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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:COL4A5-PAFAH1B1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: COL4A5-PAFAH1B1
FusionPDB ID: 18374
FusionGDB2.0 ID: 18374
HgeneTgene
Gene symbol

COL4A5

PAFAH1B1

Gene ID

1287

5048

Gene namecollagen type IV alpha 5 chainplatelet activating factor acetylhydrolase 1b regulatory subunit 1
SynonymsASLN|ATS|ATS1|CA54LIS1|LIS2|MDCR|MDS|NudF|PAFAH
Cytomap

Xq22.3

17p13.3

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-5(IV) chaincollagen IV, alpha-5 polypeptidecollagen of basement membrane, alpha-5 chaincollagen, type IV, alpha 5dA149D17.3dA24A23.1platelet-activating factor acetylhydrolase IB subunit alphalissencephaly 1 proteinplatelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)platelet-activatin
Modification date2020031320200313
UniProtAcc

P29400

.
Ensembl transtripts involved in fusion geneENST idsENST00000328300, ENST00000361603, 
ENST00000477429, 
ENST00000451360, 
ENST00000572915, ENST00000397195, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 9 X 6=64818 X 14 X 8=2016
# samples 1218
** MAII scorelog2(12/648*10)=-2.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/2016*10)=-3.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: COL4A5 [Title/Abstract] AND PAFAH1B1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)COL4A5(107840798)-PAFAH1B1(2585023), # samples:1
Anticipated loss of major functional domain due to fusion event.COL4A5-PAFAH1B1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
COL4A5-PAFAH1B1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
COL4A5-PAFAH1B1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
COL4A5-PAFAH1B1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
* 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
TgenePAFAH1B1

GO:0007017

microtubule-based process

11940666


check buttonFusion gene breakpoints across COL4A5 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PAFAH1B1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4GBMTCGA-06-0190-01ACOL4A5chrX

107840798

+PAFAH1B1chr17

2585023

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000328300COL4A5chrX107840798+ENST00000397195PAFAH1B1chr172585023+591020232442064606
ENST00000361603COL4A5chrX107840798+ENST00000397195PAFAH1B1chr172585023+591020232442064606

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
ENST00000328300ENST00000397195COL4A5chrX107840798+PAFAH1B1chr172585023+0.0007321450.9992679
ENST00000361603ENST00000397195COL4A5chrX107840798+PAFAH1B1chr172585023+0.0007321450.9992679

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>18374_18374_1_COL4A5-PAFAH1B1_COL4A5_chrX_107840798_ENST00000328300_PAFAH1B1_chr17_2585023_ENST00000397195_length(amino acids)=606AA_BP=
MKLRGVSLAAGLFLLALSLWGQPAEAAACYGCSPGSKCDCSGIKGEKGERGFPGLEGHPGLPGFPGPEGPPGPRGQKGDDGIPGPPGPKG
IRGPPGLPGFPGTPGLPGMPGHDGAPGPQGIPGCNGTKGERGFPGSPGFPGLQGPPGPPGIPGMKGEPGSIIMSSLPGPKGNPGYPGPPG
IQGLPGPTGIPGPIGPPGPPGLMGPPGPPGLPGPKGNMGLNFQGPKGEKGEQGLQGPPGPPGQISEQKRPIDVEFQKGDQGLPGDRGPPG
PPGIRGPPGPPGGEKGEKGEQGEPGKRGKPGKDGENGQPGIPGLPGDPGYPGEPGRDGEKGQKGDTGPPGPPGLVIPRPGTGITIGEKGN
IGLPGLPGEKGERGFPGIQGPPGLPGPPGAAVMGPPGPPGFPGERGQKGDEGPPGISIPGPPGLDGQPGAPGLPGPPGPAGPHIPPSDEI
CEPGPPGPPGSPGDKGLQGEQGVKGDKGDTCFNCIGTGISGPPGQPGLPGLPGPPGSLGFPGQKGEKGQAGATGPKGLPGIPGAPGAPGF

