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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: 41572

FusionGeneSummary for VPS29_MGME1

check button Fusion gene summary
Fusion gene informationFusion gene name: VPS29_MGME1
Fusion gene ID: 41572
HgeneTgene
Gene symbol

VPS29

MGME1

Gene ID

51699

92667

Gene nameVPS29, retromer complex componentmitochondrial genome maintenance exonuclease 1
SynonymsDC15|DC7|PEP11C20orf72|DDK1|MTDPS11|bA504H3.4
Cytomap

12q24.11

20p11.23

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 29PEP11 homologhVPS29retromer proteinvacuolar protein sorting 29 homologvacuolar sorting protein VPS29/PEP11vesicle protein sorting 29x 007 proteinmitochondrial genome maintenance exonuclease 1
Modification date2018052320180526
UniProtAcc

Q9UBQ0

Q9BQP7

Ensembl transtripts involved in fusion geneENST00000549578, ENST00000360579, 
ENST00000552130, ENST00000447578, 
ENST00000546588, ENST00000549970, 
ENST00000551655, 		ENST00000377710, 
ENST00000377709, ENST00000377704, 
ENST00000467391, 
Fusion gene scores* DoF score6 X 7 X 5=2103 X 2 X 2=12
# samples 123
** MAII scorelog2(12/210*10)=-0.807354922057604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: VPS29 [Title/Abstract] AND MGME1 [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
TCGALDLUSCTCGA-68-A59I-01AVPS29chr12

110939854

-MGME1chr20

17968809

+
* 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-shiftENST00000549578ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
Frame-shiftENST00000549578ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
5CDS-intronENST00000549578ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
5CDS-3UTRENST00000549578ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+
Frame-shiftENST00000360579ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
Frame-shiftENST00000360579ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
5CDS-intronENST00000360579ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
5CDS-3UTRENST00000360579ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+
intron-3CDSENST00000552130ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
intron-3CDSENST00000552130ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
intron-intronENST00000552130ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
intron-3UTRENST00000552130ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000447578ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000447578ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-intronENST00000447578ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3UTRENST00000447578ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000546588ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000546588ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-intronENST00000546588ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3UTRENST00000546588ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000549970ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000549970ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-intronENST00000549970ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3UTRENST00000549970ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000551655ENST00000377710VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3CDSENST00000551655ENST00000377709VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-intronENST00000551655ENST00000377704VPS29chr12

110939854

-MGME1chr20

17968809

+
5UTR-3UTRENST00000551655ENST00000467391VPS29chr12

110939854

-MGME1chr20

17968809

+

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FusionProtFeatures for VPS29_MGME1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VPS29

Q9UBQ0

MGME1

Q9BQP7

Acts as component of the retromer cargo-selectivecomplex (CSC). The CSC is believed to be the core functionalcomponent of retromer or respective retromer complex variantsacting to prevent missorting of selected transmembrane cargoproteins into the lysosomal degradation pathway. The recruitmentof the CSC to the endosomal membrane involves RAB7A and SNX3. TheSNX-BAR retromer mediates retrograde transport of cargo proteinsfrom endosomes to the trans-Golgi network (TGN) and is involved inendosome-to-plasma membrane transport for cargo protein recycling.The SNX3-retromer mediates the retrograde endosome-to-TGNtransport of WLS distinct from the SNX-BAR retromer pathway. TheSNX27-retromer is believed to be involved in endosome-to-plasmamembrane trafficking and recycling of a broad spectrum of cargoproteins. The CSC seems to act as recruitment hub for otherproteins, such as the WASH complex and TBC1D5. Required toregulate transcytosis of the polymeric immunoglobulin receptor(pIgR-pIgA) (Probable). Involved in GLUT1 endosome-to-plasmamembrane trafficking; the function is dependent of associationwith ANKRD27 (PubMed:24856514). {ECO:0000250|UniProtKB:Q9QZ88,ECO:0000269|PubMed:16737443, ECO:0000269|PubMed:24856514,ECO:0000303|PubMed:15247922, ECO:0000303|PubMed:21725319,ECO:0000303|PubMed:23563491}. Metal-dependent single-stranded DNA (ssDNA) exonucleaseinvolved in mitochondrial genome maintenance. Has preference for5'-3' exonuclease activity but is also capable of endoducleaseactivity on linear substrates. Necessary for maintenance of proper7S DNA levels. Probably involved in mitochondrial DNA (mtDNA)repair, possibly via the processing of displaced DNA containingOkazaki fragments during RNA-primed DNA synthesis on the laggingstrand or via processing of DNA flaps during long-patch baseexcision repair. Specifically binds 5-hydroxymethylcytosine(5hmC)-containing DNA in stem cells. {ECO:0000255|HAMAP-Rule:MF_03030, ECO:0000269|PubMed:23313956,ECO:0000269|PubMed:23358826}.

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 VPS29_MGME1


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 VPS29_MGME1


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
VPS29FRA10AC1, RGS2, TBC1D5, APP, VPS35, VPS26A, VPS26B, SNX2, HDLBP, NADK2, NDUFV1, VPS25, TMEM9, YRDC, ZFR, VPS36, UBL7, ZNHIT2, VPS33B, TTC4, UBAP2, TSN, SEC22B, UBE4B, USP7, FAM129B, GTF2F1, H3F3A, JMJD6, NAA10, NUDC, PPM1G, PSAP, PUF60, SEC24D, SNX6, STAT1, TOLLIP, ATP6V1C1, PAWR, PUS1, SHMT1, TBCD, WDR12, MCM7, RAB7A, GRHPR, HAT1, KIAA1598, OTUB1, PSMD6, SAC3D1, PPP1R7, SNX1, CCDC22, CCDC93, DUSP4, DUSP8, ANKRD27, C16orf62, COMMD10, DSCR3, COMMD9, COMMD5, COMMD7, FAM45A, COMMD1, COMMD6, COMMD3, COMMD8, COMMD2, COMMD4, FAM21C, KIAA0196, FKBP15MGME1MAGEA11, CDCA5, MRPL46, HMGCL, ECSIT, OXLD1, SMC1A, FOXA1, TRIM45, MIPEP, LUZP1, POLG, FKBP4, THNSL1, WDHD1, CBLC, 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 VPS29_MGME1


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 VPS29_MGME1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneMGME1C0013911Emaciation1CTD_human
TgeneMGME1C0029089Ophthalmoplegia1CTD_human
TgeneMGME1C0035229Respiratory Insufficiency1CTD_human
TgeneMGME1C0751651Mitochondrial Diseases1CTD_human
TgeneMGME1C3554462MITOCHONDRIAL DNA DEPLETION SYNDROME 111ORPHANET;UNIPROT