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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: 41498

FusionGeneSummary for VMP1_SMARCD2

check button Fusion gene summary
Fusion gene informationFusion gene name: VMP1_SMARCD2
Fusion gene ID: 41498
HgeneTgene
Gene symbol

VMP1

SMARCD2

Gene ID

81671

6603

Gene namevacuole membrane protein 1SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2
SynonymsEPG3|TANGO5|TMEM49BAF60B|CRACD2|PRO2451|Rsc6p|SGD2
Cytomap

17q23.1

17q23.3

Type of geneprotein-codingprotein-coding
Descriptionvacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homologSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 260 kDa BRG-1/Brm-associated factor subunit BBRG1-associated factor 60BSWI/SNF complex 60 kDa subunit BSwp73-like proteinchromatin remodeling complex BAF60B s
Modification date2018052320180519
UniProtAcc

Q96GC9

Q92925

Ensembl transtripts involved in fusion geneENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
ENST00000448276, ENST00000323347, 
ENST00000225742, 
Fusion gene scores* DoF score19 X 10 X 9=17103 X 3 X 2=18
# samples 183
** MAII scorelog2(18/1710*10)=-3.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: VMP1 [Title/Abstract] AND SMARCD2 [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
TgeneSMARCD2

GO:0006337

nucleosome disassembly

8895581

TgeneSMARCD2

GO:0006338

chromatin remodeling

11726552


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
TCGALDBRCATCGA-AO-A12C-01AVMP1chr17

57808883

+SMARCD2chr17

61910351

-
* 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-shitENST00000262291ENST00000448276VMP1chr17

57808883

+SMARCD2chr17

61910351

-
Frame-shitENST00000262291ENST00000323347VMP1chr17

57808883

+SMARCD2chr17

61910351

-
Frame-shitENST00000262291ENST00000225742VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000537567ENST00000448276VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000537567ENST00000323347VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000537567ENST00000225742VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000539763ENST00000448276VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000539763ENST00000323347VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000539763ENST00000225742VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000536180ENST00000448276VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000536180ENST00000323347VMP1chr17

57808883

+SMARCD2chr17

61910351

-
5UTR-3CDSENST00000536180ENST00000225742VMP1chr17

57808883

+SMARCD2chr17

61910351

-
Frame-shitENST00000545362ENST00000448276VMP1chr17

57808883

+SMARCD2chr17

61910351

-
Frame-shitENST00000545362ENST00000323347VMP1chr17

57808883

+SMARCD2chr17

61910351

-
Frame-shitENST00000545362ENST00000225742VMP1chr17

57808883

+SMARCD2chr17

61910351

-
intron-3CDSENST00000588617ENST00000448276VMP1chr17

57808883

+SMARCD2chr17

61910351

-
intron-3CDSENST00000588617ENST00000323347VMP1chr17

57808883

+SMARCD2chr17

61910351

-
intron-3CDSENST00000588617ENST00000225742VMP1chr17

57808883

+SMARCD2chr17

61910351

-

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FusionProtFeatures for VMP1_SMARCD2


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VMP1

Q96GC9

SMARCD2

Q92925

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}. Involved in transcriptional activation and repression ofselect genes by chromatin remodeling (alteration of DNA-nucleosometopology). Component of SWI/SNF chromatin remodeling complexesthat carry out key enzymatic activities, changing chromatinstructure by altering DNA-histone contacts within a nucleosome inan ATP-dependent manner (PubMed:22952240, PubMed:26601204).Critical regulator of myeloid differentiation, controllinggranulocytopoiesis and the expression of genes involved inneutrophil granule formation (PubMed:28369036).{ECO:0000269|PubMed:28369036, ECO:0000303|PubMed:22952240,ECO:0000303|PubMed:26601204}.

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 VMP1_SMARCD2


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 VMP1_SMARCD2


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
VMP1HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNASMARCD2XRN1, BRCA1, TP53, TP63, TP73, SMARCA4, SMARCA2, UNKL, SMARCAD1, SMARCC2, SMARCE1, SMARCD1, CUL3, SMARCB1, ARID1A, SMARCC1, BAZ1B, TOP2B, KYNU, RBBP5, NUDCD2, BPTF, SIRT1, NOTCH2NL, RNF2, BMI1, QPRT, DPF3, NUP50, DPF2, SS18, NTRK1, ACTL6A, ARID1B, BCL7A, BCL7B, BCL7C, MDC1, TBL1X, TBL1XR1, UPF2, PCM1, KPNA1, PTPN1, NUP153, SAMHD1, NFATC1, NFATC2, RELB, TEX13A, FANCA, TRIM25


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 VMP1_SMARCD2


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 VMP1_SMARCD2


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