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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 7965

FusionGeneSummary for COL4A4_VPS26B

check button Fusion gene summary
Fusion gene informationFusion gene name: COL4A4_VPS26B
Fusion gene ID: 7965
HgeneTgene
Gene symbol

COL4A4

VPS26B

Gene ID

1286

112936

Gene namecollagen type IV alpha 4 chainVPS26, retromer complex component B
SynonymsCA44Pep8b
Cytomap

2q36.3

11q25

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-4(IV) chainCollagen IV, alpha-4 polypeptidecollagen of basement membrane, alpha-4 chaincollagen, type IV, alpha 4vacuolar protein sorting-associated protein 26Bvesicle protein sorting 26B
Modification date2018052320180523
UniProtAcc

P53420

Q4G0F5

Ensembl transtripts involved in fusion geneENST00000396625, ENST00000329662, 
ENST00000281187, ENST00000525095, 
ENST00000530402, 
Fusion gene scores* DoF score1 X 1 X 1=13 X 3 X 2=18
# samples 13
** MAII scorelog2(1/1*10)=3.32192809488736log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: COL4A4 [Title/Abstract] AND VPS26B [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1BF376481COL4A4chr2

227972900

+VPS26Bchr11

134116898

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-3UTRENST00000396625ENST00000281187COL4A4chr2

227972900

+VPS26Bchr11

134116898

+
intron-intronENST00000396625ENST00000525095COL4A4chr2

227972900

+VPS26Bchr11

134116898

+
intron-intronENST00000396625ENST00000530402COL4A4chr2

227972900

+VPS26Bchr11

134116898

+
intron-3UTRENST00000329662ENST00000281187COL4A4chr2

227972900

+VPS26Bchr11

134116898

+
intron-intronENST00000329662ENST00000525095COL4A4chr2

227972900

+VPS26Bchr11

134116898

+
intron-intronENST00000329662ENST00000530402COL4A4chr2

227972900

+VPS26Bchr11

134116898

+

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FusionProtFeatures for COL4A4_VPS26B


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL4A4

P53420

VPS26B

Q4G0F5

Type IV collagen is the major structural component ofglomerular basement membranes (GBM), forming a 'chicken-wire'meshwork together with laminins, proteoglycans andentactin/nidogen. Acts as component of the retromer cargo-selectivecomplex (CSC). The CSC is believed to be the core functionalcomponent of retromer or respective retromer complex variantsacting to prevent missorting of selected transmembrane cargoproteins into the lysosomal degradation pathway. The recruitmentof the CSC to the endosomal membrane involves RAB7A and SNX3. TheSNX-BAR retromer mediates retrograde transport of cargo proteinsfrom endosomes to the trans-Golgi network (TGN) and is involved inendosome-to-plasma membrane transport for cargo protein recycling.The SNX3-retromer mediates the retrograde transport of WLSdistinct from the SNX-BAR retromer pathway. The SNX27-retromer isbelieved to be involved in endosome-to-plasma membrane traffickingand recycling of a broad spectrum of cargo proteins. The CSC seemsto act as recruitment hub for other proteins, such as the WASHcomplex and TBC1D5. May be involved in retrograde transport ofSORT1 but not of IGF2R. Acts redundantly with VSP26A in SNX-27mediated endocytic recycling of SLC2A1/GLUT1 (By similarity).{ECO:0000250|UniProtKB:O75436, ECO:0000250|UniProtKB:Q8C0E2}.

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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FusionGeneSequence for COL4A4_VPS26B


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for COL4A4_VPS26B


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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RelatedDrugs for COL4A4_VPS26B


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for COL4A4_VPS26B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL4A4C0241908Hematuria, Benign Familial3UNIPROT
HgeneCOL4A4C1567744Alport Syndrome, Autosomal Recessive2ORPHANET;UNIPROT