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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:COL4A1-COL4A1 (FusionGDB2 ID:18348)

Fusion Gene Summary for COL4A1-COL4A1

check button Fusion gene summary
Fusion gene informationFusion gene name: COL4A1-COL4A1
Fusion gene ID: 18348
HgeneTgene
Gene symbol

COL4A1

COL4A1

Gene ID

1282

1282

Gene namecollagen type IV alpha 1 chaincollagen type IV alpha 1 chain
SynonymsBSVD|BSVD1|PADMAL|RATORBSVD|BSVD1|PADMAL|RATOR
Cytomap

13q34

13q34

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(IV) chainCOL4A1 NC1 domainarrestencollagen IV, alpha-1 polypeptidecollagen of basement membrane, alpha-1 chaincollagen alpha-1(IV) chainCOL4A1 NC1 domainarrestencollagen IV, alpha-1 polypeptidecollagen of basement membrane, alpha-1 chain
Modification date2020031320200313
UniProtAcc.

P02462

Ensembl transtripts involved in fusion geneENST00000375820, ENST00000543140, 
ENST00000467182, 		ENST00000375820, 
ENST00000543140, ENST00000467182, 
Fusion gene scores* DoF score13 X 15 X 8=156014 X 14 X 7=1372
# samples 1516
** MAII scorelog2(15/1560*10)=-3.37851162325373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1372*10)=-3.10013667128545
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL4A1 [Title/Abstract] AND COL4A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCOL4A1(110801739)-COL4A1(110801827), # samples:1
COL4A1(110802192)-COL4A1(110814754), # samples:1
COL4A1(110801502)-COL4A1(110801974), # 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 COL4A1 (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 COL4A1 (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
ChiTaRS5.0N/ABF911869COL4A1chr13

110801739

-COL4A1chr13

110801827

+
ChiTaRS5.0N/ABP422422COL4A1chr13

110802192

+COL4A1chr13

110814754

-
ChiTaRS5.0N/AW58624COL4A1chr13

110801502

+COL4A1chr13

110801974

-


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Fusion Gene ORF analysis for COL4A1-COL4A1

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-3UTRENST00000375820ENST00000375820COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-intronENST00000375820ENST00000543140COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-intronENST00000375820ENST00000467182COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-3UTRENST00000543140ENST00000375820COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-intronENST00000543140ENST00000543140COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-intronENST00000543140ENST00000467182COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-3UTRENST00000467182ENST00000375820COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-intronENST00000467182ENST00000543140COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-intronENST00000467182ENST00000467182COL4A1chr13

110801739

-COL4A1chr13

110801827

+
intron-3CDSENST00000375820ENST00000375820COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-intronENST00000375820ENST00000543140COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-5UTRENST00000375820ENST00000467182COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-3CDSENST00000543140ENST00000375820COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-intronENST00000543140ENST00000543140COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-5UTRENST00000543140ENST00000467182COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-3CDSENST00000467182ENST00000375820COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-intronENST00000467182ENST00000543140COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-5UTRENST00000467182ENST00000467182COL4A1chr13

110802192

+COL4A1chr13

110814754

-
intron-3UTRENST00000375820ENST00000375820COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-intronENST00000375820ENST00000543140COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-intronENST00000375820ENST00000467182COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-3UTRENST00000543140ENST00000375820COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-intronENST00000543140ENST00000543140COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-intronENST00000543140ENST00000467182COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-3UTRENST00000467182ENST00000375820COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-intronENST00000467182ENST00000543140COL4A1chr13

110801502

+COL4A1chr13

110801974

-
intron-intronENST00000467182ENST00000467182COL4A1chr13

110801502

+COL4A1chr13

110801974

-

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 COL4A1-COL4A1


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 COL4A1-COL4A1


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
.COL4A1

P02462

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen. {ECO:0000250|UniProtKB:P02463}.; FUNCTION: Arresten, comprising the C-terminal NC1 domain, inhibits angiogenesis and tumor formation. The C-terminal half is found to possess the anti-angiogenic activity. Specifically inhibits endothelial cell proliferation, migration and tube formation. {ECO:0000269|PubMed:10811134, ECO:0000269|PubMed:18775695}.

