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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: 25779

FusionGeneSummary for PAFAH1B1_VPS53

check button Fusion gene summary
Fusion gene informationFusion gene name: PAFAH1B1_VPS53
Fusion gene ID: 25779
HgeneTgene
Gene symbol

PAFAH1B1

VPS53

Gene ID

5048

55275

Gene nameplatelet activating factor acetylhydrolase 1b regulatory subunit 1VPS53, GARP complex subunit
SynonymsLIS1|LIS2|MDCR|MDS|NudF|PAFAHHCCS1|PCH2E|hVps53L|pp13624
Cytomap

17p13.3

17p13.3

Type of geneprotein-codingprotein-coding
Descriptionplatelet-activating factor acetylhydrolase IB subunit alphalissencephaly 1 proteinplatelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit (45kD)platelet-activatinvacuolar protein sorting-associated protein 53 homolog
Modification date2018052320180523
UniProtAcc

P43034

Q5VIR6

Ensembl transtripts involved in fusion geneENST00000397195, ENST00000572915, 
ENST00000451360, 
ENST00000437048, 
ENST00000574029, ENST00000576149, 
ENST00000446250, ENST00000291074, 
ENST00000571805, ENST00000401468, 
Fusion gene scores* DoF score9 X 6 X 3=1628 X 5 X 6=240
# samples 97
** MAII scorelog2(9/162*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/240*10)=-1.77760757866355
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PAFAH1B1 [Title/Abstract] AND VPS53 [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
HgenePAFAH1B1

GO:0007017

microtubule-based process

11940666


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
TCGALDOVTCGA-61-2012-01APAFAH1B1chr17

2541614

+VPS53chr17

505136

-
* 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-shiftENST00000397195ENST00000437048PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
5CDS-intronENST00000397195ENST00000574029PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
5CDS-5UTRENST00000397195ENST00000576149PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
5CDS-5UTRENST00000397195ENST00000446250PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
5CDS-5UTRENST00000397195ENST00000291074PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
5CDS-5UTRENST00000397195ENST00000571805PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
5CDS-5UTRENST00000397195ENST00000401468PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-3CDSENST00000572915ENST00000437048PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-intronENST00000572915ENST00000574029PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-5UTRENST00000572915ENST00000576149PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-5UTRENST00000572915ENST00000446250PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-5UTRENST00000572915ENST00000291074PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-5UTRENST00000572915ENST00000571805PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
3UTR-5UTRENST00000572915ENST00000401468PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-3CDSENST00000451360ENST00000437048PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-intronENST00000451360ENST00000574029PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-5UTRENST00000451360ENST00000576149PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-5UTRENST00000451360ENST00000446250PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-5UTRENST00000451360ENST00000291074PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-5UTRENST00000451360ENST00000571805PAFAH1B1chr17

2541614

+VPS53chr17

505136

-
intron-5UTRENST00000451360ENST00000401468PAFAH1B1chr17

2541614

+VPS53chr17

505136

-

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FusionProtFeatures for PAFAH1B1_VPS53


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PAFAH1B1

P43034

VPS53

Q5VIR6

Required for proper activation of Rho GTPases and actinpolymerization at the leading edge of locomoting cerebellarneurons and postmigratory hippocampal neurons in response tocalcium influx triggered via NMDA receptors. Non-catalytic subunitof an acetylhydrolase complex which inactivates platelet-activating factor (PAF) by removing the acetyl group at the SN-2position (By similarity). Positively regulates the activity of theminus-end directed microtubule motor protein dynein. May enhancedynein-mediated microtubule sliding by targeting dynein to themicrotubule plus end. Required for several dynein- andmicrotubule-dependent processes such as the maintenance of Golgiintegrity, the peripheral transport of microtubule fragments andthe coupling of the nucleus and centrosome. Required during braindevelopment for the proliferation of neuronal precursors and themigration of newly formed neurons from theventricular/subventricular zone toward the cortical plate.Neuronal migration involves a process called nucleokinesis,whereby migrating cells extend an anterior process into which thenucleus subsequently translocates. During nucleokinesis dynein atthe nuclear surface may translocate the nucleus towards thecentrosome by exerting force on centrosomal microtubules. May alsoplay a role in other forms of cell locomotion including themigration of fibroblasts during wound healing. Required for dyneinrecruitment to microtubule plus ends and BICD2-bound cargos(PubMed:22956769). {ECO:0000250|UniProtKB:P63005,ECO:0000269|PubMed:15173193, ECO:0000269|PubMed:22956769}. 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:15878329, PubMed:18367545). Acts as component of the EARPcomplex that is involved in endocytic recycling. The EARP complexassociates with Rab4-positive endosomes and promotes recycling ofinternalized transferrin receptor (TFRC) to the plasma membrane(PubMed:25799061). {ECO:0000269|PubMed:15878329,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 PAFAH1B1_VPS53


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 PAFAH1B1_VPS53


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
PAFAH1B1NDEL1, CSNK2A1, KARS, NUDC, TUBA1A, PAFAH1B1, DCTN2, DYNC1H1, DCTN1, DCX, CLIP1, PAFAH1B2, PAFAH1B3, WDR5, DISC1, TNIK, ISG15, CDK2, DYNLL1, HSP90AA1, DYNC1I1, KATNA1, KATNB1, NDE1, NUDCD2, PDE4B, PDE4D, IQCB1, ASNS, HMGB3, HSP90AA4P, ATIC, CAPN2, CAPNS1, EIF5, FH, ISOC1, MAPRE1, MSN, MYO1E, PAPSS1, PDIA4, SNRPD2, TATDN1, UBXN1, YWHAG, YWHAH, PAK2, SNRPF, BICD2, AP1G1, CHID1, CHMP2B, CSTF1, SBDS, SCLY, NTRK1, CEP128, CEP135, DCDC5, DYNC1LI1, DYNC1I2, DYNLT3, DYNLT1, TCTEX1D2, GID8, MAPRE2, DYNLRB2, AHI1, TRIM25, NUDCD3VPS53VPS52, VPS51, EXOC2, VPS53, VPS54, STX6, VAMP4, THOC2, THOC1, USP7, TXNDC9, VCP, SNAP29, BSG, PSMD7, CCDC132, DTNBP1, TSSC1, C10orf76, PTAR1, RAB1A, CCDC40, EXOC1, EXOC6, SYCE3, PRAF2, CEP170, PKN3, NCKAP5L, TFPT, CCHCR1, YEATS4, TUFT1, RABGAP1L, GOLGA5, CLOCK, PSMD9, DZIP3, GRIPAP1, RCOR1, HMG20A, CCDC93, OIP5, PHF21A, PTRF, PHLDB3, HAUS6, GIT2, RPRD1A, ARNTL, MAX, RABGEF1, NUF2, THAP11, KDM1A, RABEP1, 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 PAFAH1B1_VPS53


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 PAFAH1B1_VPS53


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePAFAH1B1C0431375Classical Lissencephaly5ORPHANET;UNIPROT
HgenePAFAH1B1C0036341Schizophrenia1PSYGENET
HgenePAFAH1B1C0596263Carcinogenesis1CTD_human
TgeneVPS53C4014488PONTOCEREBELLAR HYPOPLASIA, TYPE 2E1UNIPROT