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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:NCKAP1-PACRGL (FusionGDB2 ID:57278)

Fusion Gene Summary for NCKAP1-PACRGL

check button Fusion gene summary
Fusion gene informationFusion gene name: NCKAP1-PACRGL
Fusion gene ID: 57278
HgeneTgene
Gene symbol

NCKAP1

PACRGL

Gene ID

10787

133015

Gene nameNCK associated protein 1parkin coregulated like
SynonymsHEM2|NAP1|NAP125|p125Nap1C4orf28
Cytomap

2q32.1

4p15.31

Type of geneprotein-codingprotein-coding
Descriptionnck-associated protein 1membrane-associated protein HEM-2PACRG-like proteinPARK2 co-regulated likePARK2 coregulated like
Modification date2020032720200313
UniProtAcc

Q9Y2A7

.
Ensembl transtripts involved in fusion geneENST00000361354, ENST00000360982, 
ENST00000478449, 		ENST00000503585, 
ENST00000360916, ENST00000295290, 
ENST00000444671, ENST00000502374, 
ENST00000538990, ENST00000502938, 
ENST00000507634, ENST00000513459, 
ENST00000508753, 
Fusion gene scores* DoF score9 X 9 X 7=5674 X 6 X 2=48
# samples 135
** MAII scorelog2(13/567*10)=-2.12483711191377
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/48*10)=0.0588936890535686
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: NCKAP1 [Title/Abstract] AND PACRGL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNCKAP1(183843562)-PACRGL(20726428), # samples:1
Anticipated loss of major functional domain due to fusion event.NCKAP1-PACRGL seems lost the major protein functional domain in Hgene 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
HgeneNCKAP1

GO:0016601

Rac protein signal transduction

21107423

HgeneNCKAP1

GO:2000601

positive regulation of Arp2/3 complex-mediated actin nucleation

21107423


check buttonFusion gene breakpoints across NCKAP1 (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 PACRGL (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/ADA496585NCKAP1chr2

183843562

-PACRGLchr4

20726428

+


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Fusion Gene ORF analysis for NCKAP1-PACRGL

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-shiftENST00000361354ENST00000503585NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000360916NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000295290NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000444671NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000502374NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000538990NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000502938NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000507634NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000513459NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000361354ENST00000508753NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
Frame-shiftENST00000360982ENST00000503585NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000360916NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000295290NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000444671NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000502374NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000538990NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000502938NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000507634NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000513459NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
5CDS-intronENST00000360982ENST00000508753NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-3CDSENST00000478449ENST00000503585NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000360916NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000295290NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000444671NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000502374NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000538990NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000502938NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000507634NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000513459NCKAP1chr2

183843562

-PACRGLchr4

20726428

+
intron-intronENST00000478449ENST00000508753NCKAP1chr2

183843562

-PACRGLchr4

20726428

+

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 NCKAP1-PACRGL


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)
NCKAP1chr2183843561-PACRGLchr420726430+1.93E-050.9999807
NCKAP1chr2183843561-PACRGLchr420726430+1.93E-050.9999807

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 NCKAP1-PACRGL


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
NCKAP1

Q9Y2A7

.
FUNCTION: Part of the WAVE complex that regulates lamellipodia formation. The WAVE complex regulates actin filament reorganization via its interaction with the Arp2/3 complex. Actin remodeling activity is regulated by RAC1. As component of the WAVE1 complex, required for BDNF-NTRK2 endocytic trafficking and signaling from early endosomes. {ECO:0000250|UniProtKB:P28660}.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.

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 NCKAP1-PACRGL


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 NCKAP1-PACRGL


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 NCKAP1-PACRGL


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 NCKAP1-PACRGL


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneNCKAP1C1535926Neurodevelopmental Disorders1CTD_human