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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:ARID2-NPC1 (FusionGDB2 ID:HG196528TG4864)

Fusion Gene Summary for ARID2-NPC1

check button Fusion gene summary
Fusion gene informationFusion gene name: ARID2-NPC1
Fusion gene ID: hg196528tg4864
HgeneTgene
Gene symbol

ARID2

NPC1

Gene ID

196528

4864

Gene nameAT-rich interaction domain 2NPC intracellular cholesterol transporter 1
SynonymsBAF200|CSS6|p200NPC|POGZ|SLC65A1
Cytomap('ARID2')('NPC1')

12q12

18q11.2

Type of geneprotein-codingprotein-coding
DescriptionAT-rich interactive domain-containing protein 2ARID domain-containing protein 2AT rich interactive domain 2 (ARID, RFX-like)BRG1-associated factor 200zinc finger protein with activation potentialzipzap/p200NPC intracellular cholesterol transporter 1Niemann-Pick C1 proteintruncated Niemann-Pick C1
Modification date2020032020200315
UniProtAcc.

O15118

Ensembl transtripts involved in fusion geneENST00000334344, ENST00000444670, 
ENST00000457135, ENST00000479608, 
ENST00000422737, 
Fusion gene scores* DoF score17 X 9 X 12=183612 X 11 X 5=660
# samples 1713
** MAII scorelog2(17/1836*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/660*10)=-2.34395440121736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ARID2 [Title/Abstract] AND NPC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointARID2(46300326)-NPC1(21096711), # 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
HgeneARID2

GO:0006337

nucleosome disassembly

8895581

HgeneARID2

GO:0008285

negative regulation of cell proliferation

26169693

HgeneARID2

GO:0030336

negative regulation of cell migration

26169693

TgeneNPC1

GO:0006486

protein glycosylation

10821832

TgeneNPC1

GO:0030301

cholesterol transport

18772377

TgeneNPC1

GO:0033344

cholesterol efflux

16141411

TgeneNPC1

GO:0042632

cholesterol homeostasis

12719428

TgeneNPC1

GO:0090150

establishment of protein localization to membrane

23360953



check button Fusion gene information
* 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


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Fusion Gene ORF analysis for ARID2-NPC1

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

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 ARID2-NPC1


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 ARID2-NPC1


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/:46300326/:21096711)
- 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
.NPC1

O15118

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Intracellular cholesterol transporter which acts in concert with NPC2 and plays an important role in the egress of cholesterol from the endosomal/lysosomal compartment (PubMed:9211849, PubMed:9927649, PubMed:10821832, PubMed:18772377, PubMed:27238017, PubMed:12554680). Unesterified cholesterol that has been released from LDLs in the lumen of the late endosomes/lysosomes is transferred by NPC2 to the cholesterol-binding pocket in the N-terminal domain of NPC1 (PubMed:9211849, PubMed:9927649, PubMed:18772377, PubMed:19563754, PubMed:27238017, PubMed:28784760). Cholesterol binds to NPC1 with the hydroxyl group buried in the binding pocket (PubMed:19563754). Binds oxysterol with higher affinity than cholesterol. May play a role in vesicular trafficking in glia, a process that may be crucial for maintaining the structural and functional integrity of nerve terminals (Probable). {ECO:0000269|PubMed:10821832, ECO:0000269|PubMed:12554680, ECO:0000269|PubMed:18772377, ECO:0000269|PubMed:19563754, ECO:0000269|PubMed:27238017, ECO:0000269|PubMed:28784760, ECO:0000269|PubMed:9211849, ECO:0000269|PubMed:9927649, ECO:0000305}.; FUNCTION: (Microbial infection) Acts as an endosomal entry receptor for ebolavirus. {ECO:0000269|PubMed:21866103, ECO:0000269|PubMed:25855742, ECO:0000269|PubMed:32855215}.

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 ARID2-NPC1


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 ARID2-NPC1


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 ARID2-NPC1


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 ARID2-NPC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneARID2C2239176Liver carcinoma2CGI;CTD_human
HgeneARID2C0033578Prostatic Neoplasms1CTD_human
HgeneARID2C0265338Coffin-Siris syndrome1ORPHANET
HgeneARID2C0376358Malignant neoplasm of prostate1CTD_human
TgeneC3179455Niemann-Pick Disease, Type C126CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0220756Niemann-Pick Disease, Type C3CTD_human;GENOMICS_ENGLAND
TgeneC0268247Niemann-Pick Disease, Type D2CTD_human;GENOMICS_ENGLAND
TgeneC0004134Ataxia1CTD_human
TgeneC0004153Atherosclerosis1CTD_human
TgeneC0006309Brucellosis1CTD_human
TgeneC0013362Dysarthria1CTD_human
TgeneC0023890Liver Cirrhosis1CTD_human
TgeneC0023895Liver diseases1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0029089Ophthalmoplegia1CTD_human
TgeneC0086565Liver Dysfunction1CTD_human
TgeneC0162292External Ophthalmoplegia1CTD_human
TgeneC0238198Gastrointestinal Stromal Tumors1CTD_human
TgeneC0239946Fibrosis, Liver1CTD_human
TgeneC0240952Dysarthria, Scanning1CTD_human
TgeneC0240991Ataxia, Sensory1CTD_human
TgeneC0278161Ataxia, Motor1CTD_human
TgeneC0339693Internal Ophthalmoplegia1CTD_human
TgeneC0427190Ataxia, Truncal1CTD_human
TgeneC0454596Dysarthria, Spastic1CTD_human
TgeneC0454597Dysarthria, Flaccid1CTD_human
TgeneC0454598Dysarthria, Mixed1CTD_human
TgeneC0520966Abnormal coordination1CTD_human
TgeneC0750937Ataxia, Appendicular1CTD_human
TgeneC0750940Tremor, Rubral1CTD_human
TgeneC0751401Ophthalmoparesis1CTD_human
TgeneC1563666Dysarthria, Guttural1CTD_human
TgeneC1563937Atherogenesis1CTD_human
TgeneC2231324Brucellosis, Pulmonary1CTD_human
TgeneC3179349Gastrointestinal Stromal Sarcoma1CTD_human