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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:NPHP4-ACOT7 (FusionGDB2 ID:59903)

Fusion Gene Summary for NPHP4-ACOT7

check button Fusion gene summary
Fusion gene informationFusion gene name: NPHP4-ACOT7
Fusion gene ID: 59903
HgeneTgene
Gene symbol

NPHP4

ACOT7

Gene ID

261734

11332

Gene namenephrocystin 4acyl-CoA thioesterase 7
SynonymsPOC10|SLSN4ACH1|ACT|BACH|CTE-II|LACH|LACH1|hBACH
Cytomap

1p36.31

1p36.31

Type of geneprotein-codingprotein-coding
Descriptionnephrocystin-4POC10 centriolar protein homolognephroretinincytosolic acyl coenzyme A thioester hydrolaseCTE-IIaacyl-CoA thioesterase 2acyl-CoA thioesterase, long chainbrain acyl-CoA hydrolaselong chain acyl-CoA thioester hydrolase
Modification date2020032020200313
UniProtAcc

O75161

O00154

Ensembl transtripts involved in fusion geneENST00000378156, ENST00000478423, 
ENST00000541130, ENST00000361521, 
ENST00000377842, ENST00000377845, 
ENST00000377855, ENST00000545482, 
ENST00000608083, 
Fusion gene scores* DoF score7 X 10 X 5=3509 X 8 X 7=504
# samples 1013
** MAII scorelog2(10/350*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/504*10)=-1.95491211047146
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NPHP4 [Title/Abstract] AND ACOT7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNPHP4(6052304)-ACOT7(6355040), # samples:3
ACOT7(6409809)-NPHP4(5993389), # samples:2
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
HgeneNPHP4

GO:0090090

negative regulation of canonical Wnt signaling pathway

22654112

TgeneACOT7

GO:0015937

coenzyme A biosynthetic process

10578051

TgeneACOT7

GO:0036114

medium-chain fatty-acyl-CoA catabolic process

10578051

TgeneACOT7

GO:0036116

long-chain fatty-acyl-CoA catabolic process

10578051

TgeneACOT7

GO:0051792

medium-chain fatty acid biosynthetic process

10578051

TgeneACOT7

GO:1900535

palmitic acid biosynthetic process

10578051


check buttonFusion gene breakpoints across NPHP4 (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 ACOT7 (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
ChimerDB4LGGTCGA-DU-6395-01ANPHP4chr1

6052304

-ACOT7chr1

6355040

-
ChimerDB4LGGTCGA-DU-6395NPHP4chr1

6052304

-ACOT7chr1

6355040

-
ChimerDB4STADTCGA-VQ-A91N-01ANPHP4chr1

6038330

-ACOT7chr1

6341346

-
ChimerDB4STADTCGA-VQ-A91NNPHP4chr1

6038329

-ACOT7chr1

6341346

-


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Fusion Gene ORF analysis for NPHP4-ACOT7

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-intronENST00000378156ENST00000541130NPHP4chr1

6038330

-ACOT7chr1

6341346

-
5CDS-intronENST00000378156ENST00000541130NPHP4chr1

6038329

-ACOT7chr1

6341346

-
5UTR-3CDSENST00000378156ENST00000361521NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000378156ENST00000377842NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000378156ENST00000377845NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000378156ENST00000377855NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000378156ENST00000545482NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000378156ENST00000608083NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000478423ENST00000361521NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000478423ENST00000377842NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000478423ENST00000377845NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000478423ENST00000377855NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000478423ENST00000545482NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-3CDSENST00000478423ENST00000608083NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-intronENST00000378156ENST00000541130NPHP4chr1

6052304

-ACOT7chr1

6355040

-
5UTR-intronENST00000478423ENST00000541130NPHP4chr1

6052304

-ACOT7chr1

6355040

-
Frame-shiftENST00000378156ENST00000361521NPHP4chr1

6038330

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000361521NPHP4chr1

6038329

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000377842NPHP4chr1

6038330

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000377842NPHP4chr1

6038329

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000377845NPHP4chr1

6038330

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000377845NPHP4chr1

6038329

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000377855NPHP4chr1

6038330

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000377855NPHP4chr1

6038329

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000545482NPHP4chr1

6038330

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000545482NPHP4chr1

6038329

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000608083NPHP4chr1

6038330

-ACOT7chr1

6341346

-
Frame-shiftENST00000378156ENST00000608083NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000361521NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000361521NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000377842NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000377842NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000377845NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000377845NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000377855NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000377855NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000545482NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000545482NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000608083NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-3CDSENST00000478423ENST00000608083NPHP4chr1

6038329

-ACOT7chr1

6341346

-
intron-intronENST00000478423ENST00000541130NPHP4chr1

6038330

-ACOT7chr1

6341346

-
intron-intronENST00000478423ENST00000541130NPHP4chr1

6038329

-ACOT7chr1

6341346

-

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 NPHP4-ACOT7


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 NPHP4-ACOT7


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/:6052304/:6355040)
- 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
NPHP4

O75161

ACOT7

O00154

FUNCTION: Involved in the organization of apical junctions; the function is proposed to implicate a NPHP1-4-8 module (PubMed:19755384, PubMed:21565611). Does not seem to be strictly required for ciliogenesis (PubMed:21565611). Required for building functional cilia. Involved in the organization of the subapical actin network in multiciliated epithelial cells. Seems to recruit INT to basal bodies of motile cilia which subsequently interacts with actin-modifying proteins such as DAAM1 (By similarity). In cooperation with INVS may downregulate the canonical Wnt pathway and promote the Wnt-PCP pathway by regulating expression and subcellular location of disheveled proteins. Stabilizes protein levels of JADE1 and promotes its translocation to the nucleus leading to cooperative inhibition of canonical Wnt signaling (PubMed:21498478, PubMed:22654112). Acts as negative regulator of the hippo pathway by association with LATS1 and modifying LATS1-dependent phosphorylation and localization of WWTR1/TAZ (PubMed:21555462). {ECO:0000250|UniProtKB:B0DOB4, ECO:0000250|UniProtKB:P59240, ECO:0000269|PubMed:21498478, ECO:0000269|PubMed:21555462, ECO:0000269|PubMed:21565611, ECO:0000269|PubMed:22654112, ECO:0000305|PubMed:19755384}.FUNCTION: Acyl-CoA thioesterases are a group of enzymes that catalyze the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH), providing the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH (PubMed:10578051). Acyl-coenzyme A thioesterase 7/ACOT7 preferentially hydrolyzes palmitoyl-CoA, but has a broad specificity acting on other fatty acyl-CoAs with chain-lengths of C8-C18 (PubMed:10578051). May play an important physiological function in brain (PubMed:10578051). {ECO:0000269|PubMed:10578051, ECO:0000303|PubMed:10578051}.

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 NPHP4-ACOT7


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 NPHP4-ACOT7


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 NPHP4-ACOT7


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 NPHP4-ACOT7


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