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 COL4A1-COL4A1


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 COL4A1-COL4A1


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 COL4A1-COL4A1


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 COL4A1-COL4A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL4A1C4551998Porencephaly, Type 1, Autosomal Dominant18CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL4A1C2673195Angiopathy, Hereditary, With Nephropathy, Aneurysms, And Muscle Cramps6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCOL4A1C1843512BRAIN SMALL VESSEL DISEASE WITH HEMORRHAGE4CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneCOL4A1C0018965Hematuria3GENOMICS_ENGLAND
HgeneCOL4A1C0266548Axenfeld anomaly (disorder)3CTD_human;GENOMICS_ENGLAND
HgeneCOL4A1C1860475Retinal vascular tortuosity3GENOMICS_ENGLAND
HgeneCOL4A1C0011881Diabetic Nephropathy2CTD_human
HgeneCOL4A1C0017667Nodular glomerulosclerosis2CTD_human
HgeneCOL4A1C0017668Focal glomerulosclerosis2CTD_human
HgeneCOL4A1C0086432Hyalinosis, Segmental Glomerular2CTD_human
HgeneCOL4A1C0265341Rieger syndrome2CTD_human
HgeneCOL4A1C0266484Schizencephaly2CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCOL4A1C0302892Congenital porencephaly2CTD_human
HgeneCOL4A1C1280768Axenfeld syndrome2CTD_human
HgeneCOL4A1C1867983PORENCEPHALY, FAMILIAL2CTD_human;ORPHANET
HgeneCOL4A1C2675650Brain Small Vessel Disease With Axenfeld-Rieger Anomaly2CTD_human
HgeneCOL4A1C2678503AXENFELD-RIEGER SYNDROME, TYPE 32CTD_human
HgeneCOL4A1C3281105HEMORRHAGE, INTRACEREBRAL, SUSCEPTIBILITY TO2GENOMICS_ENGLAND;UNIPROT
HgeneCOL4A1C3495488Axenfeld-Rieger syndrome2CTD_human
HgeneCOL4A1C3698507Post-traumatic Porencephaly2CTD_human
HgeneCOL4A1C3714873Axenfeld-Rieger Syndrome, Type 12CTD_human
HgeneCOL4A1C4082173Porencephaly2CTD_human
HgeneCOL4A1C4082301Developmental Porencephaly2CTD_human
HgeneCOL4A1C0002878Anemia, Hemolytic1CTD_human
HgeneCOL4A1C0002879Anemia, Hemolytic, Acquired1CTD_human
HgeneCOL4A1C0002889Anemia, Microangiopathic1CTD_human
HgeneCOL4A1C0015393Eye Abnormalities1CTD_human
HgeneCOL4A1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneCOL4A1C0026848Myopathy1GENOMICS_ENGLAND
HgeneCOL4A1C0027726Nephrotic Syndrome1CTD_human
HgeneCOL4A1C0036572Seizures1GENOMICS_ENGLAND
HgeneCOL4A1C0038454Cerebrovascular accident1GENOMICS_ENGLAND
HgeneCOL4A1C0149931Migraine Disorders1GENOMICS_ENGLAND
HgeneCOL4A1C0221021Microangiopathic hemolytic anemia1CTD_human
HgeneCOL4A1C0265221Walker-Warburg congenital muscular dystrophy1ORPHANET
HgeneCOL4A1C0270612Leukoencephalopathy1CTD_human
HgeneCOL4A1C0338656Impaired cognition1GENOMICS_ENGLAND
HgeneCOL4A1C0424605Developmental delay (disorder)1GENOMICS_ENGLAND
HgeneCOL4A1C0497327Dementia1GENOMICS_ENGLAND
HgeneCOL4A1C0557874Global developmental delay1GENOMICS_ENGLAND
HgeneCOL4A1C1135196Heart Failure, Diastolic1CTD_human
HgeneCOL4A1C1858991Childhood Ataxia with Central Nervous System Hypomyelinization1CTD_human
HgeneCOL4A1C1867327RETINAL ARTERIES, TORTUOSITY OF1CTD_human;ORPHANET;UNIPROT
HgeneCOL4A1C2733158Cerebral Small Vessel Diseases1GENOMICS_ENGLAND
HgeneCOL4A1C2930808Familial vascular leukoencephalopathy1ORPHANET
