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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: 41548

FusionGeneSummary for VPS13C_RB1CC1

check button Fusion gene summary
Fusion gene informationFusion gene name: VPS13C_RB1CC1
Fusion gene ID: 41548
HgeneTgene
Gene symbol

VPS13C

RB1CC1

Gene ID

54832

9821

Gene namevacuolar protein sorting 13 homolog CRB1 inducible coiled-coil 1
SynonymsPARK23ATG17|CC1|FIP200|PPP1R131
Cytomap

15q22.2

8q11.23

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 13CRB1-inducible coiled-coil protein 1200 kDa FAK family kinase-interacting proteinFAK family kinase-interacting protein of 200 kDaphosphatase 1, regulatory subunit 131
Modification date2018052320180527
UniProtAcc

Q709C8

Q8TDY2

Ensembl transtripts involved in fusion geneENST00000249837, ENST00000261517, 
ENST00000395896, ENST00000395898, 
ENST00000558919, 
ENST00000025008, 
ENST00000435644, ENST00000521611, 
ENST00000539297, 
Fusion gene scores* DoF score13 X 13 X 7=11837 X 7 X 5=245
# samples 137
** MAII scorelog2(13/1183*10)=-3.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/245*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VPS13C [Title/Abstract] AND RB1CC1 [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
TCGARVKICHTCGA-KL-8341-01AVPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
* 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-5UTRENST00000249837ENST00000025008VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000249837ENST00000435644VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000249837ENST00000521611VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-intronENST00000249837ENST00000539297VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000261517ENST00000025008VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000261517ENST00000435644VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000261517ENST00000521611VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-intronENST00000261517ENST00000539297VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000395896ENST00000025008VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000395896ENST00000435644VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000395896ENST00000521611VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-intronENST00000395896ENST00000539297VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000395898ENST00000025008VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000395898ENST00000435644VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-5UTRENST00000395898ENST00000521611VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
5CDS-intronENST00000395898ENST00000539297VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
intron-5UTRENST00000558919ENST00000025008VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
intron-5UTRENST00000558919ENST00000435644VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
intron-5UTRENST00000558919ENST00000521611VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-
intron-intronENST00000558919ENST00000539297VPS13Cchr15

62292763

-RB1CC1chr8

53599527

-

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FusionProtFeatures for VPS13C_RB1CC1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VPS13C

Q709C8

RB1CC1

Q8TDY2

Necessary for proper mitochondrial function andmaintenance of mitochondrial transmembrane potential. Involved inthe regulation of PINK1/PRKN-mediated mitophagy in response tomitochondrial depolarization. {ECO:0000269|PubMed:26942284}. Involved in autophagy (PubMed:21775823). Regulates earlyevents but also late events of autophagosome formation throughdirect interaction with Atg16L1 (PubMed:23392225). Required forthe formation of the autophagosome-like double-membrane structurethat surrounds the Salmonella-containing vacuole (SCV) duringS.typhimurium infection and subsequent xenophagy (By similarity).Involved in repair of DNA damage caused by ionizing radiation,which subsequently improves cell survival by decreasing apoptosis(By similarity). Inhibits PTK2/FAK1 and PTK2B/PYK2 kinaseactivity, affecting their downstream signaling pathways(PubMed:10769033, PubMed:12221124). Plays a role as a modulator ofTGF-beta-signaling by restricting substrate specificity of RNF111(By similarity). Functions as a DNA-binding transcription factor(PubMed:12095676). Is a potent regulator of the RB1 pathwaythrough induction of RB1 expression (PubMed:14533007). Plays acrucial role in muscular differentiation (PubMed:12163359). Playsan indispensable role in fetal hematopoiesis and in the regulationof neuronal homeostasis (By similarity).{ECO:0000250|UniProtKB:Q9ESK9, ECO:0000269|PubMed:10769033,ECO:0000269|PubMed:12095676, ECO:0000269|PubMed:12163359,ECO:0000269|PubMed:12221124, ECO:0000269|PubMed:14533007,ECO:0000269|PubMed:21775823, ECO:0000269|PubMed:23392225}.

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 VPS13C_RB1CC1


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 VPS13C_RB1CC1


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
VPS13CLGALS12, FAF2, UBXN4, DNAJC7, RNF19B, RAB9A, IER3IP1, VAPA, RAB1A, RAB30, FAM78B, HMGCLL1, LINC01587, ARPC5, VAPBRB1CC1ERCC6L, CDK19, MOB4, DBNL, MAP3K5, TRAF2, PTK2B, PTK2, ATG13, MAP1LC3C, PRKAA2, PRKAB2, SMCR8, HSBP1, ATG101, TBK1, RPA1, SAFB2, SAFB, RPA2, RBMX, YLPM1, ULK1, ULK2, SMARCB1, TP53, TBKBP1, RNF111, SKI, SKIL, VHL, CTNNB1, UBC, GABARAP, GABARAPL1, RFWD2, PINK1, CALCOCO2, DYRK2, ATG16L1, EXOC1, ATG5, SESN2, CCDC8, VAPB, BAP1, BLID, EPSTI1, ERRFI1, GLCE, GREB1, IL13RA2, IL24, ITIH5, LYPD3, MRC2, PSMC3IP, RNF20, THRSP, VPS45, WHSC1L1, WIF1, HBP1, MADD, SYN1, UMPS, DLG3, TACC1, HUWE1, SGTB, TCEAL4, SGOL1, NANOG, CDH1, MTMR4, DUPD1, FAM221B, CCDC53, DENR, VAPA, SYCE3, TRAF1, 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 VPS13C_RB1CC1


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 VPS13C_RB1CC1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVPS13CC4225186PARKINSON DISEASE 23, AUTOSOMAL RECESSIVE EARLY-ONSET1UNIPROT
TgeneRB1CC1C0036341Schizophrenia1CTD_human
TgeneRB1CC1C1458155Mammary Neoplasms1CTD_human