3ATP2C1A|BCPM|HHD|PMR1|SPCA1|hSPCA1
Cytomap

4q34.3-q35.1

3q22.1

Type of geneprotein-codingprotein-coding
Descriptionteneurin-3ODZ3-like proteinodz, odd Oz/ten-m homolog 3protein Odd Oz/ten-m homolog 3tenascin-M3testicular tissue protein Li 195calcium-transporting ATPase type 2C member 1ATP-dependent Ca(2+) pump PMR1ATPase 2C1ATPase, Ca(2+)-sequesteringATPase, Ca++ transporting, type 2C, member 1HUSSY-28secretory pathway Ca2+/Mn2+ ATPase 1
Modification date2020031320200313
UniProtAcc.

P98194

Ensembl transtripts involved in fusion geneENST00000511685, ENST00000406950, 
ENST00000502950, 		ENST00000505330, 
ENST00000504381, ENST00000507488, 
ENST00000393221, ENST00000533801, 
ENST00000510168, ENST00000508532, 
ENST00000504948, ENST00000513801, 
ENST00000328560, ENST00000428331, 
ENST00000359644, ENST00000422190, 
ENST00000509150, 
Fusion gene scores* DoF score10 X 10 X 2=20011 X 11 X 6=726
# samples 1012
** MAII scorelog2(10/200*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/726*10)=-2.59693514238723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TENM3 [Title/Abstract] AND ATP2C1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTENM3(183498757)-ATP2C1(130698240), # 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
TgeneATP2C1

GO:0006816

calcium ion transport

12810057

TgeneATP2C1

GO:0006874

cellular calcium ion homeostasis

12810057


check buttonFusion gene breakpoints across TENM3 (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 ATP2C1 (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/AEC558774TENM3chr4

183498757

+ATP2C1chr3

130698240

+


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Fusion Gene ORF analysis for TENM3-ATP2C1

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-3CDSENST00000511685ENST00000505330TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000504381TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000507488TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000393221TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000533801TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000510168TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000508532TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000504948TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000513801TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000328560TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000428331TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000359644TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000511685ENST00000422190TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-intronENST00000511685ENST00000509150TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000505330TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000504381TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000507488TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000393221TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000533801TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000510168TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000508532TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000504948TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000513801TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000328560TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000428331TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000359644TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000406950ENST00000422190TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-intronENST00000406950ENST00000509150TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000505330TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000504381TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000507488TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000393221TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000533801TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000510168TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000508532TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000504948TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000513801TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000328560TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000428331TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000359644TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-3CDSENST00000502950ENST00000422190TENM3chr4

183498757

+ATP2C1chr3

130698240

+
intron-intronENST00000502950ENST00000509150TENM3chr4

183498757

+ATP2C1chr3

130698240

+

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 TENM3-ATP2C1


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 TENM3-ATP2C1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.ATP2C1

P98194

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: This magnesium-dependent enzyme catalyzes the hydrolysis of ATP coupled with the transport of the calcium.

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 TENM3-ATP2C1


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 TENM3-ATP2C1


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 TENM3-ATP2C1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneATP2C1P98194DB00228EnfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB00228EnfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB00228EnfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB00228EnfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB01028MethoxyfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB01028MethoxyfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB01028MethoxyfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB01028MethoxyfluraneInhibitorSmall moleculeApproved|Investigational|Vet_approved
TgeneATP2C1P98194DB00753IsofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB00753IsofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB00753IsofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB00753IsofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB01236SevofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB01236SevofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB01236SevofluraneInhibitorSmall moleculeApproved|Vet_approved
TgeneATP2C1P98194DB01236SevofluraneInhibitorSmall moleculeApproved|Vet_approved

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Related Diseases for TENM3-ATP2C1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTENM3C0009171Cocaine Abuse1CTD_human
HgeneTENM3C0236736Cocaine-Related Disorders1CTD_human
HgeneTENM3C0264423Asthma, Occupational1CTD_human
HgeneTENM3C0600427Cocaine Dependence1CTD_human
HgeneTENM3C2931501Microphthalmia associated with colobomatous cyst1ORPHANET
HgeneTENM3C3554592MICROPHTHALMIA, ISOLATED, WITH COLOBOMA 91CTD_human;GENOMICS_ENGLAND
TgeneATP2C1C0085106Familial benign pemphigus8CTD_human;ORPHANET;UNIPROT