--------------------------------------------------------------

>18374_18374_2_COL4A5-PAFAH1B1_COL4A5_chrX_107840798_ENST00000361603_PAFAH1B1_chr17_2585023_ENST00000397195_length(amino acids)=606AA_BP=
MKLRGVSLAAGLFLLALSLWGQPAEAAACYGCSPGSKCDCSGIKGEKGERGFPGLEGHPGLPGFPGPEGPPGPRGQKGDDGIPGPPGPKG
IRGPPGLPGFPGTPGLPGMPGHDGAPGPQGIPGCNGTKGERGFPGSPGFPGLQGPPGPPGIPGMKGEPGSIIMSSLPGPKGNPGYPGPPG
IQGLPGPTGIPGPIGPPGPPGLMGPPGPPGLPGPKGNMGLNFQGPKGEKGEQGLQGPPGPPGQISEQKRPIDVEFQKGDQGLPGDRGPPG
PPGIRGPPGPPGGEKGEKGEQGEPGKRGKPGKDGENGQPGIPGLPGDPGYPGEPGRDGEKGQKGDTGPPGPPGLVIPRPGTGITIGEKGN
IGLPGLPGEKGERGFPGIQGPPGLPGPPGAAVMGPPGPPGFPGERGQKGDEGPPGISIPGPPGLDGQPGAPGLPGPPGPAGPHIPPSDEI
CEPGPPGPPGSPGDKGLQGEQGVKGDKGDTCFNCIGTGISGPPGQPGLPGLPGPPGSLGFPGQKGEKGQAGATGPKGLPGIPGAPGAPGF

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Fusion Protein Functional Features


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/chrX:107840798/chr17:2585023)
- 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
COL4A5

P29400

.
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.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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOL4A5chrX:107840798chr17:2585023ENST00000328300+245327_41593.01692.0RegionNote=Nonhelical region (NC2)
HgeneCOL4A5chrX:107840798chr17:2585023ENST00000361603+245127_41593.01686.0RegionNote=Nonhelical region (NC2)

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCOL4A5chrX:107840798chr17:2585023ENST00000328300+24531461_1685593.01692.0DomainCollagen IV NC1
HgeneCOL4A5chrX:107840798chr17:2585023ENST00000361603+24511461_1685593.01686.0DomainCollagen IV NC1
HgeneCOL4A5chrX:107840798chr17:2585023ENST00000328300+245342_1456593.01692.0RegionNote=Triple-helical region
HgeneCOL4A5chrX:107840798chr17:2585023ENST00000361603+245142_1456593.01686.0RegionNote=Triple-helical region
TgenePAFAH1B1chrX:107840798chr17:2585023ENST0000039719591156_82386.3333333333333411.0Coiled coilOntology_term=ECO:0000255
TgenePAFAH1B1chrX:107840798chr17:2585023ENST000003971959117_39386.3333333333333411.0DomainLisH
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911106_147386.3333333333333411.0RepeatNote=WD 1
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911148_187386.3333333333333411.0RepeatNote=WD 2
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911190_229386.3333333333333411.0RepeatNote=WD 3
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911232_271386.3333333333333411.0RepeatNote=WD 4
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911274_333386.3333333333333411.0RepeatNote=WD 5
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911336_377386.3333333333333411.0RepeatNote=WD 6
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911378_410386.3333333333333411.0RepeatNote=WD 7


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
COL4A5
PAFAH1B1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
TgenePAFAH1B1chrX:107840798chr17:2585023ENST00000397195911367_409386.3333333333333411.0DCX
TgenePAFAH1B1chrX:107840798chr17:2585023ENST0000039719591183_410386.3333333333333411.0dynein and dynactin
TgenePAFAH1B1chrX:107840798chr17:2585023ENST000003971959111_66386.3333333333333411.0NDE1
TgenePAFAH1B1chrX:107840798chr17:2585023ENST000003971959111_102386.3333333333333411.0NDEL1


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Related Drugs to COL4A5-PAFAH1B1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to COL4A5-PAFAH1B1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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