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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: 41484

FusionGeneSummary for VMP1_AP1S2

check button Fusion gene summary
Fusion gene informationFusion gene name: VMP1_AP1S2
Fusion gene ID: 41484
HgeneTgene
Gene symbol

VMP1

AP1S2

Gene ID

81671

8905

Gene namevacuole membrane protein 1adaptor related protein complex 1 subunit sigma 2
SynonymsEPG3|TANGO5|TMEM49DC22|MRX59|MRXS21|MRXS5|MRXSF|PGS|SIGMA1B
Cytomap

17q23.1

Xp22.2

Type of geneprotein-codingprotein-coding
Descriptionvacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homologAP-1 complex subunit sigma-2adapter-related protein complex 1 sigma-1B subunitadaptor protein complex AP-1 sigma-1B subunitadaptor related protein complex 1 sigma 2 subunitadaptor-related protein complex 1 subunit sigma-1Bclathrin adaptor complex AP1
Modification date2018052320180519
UniProtAcc

Q96GC9

P56377

Ensembl transtripts involved in fusion geneENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
ENST00000329235, ENST00000380291, 
ENST00000479184, ENST00000545766, 
ENST00000421527, 
Fusion gene scores* DoF score19 X 10 X 9=17102 X 2 X 2=8
# samples 182
** MAII scorelog2(18/1710*10)=-3.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: VMP1 [Title/Abstract] AND AP1S2 [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
TCGALDBRCATCGA-A1-A0SN-01AVMP1chr17

57816308

+AP1S2chrX

15849691

-
* 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
5CDS-intronENST00000262291ENST00000329235VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-3UTRENST00000262291ENST00000380291VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-5UTRENST00000262291ENST00000479184VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-5UTRENST00000262291ENST00000545766VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-intronENST00000262291ENST00000421527VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-intronENST00000537567ENST00000329235VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-3UTRENST00000537567ENST00000380291VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-5UTRENST00000537567ENST00000479184VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-5UTRENST00000537567ENST00000545766VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-intronENST00000537567ENST00000421527VMP1chr17

57816308

+AP1S2chrX

15849691

-
5UTR-intronENST00000539763ENST00000329235VMP1chr17

57816308

+AP1S2chrX

15849691

-
5UTR-3UTRENST00000539763ENST00000380291VMP1chr17

57816308

+AP1S2chrX

15849691

-
5UTR-5UTRENST00000539763ENST00000479184VMP1chr17

57816308

+AP1S2chrX

15849691

-
5UTR-5UTRENST00000539763ENST00000545766VMP1chr17

57816308

+AP1S2chrX

15849691

-
5UTR-intronENST00000539763ENST00000421527VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-intronENST00000536180ENST00000329235VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-3UTRENST00000536180ENST00000380291VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-5UTRENST00000536180ENST00000479184VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-5UTRENST00000536180ENST00000545766VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-intronENST00000536180ENST00000421527VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-intronENST00000545362ENST00000329235VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-3UTRENST00000545362ENST00000380291VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-5UTRENST00000545362ENST00000479184VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-5UTRENST00000545362ENST00000545766VMP1chr17

57816308

+AP1S2chrX

15849691

-
5CDS-intronENST00000545362ENST00000421527VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-intronENST00000588617ENST00000329235VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-3UTRENST00000588617ENST00000380291VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-5UTRENST00000588617ENST00000479184VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-5UTRENST00000588617ENST00000545766VMP1chr17

57816308

+AP1S2chrX

15849691

-
intron-intronENST00000588617ENST00000421527VMP1chr17

57816308

+AP1S2chrX

15849691

-

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FusionProtFeatures for VMP1_AP1S2


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

Q96GC9

AP1S2

P56377

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}. Subunit of clathrin-associated adaptor protein complex 1that plays a role in protein sorting in the late-Golgi/trans-Golginetwork (TGN) and/or endosomes. The AP complexes mediate both therecruitment of clathrin to membranes and the recognition ofsorting signals within the cytosolic tails of transmembrane cargomolecules.

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_AP1S2


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_AP1S2


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, LMNAAP1S2AP1G1, AP1G2, ELAVL1, AP1M1, AP1B1, EGFR, AAGAB, AP1M2, AP2M1, AP2B1, TENC1, XPO1, CLTA, CPS1, GGCX, SEC13, UBE2M, ABCG1, CLINT1, NUDT3, SYNRG, SLC43A3, NOP58, HEATR5B, AFTPH, AP1AR, NBEAL1, C19orf52, CAV3, VTI1B, STX8, CORT, CCM2, RNF13, PPP6R2, POTEB3, DLD


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_AP1S2


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_AP1S2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneAP1S2C0796254DANDY-WALKER MALFORMATION WITH MENTAL RETARDATION, BASAL GANGLIA DISEASE, AND SEIZURES3CTD_human;ORPHANET
TgeneAP1S2C0023893Liver Cirrhosis, Experimental1CTD_human