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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:NLGN4Y-VAMP7 (FusionGDB2 ID:HG22829TG6845)

Fusion Gene Summary for NLGN4Y-VAMP7

check button Fusion gene summary
Fusion gene informationFusion gene name: NLGN4Y-VAMP7
Fusion gene ID: hg22829tg6845
HgeneTgene
Gene symbol

NLGN4Y

VAMP7

Gene ID

22829

6845

Gene nameneuroligin 4 Y-linkedvesicle associated membrane protein 7
SynonymsHNL4YSYBL1|TI-VAMP|TIVAMP|VAMP-7
Cytomap('NLGN4Y')('VAMP7')

Yq11.221

Xq28 and Yq12

Type of geneprotein-codingprotein-coding
Descriptionneuroligin-4, Y-linkedalternative HNL4Yvesicle-associated membrane protein 7synaptobrevin-like 1synaptobrevin-like protein 1tetanus neurotoxin-insensitive VAMPtetanus-insensitive VAMP
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000476359, ENST00000297967, 
Fusion gene scores* DoF score12 X 11 X 6=79210 X 10 X 5=500
# samples 1311
** MAII scorelog2(13/792*10)=-2.60698880705116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/500*10)=-2.18442457113743
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NLGN4Y [Title/Abstract] AND VAMP7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNLGN4Y(16734471)-VAMP7(59272371), # 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
TgeneVAMP7

GO:0006906

vesicle fusion

10888671

TgeneVAMP7

GO:0008333

endosome to lysosome transport

10888671

TgeneVAMP7

GO:0016192

vesicle-mediated transport

10888671



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
ChimerDB4HNSCTCGA-CN-4728-01ANLGN4YchrY

16734471

+VAMP7chrY

59272371

+
ChimerDB4HNSCTCGA-CN-4728NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
ChimerDB4HNSCTCGA-CN-4728NLGN4YchrY

16734471

+VAMP7chrY

59272371

+


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Fusion Gene ORF analysis for NLGN4Y-VAMP7

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-3CDSENST00000476359ENST00000286448NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
3UTR-3UTRENST00000476359ENST00000262640NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
3UTR-3UTRENST00000476359ENST00000460621NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
3UTR-3UTRENST00000476359ENST00000479687NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
3UTR-intronENST00000476359ENST00000262640NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
3UTR-intronENST00000476359ENST00000286448NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
3UTR-intronENST00000476359ENST00000460621NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
3UTR-intronENST00000476359ENST00000479687NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
5CDS-3UTRENST00000297967ENST00000262640NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
5CDS-3UTRENST00000297967ENST00000460621NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
5CDS-3UTRENST00000297967ENST00000479687NLGN4YchrY

16734471

+VAMP7chrY

59272371

+
5CDS-intronENST00000297967ENST00000262640NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
5CDS-intronENST00000297967ENST00000286448NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
5CDS-intronENST00000297967ENST00000460621NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
5CDS-intronENST00000297967ENST00000479687NLGN4YchrY

16734471

+VAMP7chrX

155169365

+
Frame-shiftENST00000297967ENST00000286448NLGN4YchrY

16734471

+VAMP7chrY

59272371

+

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 NLGN4Y-VAMP7


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)
NLGN4YchrY16734471+VAMP7chrY59272370+0.0005532180.9994468
NLGN4YchrY16734471+VAMP7chrX155169364+0.0005532180.9994468
NLGN4YchrY16734471+VAMP7chrY59272370+0.0005532180.9994468
NLGN4YchrY16734471+VAMP7chrY59272370+0.0005532180.9994468
NLGN4YchrY16734471+VAMP7chrX155169364+0.0005532180.9994468
NLGN4YchrY16734471+VAMP7chrY59272370+0.0005532180.9994468


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.
genomic feature of top 1%

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Fusion Protein Features for NLGN4Y-VAMP7


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/:16734471/:59272371)
- 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
..
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: 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}.

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 NLGN4Y-VAMP7


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 NLGN4Y-VAMP7


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 NLGN4Y-VAMP7


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 NLGN4Y-VAMP7


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0343641Human papilloma virus infection1CTD_human
TgeneC1168401Squamous cell carcinoma of the head and neck1CTD_human
TgeneC451074446,XY partial gonadal dysgenesis1ORPHANET