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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:LYST-COG2 (FusionGDB2 ID:50508)

Fusion Gene Summary for LYST-COG2

check button Fusion gene summary
Fusion gene informationFusion gene name: LYST-COG2
Fusion gene ID: 50508
HgeneTgene
Gene symbol

LYST

COG2

Gene ID

1130

22796

Gene namelysosomal trafficking regulatorcomponent of oligomeric golgi complex 2
SynonymsCHS|CHS1CDG2Q|LDLC
Cytomap

1q42.3

1q42.2

Type of geneprotein-codingprotein-coding
Descriptionlysosomal-trafficking regulatorChediak-Higashi syndrome 1beige homologconserved oligomeric Golgi complex subunit 2COG complex subunit 2brefeldin A-sensitive, peripheral Golgi proteinconserved oligomeric Golgi complex protein 2low density lipoprotein receptor defect C complementinglow density lipoprotein receptor defect
Modification date2020031320200313
UniProtAcc

Q99698

Q14746

Ensembl transtripts involved in fusion geneENST00000389793, ENST00000389794, 
ENST00000473037, ENST00000536965, 
ENST00000366669, ENST00000366668, 
ENST00000534989, ENST00000535166, 
ENST00000490900, ENST00000546013, 
Fusion gene scores* DoF score14 X 15 X 10=21004 X 3 X 4=48
# samples 184
** MAII scorelog2(18/2100*10)=-3.54432051622381
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LYST [Title/Abstract] AND COG2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLYST(236030142)-COG2(230795209), # 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

check buttonFusion gene breakpoints across LYST (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 COG2 (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
ChimerDB4OVTCGA-25-1316LYSTchr1

236030142

-COG2chr1

230795209

+


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Fusion Gene ORF analysis for LYST-COG2

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
5UTR-3CDSENST00000389793ENST00000366669LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-3CDSENST00000389794ENST00000366669LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-5UTRENST00000389793ENST00000366668LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-5UTRENST00000389793ENST00000534989LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-5UTRENST00000389793ENST00000535166LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-5UTRENST00000389794ENST00000366668LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-5UTRENST00000389794ENST00000534989LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-5UTRENST00000389794ENST00000535166LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-intronENST00000389793ENST00000490900LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-intronENST00000389793ENST00000546013LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-intronENST00000389794ENST00000490900LYSTchr1

236030142

-COG2chr1

230795209

+
5UTR-intronENST00000389794ENST00000546013LYSTchr1

236030142

-COG2chr1

230795209

+
intron-3CDSENST00000473037ENST00000366669LYSTchr1

236030142

-COG2chr1

230795209

+
intron-3CDSENST00000536965ENST00000366669LYSTchr1

236030142

-COG2chr1

230795209

+
intron-5UTRENST00000473037ENST00000366668LYSTchr1

236030142

-COG2chr1

230795209

+
intron-5UTRENST00000473037ENST00000534989LYSTchr1

236030142

-COG2chr1

230795209

+
intron-5UTRENST00000473037ENST00000535166LYSTchr1

236030142

-COG2chr1

230795209

+
intron-5UTRENST00000536965ENST00000366668LYSTchr1

236030142

-COG2chr1

230795209

+
intron-5UTRENST00000536965ENST00000534989LYSTchr1

236030142

-COG2chr1

230795209

+
intron-5UTRENST00000536965ENST00000535166LYSTchr1

236030142

-COG2chr1

230795209

+
intron-intronENST00000473037ENST00000490900LYSTchr1

236030142

-COG2chr1

230795209

+
intron-intronENST00000473037ENST00000546013LYSTchr1

236030142

-COG2chr1

230795209

+
intron-intronENST00000536965ENST00000490900LYSTchr1

236030142

-COG2chr1

230795209

+
intron-intronENST00000536965ENST00000546013LYSTchr1

236030142

-COG2chr1

230795209

+

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 LYST-COG2


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)
LYSTchr1236030142-COG2chr1230795209+4.87E-111
LYSTchr1236030142-COG2chr1230795209+4.87E-111

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.
genomic feature of top 1%

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Fusion Protein Features for LYST-COG2


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/:236030142/:230795209)
- 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
LYST

Q99698

COG2

Q14746

FUNCTION: Adapter protein that regulates and/or fission of intracellular vesicles such as lysosomes (PubMed:11984006, PubMed:25216107). Might regulate trafficking of effectors involved in exocytosis (PubMed:25425525). In cytotoxic T-cells and natural killer (NK) cells, has role in the regulation of size, number and exocytosis of lytic granules (PubMed:26478006). In macrophages and dendritic cells, regulates phagosome maturation by controlling the conversion of early phagosomal compartments into late phagosomes (By similarity). In macrophages and dendritic cells, specifically involved in TLR3- and TLR4-induced production of pro-inflammatory cytokines by regulating the endosomal TLR3- TICAM1/TRIF and TLR4- TICAM1/TRIF signaling pathways (PubMed:27881733). {ECO:0000250|UniProtKB:P97412, ECO:0000269|PubMed:11984006, ECO:0000269|PubMed:25216107, ECO:0000269|PubMed:25425525, ECO:0000269|PubMed:26478006, ECO:0000269|PubMed:27881733}.FUNCTION: Required for normal Golgi morphology and function.

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 LYST-COG2


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 LYST-COG2


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 LYST-COG2


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 LYST-COG2


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