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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:CST3-GFAP (FusionGDB2 ID:HG1471TG2670)

Fusion Gene Summary for CST3-GFAP

check button Fusion gene summary
Fusion gene informationFusion gene name: CST3-GFAP
Fusion gene ID: hg1471tg2670
HgeneTgene
Gene symbol

CST3

GFAP

Gene ID

1471

2670

Gene namecystatin Cglial fibrillary acidic protein
SynonymsARMD11|HEL-S-2ALXDRD
Cytomap('CST3')('GFAP')

20p11.21

17q21.31

Type of geneprotein-codingprotein-coding
Descriptioncystatin-CbA218C14.4 (cystatin C)cystatin 3epididymis secretory protein Li 2gamma-traceneuroendocrine basic polypeptidepost-gamma-globulinglial fibrillary acidic protein
Modification date2020032220200327
UniProtAcc

P01034

P14136

Ensembl transtripts involved in fusion geneENST00000376925, ENST00000398409, 
ENST00000398411, 
Fusion gene scores* DoF score16 X 11 X 3=52825 X 63 X 5=7875
# samples 1651
** MAII scorelog2(16/528*10)=-1.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(51/7875*10)=-3.94871077130315
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CST3 [Title/Abstract] AND GFAP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCST3(23618371)-GFAP(42983740), # 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
HgeneCST3

GO:0006952

defense response

6203523

HgeneCST3

GO:0010466

negative regulation of peptidase activity

6203523|7890620|18256700

HgeneCST3

GO:0045861

negative regulation of proteolysis

3488317

TgeneGFAP

GO:0045109

intermediate filament organization

15732097



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
ChimerDB4LGGTCGA-HT-7680CST3chr20

23618371

-GFAPchr17

42983740

-
ChimerDB4LGGTCGA-TM-A84CCST3chr20

23618371

-GFAPchr17

42983740

-


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Fusion Gene ORF analysis for CST3-GFAP

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
intron-3UTRENST00000376925ENST00000253408CST3chr20

23618371

-GFAPchr17

42983740

-
intron-3UTRENST00000398409ENST00000253408CST3chr20

23618371

-GFAPchr17

42983740

-
intron-3UTRENST00000398411ENST00000253408CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000376925ENST00000435360CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000376925ENST00000586793CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000376925ENST00000588735CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000376925ENST00000591327CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398409ENST00000435360CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398409ENST00000586793CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398409ENST00000588735CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398409ENST00000591327CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398411ENST00000435360CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398411ENST00000586793CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398411ENST00000588735CST3chr20

23618371

-GFAPchr17

42983740

-
intron-intronENST00000398411ENST00000591327CST3chr20

23618371

-GFAPchr17

42983740

-

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 CST3-GFAP


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 CST3-GFAP


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/:23618371/:42983740)
- 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
CST3

P01034

GFAP

P14136

FUNCTION: As an inhibitor of cysteine proteinases, this protein is thought to serve an important physiological role as a local regulator of this enzyme activity.FUNCTION: GFAP, a class-III intermediate filament, is a cell-specific marker that, during the development of the central nervous system, distinguishes astrocytes from other glial cells.

