FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 7947

FusionGeneSummary for COL3A1_VMP1

check button Fusion gene summary
Fusion gene informationFusion gene name: COL3A1_VMP1
Fusion gene ID: 7947
HgeneTgene
Gene symbol

COL3A1

VMP1

Gene ID

1281

81671

Gene namecollagen type III alpha 1 chainvacuole membrane protein 1
SynonymsEDS4A|EDSVASCEPG3|TANGO5|TMEM49
Cytomap

2q32.2

17q23.1

Type of geneprotein-codingprotein-coding
Descriptioncollagen alpha-1(III) chainEhlers-Danlos syndrome type IV, autosomal dominantalpha-1 type III collagenalpha1 (III) collagencollagen, fetalcollagen, type III, alpha 1vacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homolog
Modification date2018052320180523
UniProtAcc

P02461

Q96GC9

Ensembl transtripts involved in fusion geneENST00000304636, ENST00000317840, 
ENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
Fusion gene scores* DoF score24 X 18 X 11=475224 X 11 X 12=3168
# samples 2927
** MAII scorelog2(29/4752*10)=-4.03441003078583
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(27/3168*10)=-3.55254102302878
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: COL3A1 [Title/Abstract] AND VMP1 [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
HgeneCOL3A1

GO:0007160

cell-matrix adhesion

16912226

HgeneCOL3A1

GO:0007179

transforming growth factor beta receptor signaling pathway

16360482

HgeneCOL3A1

GO:0009314

response to radiation

14736764

HgeneCOL3A1

GO:0018149

peptide cross-linking

16754721

HgeneCOL3A1

GO:0034097

response to cytokine

9076960|16360482

HgeneCOL3A1

GO:0042060

wound healing

1466622


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
TCGALDLUADTCGA-05-4405-01ACOL3A1chr2

189872868

+VMP1chr17

57915656

+
* 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
Frame-shitENST00000304636ENST00000262291COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000304636ENST00000537567COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000304636ENST00000539763COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000304636ENST00000536180COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000304636ENST00000545362COL3A1chr2

189872868

+VMP1chr17

57915656

+
5CDS-intronENST00000304636ENST00000588617COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000317840ENST00000262291COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000317840ENST00000537567COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000317840ENST00000539763COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000317840ENST00000536180COL3A1chr2

189872868

+VMP1chr17

57915656

+
Frame-shitENST00000317840ENST00000545362COL3A1chr2

189872868

+VMP1chr17

57915656

+
5CDS-intronENST00000317840ENST00000588617COL3A1chr2

189872868

+VMP1chr17

57915656

+

Top

FusionProtFeatures for COL3A1_VMP1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
COL3A1

P02461

VMP1

Q96GC9

Stress-induced protein that, when overexpressed,promotes formation of intracellular vacuoles followed by celldeath. May be involved in the cytoplasmic vacuolization of acinarcells during the early stage of acute pancreatitis. Plays a rolein the initial stages of the autophagic process through itsinteraction with BECN1 (By similarity). Involved in cell-celladhesion. Plays an essential role in formation of cell junctions.{ECO:0000250, ECO:0000269|PubMed:17724469}.

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


Top

FusionGeneSequence for COL3A1_VMP1


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).

Top

FusionGenePPI for COL3A1_VMP1


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
COL3A1SPARC, THBS1, MAG, SP1, CAND1, MYOC, PDGFA, PDGFB, ERAL1VMP1HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNA


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


Top

RelatedDrugs for COL3A1_VMP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneCOL3A1P02461DB00048Collagenase clostridium histolyticumCollagen alpha-1(III) chainbiotechapproved|investigational

Top

RelatedDiseases for COL3A1_VMP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCOL3A1C0268338Ehlers-Danlos Syndrome, Type IV23ORPHANET;UNIPROT
HgeneCOL3A1C0023890Liver Cirrhosis5CTD_human
HgeneCOL3A1C0023893Liver Cirrhosis, Experimental2CTD_human
HgeneCOL3A1C1853365AORTIC ANEURYSM, FAMILIAL ABDOMINAL 12ORPHANET;UNIPROT
HgeneCOL3A1C0003504Aortic Valve Insufficiency1CTD_human
HgeneCOL3A1C0015695Fatty Liver1CTD_human
HgeneCOL3A1C0016059Fibrosis1CTD_human
HgeneCOL3A1C0020443Hypercholesterolemia1CTD_human
HgeneCOL3A1C0020456Hyperglycemia1CTD_human
HgeneCOL3A1C0020459Hyperinsulinism1CTD_human
HgeneCOL3A1C0020538Hypertensive disease1CTD_human
HgeneCOL3A1C0022548Keloid1CTD_human
HgeneCOL3A1C0023891Liver Cirrhosis, Alcoholic1CTD_human
HgeneCOL3A1C0023895Liver diseases1CTD_human
HgeneCOL3A1C0034069Pulmonary Fibrosis1CTD_human
HgeneCOL3A1C0036341Schizophrenia1CTD_human
HgeneCOL3A1C0041956Ureteral obstruction1CTD_human
HgeneCOL3A1C0149721Left Ventricular Hypertrophy1CTD_human
HgeneCOL3A1C0238288Muscular Dystrophy, Facioscapulohumeral1CTD_human
HgeneCOL3A1C0268337Ehlers-Danlos syndrome, type 3 (disorder)1CTD_human;UNIPROT
HgeneCOL3A1C0553980Endomyocardial Fibrosis1CTD_human
HgeneCOL3A1C4277682Chemical and Drug Induced Liver Injury1CTD_human