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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:ATP6V1C2-ATM (FusionGDB2 ID:HG245973TG472)

Fusion Gene Summary for ATP6V1C2-ATM

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP6V1C2-ATM
Fusion gene ID: hg245973tg472
HgeneTgene
Gene symbol

ATP6V1C2

ATM

Gene ID

245973

472

Gene nameATPase H+ transporting V1 subunit C2ATM serine/threonine kinase
SynonymsATP6C2|VMA5AT1|ATA|ATC|ATD|ATDC|ATE|TEL1|TELO1
Cytomap('ATP6V1C2')('ATM')

2p25.1

11q22.3

Type of geneprotein-codingprotein-coding
DescriptionV-type proton ATPase subunit C 2ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2V-ATPase C2 subunitvacuolar proton pump subunit C 2serine-protein kinase ATMA-T mutatedAT mutatedTEL1, telomere maintenance 1, homologataxia telangiectasia mutated
Modification date2020031320200322
UniProtAcc

Q8NEY4

Q13315

Ensembl transtripts involved in fusion geneENST00000381661, ENST00000272238, 
Fusion gene scores* DoF score6 X 6 X 3=1088 X 9 X 8=576
# samples 612
** MAII scorelog2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/576*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ATP6V1C2 [Title/Abstract] AND ATM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP6V1C2(10924263)-ATM(108172361), # 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
TgeneATM

GO:0006468

protein phosphorylation

15916964

TgeneATM

GO:0006974

cellular response to DNA damage stimulus

9733515|16213212

TgeneATM

GO:0010212

response to ionizing radiation

9733515|11375976

TgeneATM

GO:0018105

peptidyl-serine phosphorylation

9733515|26323318

TgeneATM

GO:0046777

protein autophosphorylation

9733515|15790808

TgeneATM

GO:0071044

histone mRNA catabolic process

16086026

TgeneATM

GO:0071480

cellular response to gamma radiation

9925639|16213212

TgeneATM

GO:0071481

cellular response to X-ray

26323318

TgeneATM

GO:0071500

cellular response to nitrosative stress

23878245



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/ABF329241ATP6V1C2chr2

10924263

+ATMchr11

108172361

-


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Fusion Gene ORF analysis for ATP6V1C2-ATM

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
3UTR-intronENST00000381661ENST00000278616ATP6V1C2chr2

10924263

+ATMchr11

108172361

-
3UTR-intronENST00000381661ENST00000452508ATP6V1C2chr2

10924263

+ATMchr11

108172361

-
3UTR-intronENST00000381661ENST00000525178ATP6V1C2chr2

10924263

+ATMchr11

108172361

-
intron-intronENST00000272238ENST00000278616ATP6V1C2chr2

10924263

+ATMchr11

108172361

-
intron-intronENST00000272238ENST00000452508ATP6V1C2chr2

10924263

+ATMchr11

108172361

-
intron-intronENST00000272238ENST00000525178ATP6V1C2chr2

10924263

+ATMchr11

108172361

-

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 ATP6V1C2-ATM


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 ATP6V1C2-ATM


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/:10924263/:108172361)
- 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
ATP6V1C2

Q8NEY4

ATM

Q13315

FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.FUNCTION: Serine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX at double strand breaks (DSBs), thereby regulating DNA damage response mechanism. Also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. After the introduction of DNA breaks by the RAG complex on one immunoglobulin allele, acts by mediating a repositioning of the second allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. Also involved in signal transduction and cell cycle control. May function as a tumor suppressor. Necessary for activation of ABL1 and SAPK. Phosphorylates DYRK2, CHEK2, p53/TP53, FANCD2, NFKBIA, BRCA1, CTIP, nibrin (NBN), TERF1, UFL1, RAD9, UBQLN4 and DCLRE1C (PubMed:9843217, PubMed:9733515, PubMed:10550055, PubMed:10766245, PubMed:10839545, PubMed:10910365, PubMed:10802669, PubMed:10973490, PubMed:11375976, PubMed:12086603, PubMed:15456891, PubMed:19965871, PubMed:30612738, PubMed:30886146). May play a role in vesicle and/or protein transport. Could play a role in T-cell development, gonad and neurological function. Plays a role in replication-dependent histone mRNA degradation. Binds DNA ends. Phosphorylation of DYRK2 in nucleus in response to genotoxic stress prevents its MDM2-mediated ubiquitination and subsequent proteasome degradation. Phosphorylates ATF2 which stimulates its function in DNA damage response. Phosphorylates ERCC6 which is essential for its chromatin remodeling activity at DNA double-strand breaks (PubMed:29203878). {ECO:0000269|PubMed:10550055, ECO:0000269|PubMed:10766245, ECO:0000269|PubMed:10802669, ECO:0000269|PubMed:10839545, ECO:0000269|PubMed:10910365, ECO:0000269|PubMed:10973490, ECO:0000269|PubMed:11375976, ECO:0000269|PubMed:12086603, ECO:0000269|PubMed:12556884, ECO:0000269|PubMed:14871926, ECO:0000269|PubMed:15456891, ECO:0000269|PubMed:15916964, ECO:0000269|PubMed:16086026, ECO:0000269|PubMed:16858402, ECO:0000269|PubMed:17923702, ECO:0000269|PubMed:19431188, ECO:0000269|PubMed:19965871, ECO:0000269|PubMed:29203878, ECO:0000269|PubMed:30612738, ECO:0000269|PubMed:30886146, ECO:0000269|PubMed:9733514, ECO:0000269|PubMed:9733515, ECO:0000269|PubMed:9843217}.