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 CST3-GFAP


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 CST3-GFAP


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 CST3-GFAP


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 CST3-GFAP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCST3C1527338Hereditary Cerebral Amyloid Angiopathy, Icelandic Type5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCST3C2677774Age-Related Macular Degeneration type 113CTD_human;UNIPROT
HgeneCST3C0002395Alzheimer's Disease2CTD_human
HgeneCST3C0011265Presenile dementia2CTD_human
HgeneCST3C0022658Kidney Diseases2CTD_human
HgeneCST3C0022660Kidney Failure, Acute2CTD_human
HgeneCST3C0276496Familial Alzheimer Disease (FAD)2CTD_human
HgeneCST3C0494463Alzheimer Disease, Late Onset2CTD_human
HgeneCST3C0546126Acute Confusional Senile Dementia2CTD_human
HgeneCST3C0750900Alzheimer's Disease, Focal Onset2CTD_human
HgeneCST3C0750901Alzheimer Disease, Early Onset2CTD_human
HgeneCST3C1565662Acute Kidney Insufficiency2CTD_human
HgeneCST3C2609414Acute kidney injury2CTD_human
HgeneCST3C0007222Cardiovascular Diseases1CTD_human
HgeneCST3C0013221Drug toxicity1CTD_human
HgeneCST3C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneCST3C0025286Meningioma1CTD_human
HgeneCST3C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneCST3C0029172Oral Submucous Fibrosis1CTD_human
HgeneCST3C0041755Adverse reaction to drug1CTD_human
HgeneCST3C0205834Meningiomas, Multiple1CTD_human
HgeneCST3C0259785Malignant Meningioma1CTD_human
HgeneCST3C0268393Familial Cerebral Amyloid Angiopathy1CTD_human
HgeneCST3C0281784Benign Meningioma1CTD_human
HgeneCST3C0334605Meningothelial meningioma1CTD_human
HgeneCST3C0334606Fibrous Meningioma1CTD_human
HgeneCST3C0334607Psammomatous Meningioma1CTD_human
HgeneCST3C0334608Angiomatous Meningioma1CTD_human
HgeneCST3C0334609Hemangioblastic Meningioma1CTD_human
HgeneCST3C0334610Hemangiopericytic Meningioma1CTD_human
HgeneCST3C0334611Transitional Meningioma1CTD_human
HgeneCST3C0347515Spinal Meningioma1CTD_human
HgeneCST3C0349604Intracranial Meningioma1CTD_human
HgeneCST3C0431121Clear Cell Meningioma1CTD_human
HgeneCST3C0457190Xanthomatous Meningioma1CTD_human
HgeneCST3C0751303Cerebral Convexity Meningioma1CTD_human
HgeneCST3C0751304Parasagittal Meningioma1CTD_human
HgeneCST3C1334261Intraorbital Meningioma1CTD_human
HgeneCST3C1334271Intraventricular Meningioma1CTD_human
HgeneCST3C1335107Olfactory Groove Meningioma1CTD_human
HgeneCST3C1384406Secretory meningioma1CTD_human
HgeneCST3C1384408Microcystic meningioma1CTD_human
HgeneCST3C1510489Cerebral Amyloid Angiopathy, Hereditary1CTD_human
HgeneCST3C1527197Angioblastic Meningioma1CTD_human
HgeneCST3C1565950Posterior Fossa Meningioma1CTD_human
HgeneCST3C1565951Sphenoid Wing Meningioma1CTD_human
HgeneCST3C1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
HgeneCST3C1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
HgeneCST3C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneCST3C1956349Cerebral Amyloid Angiopathy, Genetic1CTD_human
HgeneCST3C3163622Papillary Meningioma1CTD_human
HgeneCST3C4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
TgeneC0270726Alexander Disease30CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0011570Mental Depression3PSYGENET
TgeneC0011581Depressive disorder3PSYGENET
TgeneC0027765nervous system disorder3CTD_human
TgeneC0005586Bipolar Disorder2PSYGENET
TgeneC0036341Schizophrenia2PSYGENET
TgeneC0041696Unipolar Depression2PSYGENET
TgeneC1269683Major Depressive Disorder2PSYGENET
TgeneC0001973Alcoholic Intoxication, Chronic1PSYGENET
TgeneC0002736Amyotrophic Lateral Sclerosis1CTD_human
TgeneC0014544Epilepsy1CTD_human
TgeneC0017639Gliosis1CTD_human
TgeneC0020429Hyperalgesia1CTD_human
TgeneC0027873Neuromyelitis Optica1CTD_human
TgeneC0030567Parkinson Disease1CTD_human
TgeneC0036572Seizures1GENOMICS_ENGLAND
TgeneC0037917Spina Bifida Cystica1CTD_human
TgeneC0040997Trigeminal Neuralgia1CTD_human
TgeneC0086237Epilepsy, Cryptogenic1CTD_human
TgeneC0236018Aura1CTD_human
TgeneC0393554Amyotrophic Lateral Sclerosis With Dementia1CTD_human
TgeneC0393786Trigeminal Neuralgia, Idiopathic1CTD_human
TgeneC0393787Secondary Trigeminal Neuralgia1CTD_human
TgeneC0458247Allodynia1CTD_human
TgeneC0543859Amyotrophic Lateral Sclerosis, Guam Form1CTD_human
TgeneC0751111Awakening Epilepsy1CTD_human
TgeneC0751211Hyperalgesia, Primary1CTD_human
TgeneC0751212Hyperalgesia, Secondary1CTD_human
TgeneC0751213Tactile Allodynia1CTD_human
TgeneC0751214Hyperalgesia, Thermal1CTD_human
TgeneC0752347Lewy Body Disease1CTD_human
TgeneC0917813Spina Bifida, Open1CTD_human
TgeneC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
TgeneC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
TgeneC2931673Ceroid lipofuscinosis, neuronal 1, infantile1CTD_human
TgeneC2936719Mechanical Allodynia1CTD_human
TgeneC3887640Astrocytosis1CTD_human
TgeneC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
TgeneC4721453Peripheral Nervous System Diseases1CTD_human