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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: 35639

FusionGeneSummary for SPECC1_VPS54

check button Fusion gene summary
Fusion gene informationFusion gene name: SPECC1_VPS54
Fusion gene ID: 35639
HgeneTgene
Gene symbol

SPECC1

VPS54

Gene ID

92521

51542

Gene namesperm antigen with calponin homology and coiled-coil domains 1VPS54, GARP complex subunit
SynonymsCYTSB|HCMOGT-1|HCMOGT1|NSPHCC8|PPP1R164|SLP-8p|VPS54L|WR|hVps54L
Cytomap

17p11.2

2p15-p14

Type of geneprotein-codingprotein-coding
Descriptioncytospin-BNSP5cytokinesis and spindle organization Bnuclear structure protein 5sperm antigen HCMOGT-1sperm antigen with calponin-like and coiled coil domains 1structure protein NSP5a3astructure protein NSP5a3bstructure protein NSP5b3astructure prvacuolar protein sorting-associated protein 54hepatocellular carcinoma protein 8protein phosphatase 1, regulatory subunit 164tumor antigen HOM-HCC-8tumor antigen SLP-8pvacuolar protein sorting 54 homolog
Modification date2018052320180523
UniProtAcc

Q5M775

Q9P1Q0

Ensembl transtripts involved in fusion geneENST00000472876, ENST00000395527, 
ENST00000395529, ENST00000261503, 
ENST00000395530, ENST00000536879, 
ENST00000395522, ENST00000395525, 
ENST00000584527, 
ENST00000409558, 
ENST00000272322, ENST00000354504, 
Fusion gene scores* DoF score6 X 6 X 3=1085 X 5 X 4=100
# samples 65
** MAII scorelog2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SPECC1 [Title/Abstract] AND VPS54 [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
ChiTaRS3.1BC021123SPECC1chr17

20217959

+VPS54chr2

64175581

-
* 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-intronENST00000472876ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000472876ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000472876ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395527ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395527ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395527ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395529ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395529ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395529ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
3UTR-intronENST00000261503ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
3UTR-intronENST00000261503ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
3UTR-intronENST00000261503ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
3UTR-intronENST00000395530ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
3UTR-intronENST00000395530ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
3UTR-intronENST00000395530ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000536879ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000536879ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000536879ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395522ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395522ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395522ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395525ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395525ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000395525ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000584527ENST00000409558SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000584527ENST00000272322SPECC1chr17

20217959

+VPS54chr2

64175581

-
intron-intronENST00000584527ENST00000354504SPECC1chr17

20217959

+VPS54chr2

64175581

-

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FusionProtFeatures for SPECC1_VPS54


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
SPECC1

Q5M775

VPS54

Q9P1Q0

Acts as component of the GARP complex that is involvedin retrograde transport from early and late endosomes to thetrans-Golgi network (TGN). The GARP complex is required for themaintenance of the cycling of mannose 6-phosphate receptorsbetween the TGN and endosomes, this cycling is necessary forproper lysosomal sorting of acid hydrolases such as CTSD(PubMed:18367545). Within the GARP complex, required to tether thecomplex to the TGN. Not involved in endocytic recycling(PubMed:25799061). {ECO:0000269|PubMed:18367545,ECO:0000269|PubMed:25799061}.

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 SPECC1_VPS54


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 SPECC1_VPS54


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 SPECC1_VPS54


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 SPECC1_VPS54


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneVPS54C0027746Nerve Degeneration1CTD_human