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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: 35202

FusionGeneSummary for SNRPD2_VCP

check button Fusion gene summary
Fusion gene informationFusion gene name: SNRPD2_VCP
Fusion gene ID: 35202
HgeneTgene
Gene symbol

SNRPD2

VCP

Gene ID

6633

7415

Gene namesmall nuclear ribonucleoprotein D2 polypeptidevalosin containing protein
SynonymsSMD2|SNRPD1|Sm-D2CDC48|TERA|p97
Cytomap

19q13.32

9p13.3

Type of geneprotein-codingprotein-coding
Descriptionsmall nuclear ribonucleoprotein Sm D2small nuclear ribonucleoprotein D2 polypeptide 16.5kDasnRNP core protein D2transitional endoplasmic reticulum ATPase15S Mg(2+)-ATPase p97 subunitTER ATPase
Modification date2018052320180523
UniProtAcc

P62316

P55072

Ensembl transtripts involved in fusion geneENST00000342669, ENST00000585392, 
ENST00000587367, ENST00000588599, 
ENST00000391932, ENST00000588301, 
ENST00000590212, ENST00000587579, 
ENST00000358901, 
Fusion gene scores* DoF score3 X 3 X 1=95 X 8 X 1=40
# samples 38
** MAII scorelog2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(8/40*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: SNRPD2 [Title/Abstract] AND VCP [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
HgeneSNRPD2

GO:0000387

spliceosomal snRNP assembly

18984161

TgeneVCP

GO:0006302

double-strand break repair

10855792|22120668

TgeneVCP

GO:0006974

cellular response to DNA damage stimulus

16140914|22120668|23042605

TgeneVCP

GO:0016567

protein ubiquitination

22120668

TgeneVCP

GO:0030433

ubiquitin-dependent ERAD pathway

17872946

TgeneVCP

GO:0030970

retrograde protein transport, ER to cytosol

15215856

TgeneVCP

GO:0031334

positive regulation of protein complex assembly

18775313

TgeneVCP

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

9452483

TgeneVCP

GO:0036503

ERAD pathway

25088257

TgeneVCP

GO:0045732

positive regulation of protein catabolic process

11483959|18775313

TgeneVCP

GO:0090263

positive regulation of canonical Wnt signaling pathway

28689657

TgeneVCP

GO:1903006

positive regulation of protein K63-linked deubiquitination

22970133

TgeneVCP

GO:1903007

positive regulation of Lys63-specific deubiquitinase activity

22970133


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
ChiTaRS3.1BE336906SNRPD2chr19

46195195

+VCPchr9

35061616

-
* 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-3CDSENST00000342669ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000585392ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000587367ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000588599ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000391932ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000588301ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000590212ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-
intron-3CDSENST00000587579ENST00000358901SNRPD2chr19

46195195

+VCPchr9

35061616

-

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FusionProtFeatures for SNRPD2_VCP


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SNRPD2

P62316

VCP

P55072

Core component of the spliceosomal U1, U2, U4 and U5small nuclear ribonucleoproteins (snRNPs), the building blocks ofthe spliceosome. Thereby, plays an important role in the splicingof cellular pre-mRNAs. Most spliceosomal snRNPs contain a commonset of Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF andSNRPG that assemble in a heptameric protein ring on the Sm site ofthe small nuclear RNA to form the core snRNP.{ECO:0000269|PubMed:18984161, ECO:0000269|PubMed:23333303}. 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}.

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 SNRPD2_VCP


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 SNRPD2_VCP


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 SNRPD2_VCP


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneSNRPD2P62316DB11638ArtenimolSmall nuclear ribonucleoprotein Sm D2small moleculeapproved|investigational

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RelatedDiseases for SNRPD2_VCP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneVCPC1833662INCLUSION BODY MYOPATHY WITH EARLY-ONSET PAGET DISEASE AND FRONTOTEMPORAL DEMENTIA8CTD_human;ORPHANET;UNIPROT
TgeneVCPC3151403AMYOTROPHIC LATERAL SCLEROSIS 14 WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA8UNIPROT
TgeneVCPC4225244CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2Y2ORPHANET;UNIPROT
TgeneVCPC0038325Stevens-Johnson Syndrome1CTD_human