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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: 41408

FusionGeneSummary for VCP_HNRNPA2B1

check button Fusion gene summary
Fusion gene informationFusion gene name: VCP_HNRNPA2B1
Fusion gene ID: 41408
HgeneTgene
Gene symbol

VCP

HNRNPA2B1

Gene ID

7415

3181

Gene namevalosin containing proteinheterogeneous nuclear ribonucleoprotein A2/B1
SynonymsCDC48|TERA|p97HNRNPA2|HNRNPB1|HNRPA2|HNRPA2B1|HNRPB1|IBMPFD2|RNPA2|SNRPB1
Cytomap

9p13.3

7p15.2

Type of geneprotein-codingprotein-coding
Descriptiontransitional endoplasmic reticulum ATPase15S Mg(2+)-ATPase p97 subunitTER ATPaseheterogeneous nuclear ribonucleoproteins A2/B1HNRNPA2B1/MYC fusionhnRNP A2 / hnRNP B1nuclear ribonucleoprotein particle A2 protein
Modification date2018052320180523
UniProtAcc

P55072

P22626

Ensembl transtripts involved in fusion geneENST00000358901, ENST00000476233, 
ENST00000354667, ENST00000356674, 
Fusion gene scores* DoF score7 X 9 X 3=18915 X 19 X 2=570
# samples 1021
** MAII scorelog2(10/189*10)=-0.918386234446348
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/570*10)=-1.44057259138598
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VCP [Title/Abstract] AND HNRNPA2B1 [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
HgeneVCP

GO:0006302

double-strand break repair

10855792|22120668

HgeneVCP

GO:0006974

cellular response to DNA damage stimulus

16140914|22120668|23042605

HgeneVCP

GO:0016567

protein ubiquitination

22120668

HgeneVCP

GO:0030433

ubiquitin-dependent ERAD pathway

17872946

HgeneVCP

GO:0030970

retrograde protein transport, ER to cytosol

15215856

HgeneVCP

GO:0031334

positive regulation of protein complex assembly

18775313

HgeneVCP

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

9452483

HgeneVCP

GO:0036503

ERAD pathway

25088257

HgeneVCP

GO:0045732

positive regulation of protein catabolic process

11483959|18775313

HgeneVCP

GO:0090263

positive regulation of canonical Wnt signaling pathway

28689657

HgeneVCP

GO:1903006

positive regulation of protein K63-linked deubiquitination

22970133

HgeneVCP

GO:1903007

positive regulation of Lys63-specific deubiquitinase activity

22970133

TgeneHNRNPA2B1

GO:0006397

mRNA processing

2557628

TgeneHNRNPA2B1

GO:0006406

mRNA export from nucleus

10567417

TgeneHNRNPA2B1

GO:0031053

primary miRNA processing

26321680

TgeneHNRNPA2B1

GO:0050658

RNA transport

17004321

TgeneHNRNPA2B1

GO:1990428

miRNA transport

24356509


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
ChiTaRS3.1BF082148VCPchr9

35064227

-HNRNPA2B1chr7

26232909

-
* 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-intronENST00000358901ENST00000476233VCPchr9

35064227

-HNRNPA2B1chr7

26232909

-
intron-intronENST00000358901ENST00000354667VCPchr9

35064227

-HNRNPA2B1chr7

26232909

-
intron-intronENST00000358901ENST00000356674VCPchr9

35064227

-HNRNPA2B1chr7

26232909

-

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FusionProtFeatures for VCP_HNRNPA2B1


