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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:CGNL1-CLU (FusionGDB2 ID:16213)

Fusion Gene Summary for CGNL1-CLU

check button Fusion gene summary
Fusion gene informationFusion gene name: CGNL1-CLU
Fusion gene ID: 16213
HgeneTgene
Gene symbol

CGNL1

CLU

Gene ID

84952

1191

Gene namecingulin like 1clusterin
SynonymsJACOP|PCINGAAG4|APO-J|APOJ|CLI|CLU1|CLU2|KUB1|NA1/NA2|SGP-2|SGP2|SP-40|TRPM-2|TRPM2
Cytomap

15q21.3

8p21.1

Type of geneprotein-codingprotein-coding
Descriptioncingulin-like protein 1junction-associated coiled-coil proteinparacingulinclusterinaging-associated protein 4apolipoprotein Jcomplement cytolysis inhibitorcomplement lysis inhibitorcomplement-associated protein SP-40,40epididymis secretory sperm binding proteinku70-binding protein 1sulfated glycoprotein 2testosterone-r
Modification date2020031320200327
UniProtAcc

Q0VF96

Q15846

Ensembl transtripts involved in fusion geneENST00000281282, ENST00000557813, 
ENST00000316403, ENST00000546343, 
ENST00000560366, ENST00000405140, 
ENST00000523500, 
Fusion gene scores* DoF score14 X 12 X 3=50423 X 24 X 12=6624
# samples 1630
** MAII scorelog2(16/504*10)=-1.65535182861255
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(30/6624*10)=-4.46466826700344
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CGNL1 [Title/Abstract] AND CLU [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCGNL1(57839712)-CLU(27462523), # 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
TgeneCLU

GO:0000902

cell morphogenesis

15857407

TgeneCLU

GO:0001774

microglial cell activation

15857407

TgeneCLU

GO:0017038

protein import

24446231

TgeneCLU

GO:0031333

negative regulation of protein complex assembly

22179788|23106396

TgeneCLU

GO:0031334

positive regulation of protein complex assembly

22179788

TgeneCLU

GO:0032760

positive regulation of tumor necrosis factor production

15857407

TgeneCLU

GO:0045429

positive regulation of nitric oxide biosynthetic process

15857407

TgeneCLU

GO:0050821

protein stabilization

11123922|12176985

TgeneCLU

GO:0051131

chaperone-mediated protein complex assembly

17412999

TgeneCLU

GO:0051788

response to misfolded protein

19996109

TgeneCLU

GO:0061077

chaperone-mediated protein folding

11123922

TgeneCLU

GO:0061518

microglial cell proliferation

15857407

TgeneCLU

GO:1900221

regulation of amyloid-beta clearance

24446231

TgeneCLU

GO:1901214

regulation of neuron death

17412999

TgeneCLU

GO:1901216

positive regulation of neuron death

15857407

TgeneCLU

GO:1902430

negative regulation of amyloid-beta formation

12047389|17412999

TgeneCLU

GO:1905907

negative regulation of amyloid fibril formation

22179788


check buttonFusion gene breakpoints across CGNL1 (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 CLU (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
ChimerDB4THCATCGA-DJ-A2Q7-01ACGNL1chr15

57839712

+CLUchr8

27462523

-


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Fusion Gene ORF analysis for CGNL1-CLU

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-3CDSENST00000281282ENST00000316403CGNL1chr15

57839712

+CLUchr8

27462523

-
3UTR-3CDSENST00000281282ENST00000546343CGNL1chr15

57839712

+CLUchr8

27462523

-
3UTR-3CDSENST00000281282ENST00000560366CGNL1chr15

57839712

+CLUchr8

27462523

-
3UTR-3CDSENST00000281282ENST00000405140CGNL1chr15

57839712

+CLUchr8

27462523

-
3UTR-3CDSENST00000281282ENST00000523500CGNL1chr15

57839712

+CLUchr8

27462523

-
intron-3CDSENST00000557813ENST00000316403CGNL1chr15

57839712

+CLUchr8

27462523

-
intron-3CDSENST00000557813ENST00000546343CGNL1chr15

57839712

+CLUchr8

27462523

-
intron-3CDSENST00000557813ENST00000560366CGNL1chr15

57839712

+CLUchr8

27462523

-
intron-3CDSENST00000557813ENST00000405140CGNL1chr15

57839712

+CLUchr8

27462523

-
intron-3CDSENST00000557813ENST00000523500CGNL1chr15

57839712

+CLUchr8

27462523

-

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 CGNL1-CLU


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 CGNL1-CLU


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
CGNL1

Q0VF96

CLU

Q15846

FUNCTION: May be involved in anchoring the apical junctional complex, especially tight junctions, to actin-based cytoskeletons. {ECO:0000269|PubMed:22891260}.

