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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:COL1A1-SCN1A (FusionGDB2 ID:HG1277TG6323)

Fusion Gene Summary for COL1A1-SCN1A

check button Fusion gene summary
Fusion gene informationFusion gene name: COL1A1-SCN1A
Fusion gene ID: hg1277tg6323
HgeneTgene
Gene symbol

COL1A1

SCN1A

Gene ID

1277

6323

Gene namecollagen type I alpha 1 chainsodium voltage-gated channel alpha subunit 1
SynonymsCAFYD|EDSARTH1|EDSC|OI1|OI2|OI3|OI4EIEE6|FEB3|FEB3A|FHM3|GEFSP2|HBSCI|NAC1|Nav1.1|SCN1|SMEI
Cytomap('COL1A1')('SCN1A')

17q21.33

2q24.3

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(I) chainalpha-1 type I collagenalpha1(I) procollagencollagen alpha 1 chain type Icollagen alpha-1(I) chain preproproteincollagen of skin, tendon and bone, alpha-1 chaincollagen, type I, alpha 1pro-alpha-1 collagen type 1type I prosodium channel protein type 1 subunit alphasodium channel protein type I subunit alphasodium channel protein, brain I alpha subunitsodium channel voltage gated type 1 alpha subunitsodium channel, voltage-gated, type I, alpha polypeptidesodium channel
Modification date2020032220200329
UniProtAcc

P02452

.
Ensembl transtripts involved in fusion geneENST00000225964, 
Fusion gene scores* DoF score56 X 95 X 16=851201 X 1 X 1=1
# samples 861
** MAII scorelog2(86/85120*10)=-6.62901768079909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(1/1*10)=3.32192809488736
Context

PubMed: COL1A1 [Title/Abstract] AND SCN1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL1A1(48262619)-SCN1A(166871076), # 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
HgeneCOL1A1

GO:0010718

positive regulation of epithelial to mesenchymal transition

20018240

HgeneCOL1A1

GO:0030335

positive regulation of cell migration

20018240

HgeneCOL1A1

GO:0034504

protein localization to nucleus

20018240

HgeneCOL1A1

GO:0045893

positive regulation of transcription, DNA-templated

20018240

HgeneCOL1A1

GO:0090263

positive regulation of canonical Wnt signaling pathway

20018240



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
ChiTaRS5.0N/ABI495586COL1A1chr17

48262619

-SCN1Achr2

166871076

+


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Fusion Gene ORF analysis for COL1A1-SCN1A

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-intronENST00000225964ENST00000303395COL1A1chr17

48262619

-SCN1Achr2

166871076

+
intron-intronENST00000225964ENST00000375405COL1A1chr17

48262619

-SCN1Achr2

166871076

+
intron-intronENST00000225964ENST00000409050COL1A1chr17

48262619

-SCN1Achr2

166871076

+
intron-intronENST00000225964ENST00000423058COL1A1chr17

48262619

-SCN1Achr2

166871076

+

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 COL1A1-SCN1A


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 COL1A1-SCN1A


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/:48262619/:166871076)
- 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
COL1A1

P02452

.
FUNCTION: Type I collagen is a member of group I collagen (fibrillar forming collagen).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 COL1A1-SCN1A


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 COL1A1-SCN1A


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 COL1A1-SCN1A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCOL1A1P02452DB00048Collagenase clostridium histolyticumBinderBiotechApproved|Investigational
HgeneCOL1A1P02452DB12872Vonicog AlfaBinderBiotechApproved|Investigational
HgeneCOL1A1P02452DB13133Von Willebrand Factor HumanBinderBiotechApproved|Investigational
HgeneCOL1A1P02452DB11338Clove oilBiotechApproved|Nutraceutical
HgeneCOL1A1P02452DB04866HalofuginoneSmall moleculeInvestigational|Vet_approved

