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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:ATP1A1-ATG4C (FusionGDB2 ID:7855)

Fusion Gene Summary for ATP1A1-ATG4C

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP1A1-ATG4C
Fusion gene ID: 7855
HgeneTgene
Gene symbol

ATP1A1

ATG4C

Gene ID

480

84938

Gene nameATPase Na+/K+ transporting subunit alpha 4autophagy related 4C cysteine peptidase
SynonymsATP1A1|ATP1AL2APG4-C|APG4C|AUTL1|AUTL3
Cytomap

1q23.2

1p31.3

Type of geneprotein-codingprotein-coding
Descriptionsodium/potassium-transporting ATPase subunit alpha-4ATPase, Na+/K+ transporting, alpha 4 polypeptideATPase, Na+/K+ transporting, alpha polypeptide-like 2Na(+)/K(+) ATPase alpha-4 subunitNa+/K+ ATPase 4Na+/K+ ATPase, alpha-D polypeptideNa,K-ATPase sucysteine protease ATG4CAPG4 autophagy 4 homolog CATG4 autophagy related 4 homolog CAUT-like 1, cysteine endopeptidaseAUT-like 3 cysteine endopeptidaseautophagin-3autophagy-related cysteine endopeptidase 3autophagy-related protein 4 homolog Cepidid
Modification date2020031320200313
UniProtAcc.

Q96DT6

Ensembl transtripts involved in fusion geneENST00000295598, ENST00000537345, 
ENST00000369496, ENST00000491156, 
ENST00000371120, ENST00000317868, 
Fusion gene scores* DoF score16 X 18 X 7=20167 X 7 X 3=147
# samples 238
** MAII scorelog2(23/2016*10)=-3.13178987255554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/147*10)=-0.877744249949002
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATP1A1 [Title/Abstract] AND ATG4C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP1A1(116916145)-ATG4C(63329663), # samples:2
Anticipated loss of major functional domain due to fusion event.ATP1A1-ATG4C seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
ATP1A1-ATG4C seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
ATP1A1-ATG4C seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneATP1A1

GO:0030317

flagellated sperm motility

12112599

HgeneATP1A1

GO:0030641

regulation of cellular pH

12112599


check buttonFusion gene breakpoints across ATP1A1 (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 ATG4C (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
ChimerDB4SKCMTCGA-EE-A2GP-06AATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
ChimerDB4SKCMTCGA-EE-A2GPATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
ChimerDB4SKCMTCGA-EE-A2GP-06AATP1A1chr1

116916145

+ATG4Cchr1

63329663

+


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Fusion Gene ORF analysis for ATP1A1-ATG4C

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
Frame-shiftENST00000295598ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
Frame-shiftENST00000295598ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
intron-3CDSENST00000537345ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
intron-3CDSENST00000537345ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
intron-3CDSENST00000369496ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
intron-3CDSENST00000369496ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
intron-3CDSENST00000491156ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
intron-3CDSENST00000491156ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329663

+
Frame-shiftENST00000295598ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
Frame-shiftENST00000295598ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
intron-3CDSENST00000537345ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
intron-3CDSENST00000537345ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
intron-3CDSENST00000369496ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
intron-3CDSENST00000369496ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
intron-3CDSENST00000491156ENST00000371120ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+
intron-3CDSENST00000491156ENST00000317868ATP1A1chr1

116916145

+ATG4Cchr1

63329662

+

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 ATP1A1-ATG4C


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)
ATP1A1chr1116916145+ATG4Cchr163329662+0.0001894550.9998105
ATP1A1chr1116916145+ATG4Cchr163329662+0.0001894550.9998105
ATP1A1chr1116916145+ATG4Cchr163329662+0.0001894550.9998105
ATP1A1chr1116916145+ATG4Cchr163329662+0.0001894550.9998105

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 ATP1A1-ATG4C


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
.ATG4C

Q96DT6

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: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3 and GABARAPL2, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms. {ECO:0000250, ECO:0000269|PubMed:21177865}.

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 ATP1A1-ATG4C


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 ATP1A1-ATG4C


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 ATP1A1-ATG4C


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 ATP1A1-ATG4C


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATP1A1C0001430Adenoma2CTD_human
HgeneATP1A1C0205646Adenoma, Basal Cell2CTD_human
HgeneATP1A1C0205647Follicular adenoma2CTD_human
HgeneATP1A1C0205648Adenoma, Microcystic2CTD_human
HgeneATP1A1C0205649Adenoma, Monomorphic2CTD_human
HgeneATP1A1C0205650Papillary adenoma2CTD_human
HgeneATP1A1C0205651Adenoma, Trabecular2CTD_human
HgeneATP1A1C4747974CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2DD2GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneATP1A1C0005586Bipolar Disorder1PSYGENET
HgeneATP1A1C0017162Gastroenteritis, Transmissible, of Swine1CTD_human
HgeneATP1A1C0020428Hyperaldosteronism1CTD_human
HgeneATP1A1C0020538Hypertensive disease1CTD_human
HgeneATP1A1C0027051Myocardial Infarction1CTD_human
HgeneATP1A1C0027055Myocardial Reperfusion Injury1CTD_human
HgeneATP1A1C0036572Seizures1GENOMICS_ENGLAND
HgeneATP1A1C0042594Vestibular Diseases1CTD_human
HgeneATP1A1C0151723Hypomagnesemia1GENOMICS_ENGLAND
HgeneATP1A1C0151744Myocardial Ischemia1CTD_human
HgeneATP1A1C1384514Conn Syndrome1CTD_human
HgeneATP1A1C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneATP1A1C4552839Hypomagnesemia, CTCAE1GENOMICS_ENGLAND