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 ATP6V1C2-ATM


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 ATP6V1C2-ATM


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 ATP6V1C2-ATM


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneATMQ13315DB00201CaffeineInhibitorSmall moleculeApproved

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Related Diseases for ATP6V1C2-ATM


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0004135Ataxia Telangiectasia37CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0009405Hereditary Nonpolyposis Colorectal Neoplasms6CLINGEN
TgeneC1112155Hereditary non-polyposis colorectal cancer syndrome6CLINGEN
TgeneC1333990Hereditary Nonpolyposis Colorectal Cancer6CLINGEN
TgeneC1333991Hereditary Non-Polyposis Colon Cancer Type 26CLINGEN
TgeneC2936783Colorectal cancer, hereditary nonpolyposis, type 16CLINGEN
TgeneC0346153Breast Cancer, Familial5CLINGEN
TgeneC0033578Prostatic Neoplasms4CTD_human
TgeneC0376358Malignant neoplasm of prostate4CTD_human
TgeneC0023434Chronic Lymphocytic Leukemia2CTD_human;ORPHANET;UNIPROT
TgeneC0030297Pancreatic Neoplasm2CTD_human
TgeneC0346647Malignant neoplasm of pancreas2CTD_human
TgeneC0005684Malignant neoplasm of urinary bladder1CGI;CTD_human
TgeneC0005695Bladder Neoplasm1CGI;CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human;GENOMICS_ENGLAND
TgeneC0006826Malignant Neoplasms1CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0007193Cardiomyopathy, Dilated1CTD_human
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0016059Fibrosis1CTD_human
TgeneC0017638Glioma1CGI;GENOMICS_ENGLAND
TgeneC0021051Immunologic Deficiency Syndromes1GENOMICS_ENGLAND
TgeneC0023418leukemia1CGI;GENOMICS_ENGLAND
TgeneC0024299Lymphoma1CGI;GENOMICS_ENGLAND
TgeneC0024623Malignant neoplasm of stomach1CGI;CTD_human
TgeneC0025149Medulloblastoma1CGI;GENOMICS_ENGLAND
TgeneC0025202melanoma1CTD_human
TgeneC0027051Myocardial Infarction1CTD_human
TgeneC0027651Neoplasms1CTD_human
TgeneC0033054Prenatal Exposure Delayed Effects1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0038356Stomach Neoplasms1CGI;CTD_human
TgeneC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
TgeneC0079774Peripheral T-Cell Lymphoma1CTD_human
TgeneC0086543Cataract1CTD_human
TgeneC0086692Benign Neoplasm1CTD_human
TgeneC0242698Ventricular Dysfunction, Left1CTD_human
TgeneC0334634Malignant lymphoma, lymphocytic, intermediate differentiation, diffuse1CGI;GENOMICS_ENGLAND;UNIPROT
TgeneC0376407Granulomatous Slack Skin1CTD_human
TgeneC0524524Pseudoaphakia1CTD_human
TgeneC0555202Malignant lymphoma - lymphocytic, intermediate differentiation1ORPHANET
TgeneC0855095Small Lymphocytic Lymphoma1ORPHANET
TgeneC1449563Cardiomyopathy, Familial Idiopathic1CTD_human
TgeneC1510497Lens Opacities1CTD_human
TgeneC1623038Cirrhosis1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneC1843542T-CELL PROLYMPHOCYTIC LEUKEMIA, SOMATIC1GENOMICS_ENGLAND
TgeneC1868683B-CELL MALIGNANCY, LOW-GRADE1ORPHANET
TgeneC1876175Ataxia-Telangiectasia Variant1ORPHANET
TgeneC2239176Liver carcinoma1CTD_human
TgeneC2931456Prostate cancer, familial1CTD_human
TgeneC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human