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Related Diseases for COL1A1-SCN1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL1A1C0268358Osteogenesis imperfecta, dominant perinatal lethal38CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0268362Osteogenesis imperfecta type III (disorder)17CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0023931Lobstein Disease15CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0268363Osteogenesis imperfecta type IV (disorder)12GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL1A1C0023890Liver Cirrhosis4CTD_human
HgeneCOL1A1C0239946Fibrosis, Liver4CTD_human
HgeneCOL1A1C4551623EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE, 14CTD_human;GENOMICS_ENGLAND
HgeneCOL1A1C4552122EHLERS-DANLOS SYNDROME, CLASSIC TYPE, 14GENOMICS_ENGLAND;UNIPROT
HgeneCOL1A1C0020497Cortical Congenital Hyperostosis3CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL1A1C0023893Liver Cirrhosis, Experimental3CTD_human
HgeneCOL1A1C0268345EHLERS-DANLOS SYNDROME, ARTHROCHALASIA TYPE2ORPHANET
HgeneCOL1A1C0000786Spontaneous abortion1CTD_human
HgeneCOL1A1C0000822Abortion, Tubal1CTD_human
HgeneCOL1A1C0002949Aneurysm, Dissecting1CTD_human
HgeneCOL1A1C0003504Aortic Valve Insufficiency1CTD_human
HgeneCOL1A1C0004364Autoimmune Diseases1CTD_human
HgeneCOL1A1C0005398Cholestasis, Extrahepatic1CTD_human
HgeneCOL1A1C0005779Blood Coagulation Disorders1GENOMICS_ENGLAND
HgeneCOL1A1C0006663Calcinosis1CTD_human
HgeneCOL1A1C0008311Cholangitis1CTD_human
HgeneCOL1A1C0013720Ehlers-Danlos Syndrome1GENOMICS_ENGLAND
HgeneCOL1A1C0016059Fibrosis1CTD_human
HgeneCOL1A1C0018824Heart valve disease1CTD_human
HgeneCOL1A1C0020538Hypertensive disease1CTD_human
HgeneCOL1A1C0022548Keloid1CTD_human
HgeneCOL1A1C0027719Nephrosclerosis1CTD_human
HgeneCOL1A1C0027726Nephrotic Syndrome1CTD_human
HgeneCOL1A1C0029172Oral Submucous Fibrosis1CTD_human
HgeneCOL1A1C0029434Osteogenesis Imperfecta1CTD_human;GENOMICS_ENGLAND
HgeneCOL1A1C0149721Left Ventricular Hypertrophy1CTD_human
HgeneCOL1A1C0220679Ehlers-Danlos Syndrome, Autosomal Dominant, Type Unspecified1ORPHANET
HgeneCOL1A1C0263628Tumoral calcinosis1CTD_human
HgeneCOL1A1C0340643Dissection of aorta1CTD_human
HgeneCOL1A1C0521174Microcalcification1CTD_human
HgeneCOL1A1C1458140Bleeding tendency1GENOMICS_ENGLAND
HgeneCOL1A1C1619692Nephrogenic Fibrosing Dermopathy1CTD_human
HgeneCOL1A1C1623038Cirrhosis1CTD_human
HgeneCOL1A1C1846545Autoimmune Lymphoproliferative Syndrome Type 2B1GENOMICS_ENGLAND
HgeneCOL1A1C3830362Early Pregnancy Loss1CTD_human
HgeneCOL1A1C4277533Dissection, Blood Vessel1CTD_human
HgeneCOL1A1C4552766Miscarriage1CTD_human
TgeneC4551549Early Infantile Epileptic Encephalopathy 646GENOMICS_ENGLAND;UNIPROT
TgeneC1858673GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS, TYPE 232CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0751122Infantile Severe Myoclonic Epilepsy17CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneC1864987Migraine, Familial Hemiplegic, 317CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC3502809Generalized Epilepsy with Febrile Seizures Plus15CLINGEN
TgeneC0014544Epilepsy4CTD_human
TgeneC0086237Epilepsy, Cryptogenic4CTD_human
TgeneC0236018Aura4CTD_human
TgeneC0751111Awakening Epilepsy4CTD_human
TgeneC0009952Febrile Convulsions3CTD_human
TgeneC0149886Seizure, Febrile, Simple3CTD_human
TgeneC0751057Seizure, Febrile, Complex3CTD_human
TgeneC0238111Lennox-Gastaut syndrome2ORPHANET
TgeneC0393706Early infantile epileptic encephalopathy with suppression bursts2CLINGEN
TgeneC3463992EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 12CLINGEN
TgeneC4552072X-linked infantile spasms2CLINGEN
TgeneC0014548Epilepsy, Generalized1CTD_human
TgeneC0014550Myoclonic Epilepsy1CTD_human
TgeneC0017332Generalized Nonconvulsive Seizure Disorder1CTD_human
TgeneC0020796Profound Mental Retardation1CTD_human
TgeneC0025363Mental Retardation, Psychosocial1CTD_human
TgeneC0026650Movement Disorders1CTD_human
TgeneC0086236Epilepsy, Atonic1CTD_human
TgeneC0086241Epilepsy, Tonic1CTD_human
TgeneC0266487Etat Marbre1CTD_human
TgeneC0270854Symptomatic Generalized Epilepsy1CTD_human
TgeneC0311334Generalized convulsive epilepsy1CTD_human
TgeneC0338478Idiopathic Myoclonic Epilepsy1CTD_human
TgeneC0338479Symptomatic Myoclonic Epilepsy1CTD_human
TgeneC0347869Epilepsy, Akinetic1CTD_human
TgeneC0393695Early Childhood Epilepsy, Myoclonic1CTD_human
TgeneC0393702Myoclonic Astatic Epilepsy1CTD_human
TgeneC0393703Myoclonic Absence Epilepsy1CTD_human
TgeneC0438414Myoclonic Encephalopathy1CTD_human
TgeneC0751120Benign Infantile Myoclonic Epilepsy1CTD_human
TgeneC0917800Epilepsy, Myoclonic, Infantile1CTD_human
TgeneC0917816Mental deficiency1CTD_human
TgeneC1510586Autism Spectrum Disorders1CTD_human
TgeneC1535926Neurodevelopmental Disorders1CTD_human
TgeneC3496069cocaine use1PSYGENET
TgeneC3714756Intellectual Disability1CTD_human