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

P55072

HNRNPA2B1

P22626

Necessary for the fragmentation of Golgi stacks duringmitosis and for their reassembly after mitosis. Involved in theformation of the transitional endoplasmic reticulum (tER). Thetransfer of membranes from the endoplasmic reticulum to the Golgiapparatus occurs via 50-70 nm transition vesicles which derivefrom part-rough, part-smooth transitional elements of theendoplasmic reticulum (tER). Vesicle budding from the tER is anATP-dependent process. The ternary complex containing UFD1, VCPand NPLOC4 binds ubiquitinated proteins and is necessary for theexport of misfolded proteins from the ER to the cytoplasm, wherethey are degraded by the proteasome. The NPLOC4-UFD1-VCP complexregulates spindle disassembly at the end of mitosis and isnecessary for the formation of a closed nuclear envelope.Regulates E3 ubiquitin-protein ligase activity of RNF19A.Component of the VCP/p97-AMFR/gp78 complex that participates inthe final step of the sterol-mediated ubiquitination andendoplasmic reticulum-associated degradation (ERAD) of HMGCR.Involved in endoplasmic reticulum stress-induced pre-emptivequality control, a mechanism that selectively attenuates thetranslocation of newly synthesized proteins into the endoplasmicreticulum and reroutes them to the cytosol for proteasomaldegradation (PubMed:26565908). Also involved in DNA damageresponse: recruited to double-strand breaks (DSBs) sites in aRNF8- and RNF168-dependent manner and promotes the recruitment ofTP53BP1 at DNA damage sites (PubMed:22020440, PubMed:22120668).Recruited to stalled replication forks by SPRTN: may act bymediating extraction of DNA polymerase eta (POLH) to preventexcessive translesion DNA synthesis and limit the incidence ofmutations induced by DNA damage (PubMed:23042607,PubMed:23042605). Required for cytoplasmic retrotranslocation ofstressed/damaged mitochondrial outer-membrane proteins and theirsubsequent proteasomal degradation (PubMed:16186510,PubMed:21118995). Essential for the maturation of ubiquitin-containing autophagosomes and the clearance of ubiquitinatedprotein by autophagy (PubMed:20104022, PubMed:27753622). Acts as anegative regulator of type I interferon production by interactingwith DDX58/RIG-I: interaction takes place when DDX58/RIG-I isubiquitinated via 'Lys-63'-linked ubiquitin on its CARD domains,leading to recruit RNF125 and promote ubiquitination anddegradation of DDX58/RIG-I (PubMed:26471729). May play a role inthe ubiquitin-dependent sorting of membrane proteins to lysosomeswhere they undergo degradation (PubMed:21822278). May moreparticularly play a role in caveolins sorting in cells(PubMed:21822278, PubMed:23335559). By controlling the steady-state expression of the IGF1R receptor, indirectly regulates theinsulin-like growth factor receptor signaling pathway(PubMed:26692333). {ECO:0000269|PubMed:15456787,ECO:0000269|PubMed:16168377, ECO:0000269|PubMed:16186510,ECO:0000269|PubMed:20104022, ECO:0000269|PubMed:21118995,ECO:0000269|PubMed:21822278, ECO:0000269|PubMed:22020440,ECO:0000269|PubMed:22120668, ECO:0000269|PubMed:22607976,ECO:0000269|PubMed:23042605, ECO:0000269|PubMed:23042607,ECO:0000269|PubMed:23335559, ECO:0000269|PubMed:26471729,ECO:0000269|PubMed:26565908, ECO:0000269|PubMed:26692333,ECO:0000269|PubMed:27753622}. Heterogeneous nuclear ribonucleoprotein (hnRNP) thatassociates with nascent pre-mRNAs, packaging them into hnRNPparticles. The hnRNP particle arrangement on nascent hnRNA is non-random and sequence-dependent and serves to condense and stabilizethe transcripts and minimize tangling and knotting. Packagingplays a role in various processes such as transcription, pre-mRNAprocessing, RNA nuclear export, subcellular location, mRNAtranslation and stability of mature mRNAs (PubMed:19099192). FormshnRNP particles with at least 20 other different hnRNP andheterogeneous nuclear RNA in the nucleus. Involved in transport ofspecific mRNAs to the cytoplasm in oligodendrocytes and neurons:acts by specifically recognizing and binding the A2RE (21nucleotide hnRNP A2 response element) or the A2RE11 (derivative 11nucleotide oligonucleotide) sequence motifs present on some mRNAs,and promotes their transport to the cytoplasm (PubMed:10567417).Specifically binds single-stranded telomeric DNA sequences,protecting telomeric DNA repeat against endonuclease digestion (Bysimilarity). Also binds other RNA molecules, such as primary miRNA(pri-miRNAs): acts as a nuclear 'reader' of the N6-methyladenosine(m6A) mark by specifically recognizing and binding a subset ofnuclear m6A-containing pri-miRNAs. Binding to m6A-containing pri-miRNAs promotes pri-miRNA processing by enhancing binding of DGCR8to pri-miRNA transcripts (PubMed:26321680). Involved in miRNAsorting into exosomes following sumoylation, possibly by binding(m6A)-containing pre-miRNAs (PubMed:24356509). Acts as a regulatorof efficiency of mRNA splicing, possibly by binding to m6A-containing pre-mRNAs (PubMed:26321680).{ECO:0000250|UniProtKB:A7VJC2, ECO:0000269|PubMed:10567417,ECO:0000269|PubMed:24356509, ECO:0000269|PubMed:26321680,ECO:0000303|PubMed:19099192}. (Microbial infection) Involved in the transport of HIV-1genomic RNA out of the nucleus, to the microtubule organizingcenter (MTOC), and then from the MTOC to the cytoplasm: acts byspecifically recognizing and binding the A2RE (21 nucleotide hnRNPA2 response element) sequence motifs present on HIV-1 genomic RNA,and promotes its transport. {ECO:0000269|PubMed:15294897,ECO:0000269|PubMed:17004321}.

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 VCP_HNRNPA2B1


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 VCP_HNRNPA2B1


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 VCP_HNRNPA2B1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneHNRNPA2B1P22626DB11638ArtenimolHeterogeneous nuclear ribonucleoproteins A2/B1small moleculeapproved|investigational

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RelatedDiseases for VCP_HNRNPA2B1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVCPC1833662INCLUSION BODY MYOPATHY WITH EARLY-ONSET PAGET DISEASE AND FRONTOTEMPORAL DEMENTIA8CTD_human;ORPHANET;UNIPROT
HgeneVCPC3151403AMYOTROPHIC LATERAL SCLEROSIS 14 WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA8UNIPROT
HgeneVCPC4225244CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2Y2ORPHANET;UNIPROT
HgeneVCPC0038325Stevens-Johnson Syndrome1CTD_human
TgeneHNRNPA2B1C0023493Adult T-Cell Lymphoma/Leukemia1CTD_human
TgeneHNRNPA2B1C3809468INCLUSION BODY MYOPATHY WITH EARLY-ONSET PAGET DISEASE WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA 21UNIPROT