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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:ATG16L1-NGEF (FusionGDB2 ID:HG55054TG25791)

Fusion Gene Summary for ATG16L1-NGEF

check button Fusion gene summary
Fusion gene informationFusion gene name: ATG16L1-NGEF
Fusion gene ID: hg55054tg25791
HgeneTgene
Gene symbol

ATG16L1

NGEF

Gene ID

55054

25791

Gene nameautophagy related 16 like 1neuronal guanine nucleotide exchange factor
SynonymsAPG16L|ATG16A|ATG16L|IBD10|WDR30ARHGEF27|EPHEXIN
Cytomap('ATG16L1')('NGEF')

2q37.1

2q37.1

Type of geneprotein-codingprotein-coding
Descriptionautophagy-related protein 16-1APG16L betaATG16 autophagy related 16-like 1WD repeat domain 30ephexin-1eph-interacting exchange proteinephexin1
Modification date2020032020200313
UniProtAcc.

Q8N5V2

Ensembl transtripts involved in fusion geneENST00000347464, ENST00000373525, 
ENST00000392017, ENST00000392018, 
ENST00000392020, ENST00000498620, 
Fusion gene scores* DoF score5 X 4 X 4=803 X 4 X 3=36
# samples 54
** MAII scorelog2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ATG16L1 [Title/Abstract] AND NGEF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATG16L1(234202003)-NGEF(233785295), # samples:3
Anticipated loss of major functional domain due to fusion event.ATG16L1-NGEF seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATG16L1-NGEF 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


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
ChimerDB4LGGTCGA-E1-A7Z2-01AATG16L1chr2

234202003

-NGEFchr2

233785295

-
ChimerDB4LGGTCGA-E1-A7Z2-01AATG16L1chr2

234202003

+NGEFchr2

233785295

-
ChimerDB4LGGTCGA-E1-A7Z2ATG16L1chr2

234202003

+NGEFchr2

233785295

-


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Fusion Gene ORF analysis for ATG16L1-NGEF

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-intronENST00000347464ENST00000409079ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000347464ENST00000539537ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000373525ENST00000409079ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000373525ENST00000539537ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000392017ENST00000409079ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000392017ENST00000539537ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000392018ENST00000409079ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000392018ENST00000539537ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000392020ENST00000409079ATG16L1chr2

234202003

+NGEFchr2

233785295

-
5CDS-intronENST00000392020ENST00000539537ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000347464ENST00000264051ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000347464ENST00000373552ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000373525ENST00000264051ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000373525ENST00000373552ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000392017ENST00000264051ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000392017ENST00000373552ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000392018ENST00000264051ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000392018ENST00000373552ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000392020ENST00000264051ATG16L1chr2

234202003

+NGEFchr2

233785295

-
Frame-shiftENST00000392020ENST00000373552ATG16L1chr2

234202003

+NGEFchr2

233785295

-
intron-3CDSENST00000498620ENST00000264051ATG16L1chr2

234202003

+NGEFchr2

233785295

-
intron-3CDSENST00000498620ENST00000373552ATG16L1chr2

234202003

+NGEFchr2

233785295

-
intron-intronENST00000498620ENST00000409079ATG16L1chr2

234202003

+NGEFchr2

233785295

-
intron-intronENST00000498620ENST00000539537ATG16L1chr2

234202003

+NGEFchr2

233785295

-

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 ATG16L1-NGEF


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 ATG16L1-NGEF


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/:234202003/:233785295)
- 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
.NGEF

Q8N5V2

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: Acts as a guanine nucleotide exchange factor (GEF) which differentially activates the GTPases RHOA, RAC1 and CDC42. Plays a role in axon guidance regulating ephrin-induced growth cone collapse and dendritic spine morphogenesis. Upon activation by ephrin through EPHA4, the GEF activity switches toward RHOA resulting in its activation. Activated RHOA promotes cone retraction at the expense of RAC1- and CDC42-stimulated growth cone extension (By similarity). {ECO:0000250}.

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 ATG16L1-NGEF


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 ATG16L1-NGEF


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 ATG16L1-NGEF


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 ATG16L1-NGEF


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneATG16L1C1970207Inflammatory Bowel Disease 1011CTD_human;UNIPROT
HgeneATG16L1C0010346Crohn Disease2CTD_human;GENOMICS_ENGLAND
HgeneATG16L1C0156147Crohn's disease of large bowel2CTD_human
HgeneATG16L1C0267380Crohn's disease of the ileum2CTD_human
HgeneATG16L1C0678202Regional enteritis2CTD_human
HgeneATG16L1C0949272IIeocolitis2CTD_human
HgeneATG16L1C0021390Inflammatory Bowel Diseases1CTD_human