HgeneCOL4A1C2931870Familial schizencephaly1ORPHANET
HgeneCOL4A1C4013035BRAIN SMALL VESSEL DISEASE WITH OR WITHOUT OCULAR ANOMALIES1GENOMICS_ENGLAND
TgeneCOL4A1C4551998Porencephaly, Type 1, Autosomal Dominant18CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneCOL4A1C2673195Angiopathy, Hereditary, With Nephropathy, Aneurysms, And Muscle Cramps6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneCOL4A1C1843512BRAIN SMALL VESSEL DISEASE WITH HEMORRHAGE4CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneCOL4A1C0018965Hematuria3GENOMICS_ENGLAND
TgeneCOL4A1C0266548Axenfeld anomaly (disorder)3CTD_human;GENOMICS_ENGLAND
TgeneCOL4A1C1860475Retinal vascular tortuosity3GENOMICS_ENGLAND
TgeneCOL4A1C0011881Diabetic Nephropathy2CTD_human
TgeneCOL4A1C0017667Nodular glomerulosclerosis2CTD_human
TgeneCOL4A1C0017668Focal glomerulosclerosis2CTD_human
TgeneCOL4A1C0086432Hyalinosis, Segmental Glomerular2CTD_human
TgeneCOL4A1C0265341Rieger syndrome2CTD_human
TgeneCOL4A1C0266484Schizencephaly2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneCOL4A1C0302892Congenital porencephaly2CTD_human
TgeneCOL4A1C1280768Axenfeld syndrome2CTD_human
TgeneCOL4A1C1867983PORENCEPHALY, FAMILIAL2CTD_human;ORPHANET
TgeneCOL4A1C2675650Brain Small Vessel Disease With Axenfeld-Rieger Anomaly2CTD_human
TgeneCOL4A1C2678503AXENFELD-RIEGER SYNDROME, TYPE 32CTD_human
TgeneCOL4A1C3281105HEMORRHAGE, INTRACEREBRAL, SUSCEPTIBILITY TO2GENOMICS_ENGLAND;UNIPROT
TgeneCOL4A1C3495488Axenfeld-Rieger syndrome2CTD_human
TgeneCOL4A1C3698507Post-traumatic Porencephaly2CTD_human
TgeneCOL4A1C3714873Axenfeld-Rieger Syndrome, Type 12CTD_human
TgeneCOL4A1C4082173Porencephaly2CTD_human
TgeneCOL4A1C4082301Developmental Porencephaly2CTD_human
TgeneCOL4A1C0002878Anemia, Hemolytic1CTD_human
TgeneCOL4A1C0002879Anemia, Hemolytic, Acquired1CTD_human
TgeneCOL4A1C0002889Anemia, Microangiopathic1CTD_human
TgeneCOL4A1C0015393Eye Abnormalities1CTD_human
TgeneCOL4A1C0023893Liver Cirrhosis, Experimental1CTD_human
TgeneCOL4A1C0026848Myopathy1GENOMICS_ENGLAND
TgeneCOL4A1C0027726Nephrotic Syndrome1CTD_human
TgeneCOL4A1C0036572Seizures1GENOMICS_ENGLAND
TgeneCOL4A1C0038454Cerebrovascular accident1GENOMICS_ENGLAND
TgeneCOL4A1C0149931Migraine Disorders1GENOMICS_ENGLAND
TgeneCOL4A1C0221021Microangiopathic hemolytic anemia1CTD_human
TgeneCOL4A1C0265221Walker-Warburg congenital muscular dystrophy1ORPHANET
TgeneCOL4A1C0270612Leukoencephalopathy1CTD_human
TgeneCOL4A1C0338656Impaired cognition1GENOMICS_ENGLAND
TgeneCOL4A1C0424605Developmental delay (disorder)1GENOMICS_ENGLAND
TgeneCOL4A1C0497327Dementia1GENOMICS_ENGLAND
TgeneCOL4A1C0557874Global developmental delay1GENOMICS_ENGLAND
TgeneCOL4A1C1135196Heart Failure, Diastolic1CTD_human
TgeneCOL4A1C1858991Childhood Ataxia with Central Nervous System Hypomyelinization1CTD_human
TgeneCOL4A1C1867327RETINAL ARTERIES, TORTUOSITY OF1CTD_human;ORPHANET;UNIPROT
TgeneCOL4A1C2733158Cerebral Small Vessel Diseases1GENOMICS_ENGLAND
TgeneCOL4A1C2930808Familial vascular leukoencephalopathy1ORPHANET
TgeneCOL4A1C2931870Familial schizencephaly1ORPHANET
TgeneCOL4A1C4013035BRAIN SMALL VESSEL DISEASE WITH OR WITHOUT OCULAR ANOMALIES1GENOMICS_ENGLAND