FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

FusionGeneSummary

leaf

FusionProtFeature

leaf

FusionGeneSequence

leaf

FusionGenePPI

leaf

RelatedDrugs

leaf

RelatedDiseases

Fusion gene ID: 41549

FusionGeneSummary for VPS13C_SH2D4A

check button Fusion gene summary
Fusion gene informationFusion gene name: VPS13C_SH2D4A
Fusion gene ID: 41549
HgeneTgene
Gene symbol

VPS13C

SH2D4A

Gene ID

54832

63898

Gene namevacuolar protein sorting 13 homolog CSH2 domain containing 4A
SynonymsPARK23PPP1R38|SH2A
Cytomap

15q22.2

8p21.3

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 13CSH2 domain-containing protein 4Aprotein SH(2)Aprotein phosphatase 1 regulatory subunit 38
Modification date2018052320180523
UniProtAcc

Q709C8

Q9H788

Ensembl transtripts involved in fusion geneENST00000249837, ENST00000261517, 
ENST00000395896, ENST00000395898, 
ENST00000558919, 		ENST00000265807, 
ENST00000518040, ENST00000519207, 
Fusion gene scores* DoF score13 X 13 X 7=11832 X 2 X 2=8
# samples 132
** MAII scorelog2(13/1183*10)=-3.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: VPS13C [Title/Abstract] AND SH2D4A [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
TgeneSH2D4A

GO:0010923

negative regulation of phosphatase activity

19389623


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
TCGARVPRADTCGA-KK-A7B1-01AVPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
* 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-shiftENST00000249837ENST00000265807VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000249837ENST00000518040VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000249837ENST00000519207VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000261517ENST00000265807VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000261517ENST00000518040VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000261517ENST00000519207VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000395896ENST00000265807VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000395896ENST00000518040VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000395896ENST00000519207VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000395898ENST00000265807VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000395898ENST00000518040VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
Frame-shiftENST00000395898ENST00000519207VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
intron-3CDSENST00000558919ENST00000265807VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
intron-3CDSENST00000558919ENST00000518040VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+
intron-3CDSENST00000558919ENST00000519207VPS13Cchr15

62269281

-SH2D4Achr8

19250829

+

Top

FusionProtFeatures for VPS13C_SH2D4A


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

Q709C8

SH2D4A

Q9H788

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}. Inhibits estrogen-induced cell proliferation bycompeting with PLCG for binding to ESR1, blocking the effect ofestrogen on PLCG and repressing estrogen-induced proliferation.May play a role in T-cell development and function.{ECO:0000269|PubMed:18641339, ECO:0000269|PubMed:19712589}.

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


Top

FusionGeneSequence for VPS13C_SH2D4A


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).

Top

FusionGenePPI for VPS13C_SH2D4A


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, VAPBSH2D4ASH3GL1, HCLS1, MAGEA11, DBNL, PPP1CB, GRB2, LYN, HDGF, ASNS, ALAS1, TRIM23, CDR2, GOLGA2, MAGEA6, TRIM27, VPS52, TACC1, TRAF2, ZBTB16, SORBS2, CASK, SKAP1, STX11, PSTPIP1, PNMA1, PDE4DIP, SORBS3, STAM2, IKZF1, SPAG5, NINL, MTUS2, LDOC1, TFIP11, NECAB2, RINT1, HMBOX1, CEP76, CEP70, USHBP1, LZTS2, UBXN11, FSD2, KRT40, NUTM1, CCDC172, NXF1, TF, PPP1R7, TUBA3C, DTD1, NDRG1, OLIG1, PPP1CA, PPP1CC


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


Top

RelatedDrugs for VPS13C_SH2D4A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

RelatedDiseases for VPS13C_SH2D4A


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