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 CGNL1-CLU


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 CGNL1-CLU


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 CGNL1-CLU


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 CGNL1-CLU


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCGNL1C0036341Schizophrenia1PSYGENET
TgeneCLUC0022660Kidney Failure, Acute6CTD_human
TgeneCLUC1565662Acute Kidney Insufficiency6CTD_human
TgeneCLUC2609414Acute kidney injury6CTD_human
TgeneCLUC0002395Alzheimer's Disease3CTD_human
TgeneCLUC0011265Presenile dementia3CTD_human
TgeneCLUC0022658Kidney Diseases3CTD_human
TgeneCLUC0276496Familial Alzheimer Disease (FAD)3CTD_human
TgeneCLUC0494463Alzheimer Disease, Late Onset3CTD_human
TgeneCLUC0546126Acute Confusional Senile Dementia3CTD_human
TgeneCLUC0750900Alzheimer's Disease, Focal Onset3CTD_human
TgeneCLUC0750901Alzheimer Disease, Early Onset3CTD_human
TgeneCLUC0013221Drug toxicity2CTD_human
TgeneCLUC0029408Degenerative polyarthritis2CTD_human
TgeneCLUC0041755Adverse reaction to drug2CTD_human
TgeneCLUC0086743Osteoarthrosis Deformans2CTD_human
TgeneCLUC0019193Hepatitis, Toxic1CTD_human
TgeneCLUC0022333Jacksonian Seizure1CTD_human
TgeneCLUC0024141Lupus Erythematosus, Systemic1CTD_human
TgeneCLUC0025202melanoma1CTD_human
TgeneCLUC0027686Pathologic Neovascularization1CTD_human
TgeneCLUC0033578Prostatic Neoplasms1CTD_human
TgeneCLUC0036341Schizophrenia1PSYGENET
TgeneCLUC0036572Seizures1CTD_human
TgeneCLUC0087031Juvenile-Onset Still Disease1CTD_human
TgeneCLUC0149958Complex partial seizures1CTD_human
TgeneCLUC0234533Generalized seizures1CTD_human
TgeneCLUC0234535Clonic Seizures1CTD_human
TgeneCLUC0234985Mental deterioration1CTD_human
TgeneCLUC0242380Libman-Sacks Disease1CTD_human
TgeneCLUC0270824Visual seizure1CTD_human
TgeneCLUC0270844Tonic Seizures1CTD_human
TgeneCLUC0270846Epileptic drop attack1CTD_human
TgeneCLUC0333641Atrophic1CTD_human
TgeneCLUC0338656Impaired cognition1CTD_human
TgeneCLUC0376358Malignant neoplasm of prostate1CTD_human
TgeneCLUC0422850Seizures, Somatosensory1CTD_human
TgeneCLUC0422852Seizures, Auditory1CTD_human
TgeneCLUC0422853Olfactory seizure1CTD_human
TgeneCLUC0422854Gustatory seizure1CTD_human
TgeneCLUC0422855Vertiginous seizure1CTD_human
TgeneCLUC0494475Tonic - clonic seizures1CTD_human
TgeneCLUC0751056Non-epileptic convulsion1CTD_human
TgeneCLUC0751110Single Seizure1CTD_human
TgeneCLUC0751123Atonic Absence Seizures1CTD_human
TgeneCLUC0751494Convulsive Seizures1CTD_human
TgeneCLUC0751495Seizures, Focal1CTD_human
TgeneCLUC0751496Seizures, Sensory1CTD_human
TgeneCLUC0860207Drug-Induced Liver Disease1CTD_human
TgeneCLUC1262760Hepatitis, Drug-Induced1CTD_human
TgeneCLUC1270972Mild cognitive disorder1CTD_human
TgeneCLUC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
TgeneCLUC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
TgeneCLUC3495559Juvenile arthritis1CTD_human
TgeneCLUC3495874Nonepileptic Seizures1CTD_human
TgeneCLUC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneCLUC3714758Juvenile psoriatic arthritis1CTD_human
TgeneCLUC4048158Convulsions1CTD_human
TgeneCLUC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneCLUC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneCLUC4316903Absence Seizures1CTD_human
TgeneCLUC4317109Epileptic Seizures1CTD_human
TgeneCLUC4317123Myoclonic Seizures1CTD_human
TgeneCLUC4505436Generalized Absence Seizures1CTD_human
TgeneCLUC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
TgeneCLUC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneCLUC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human