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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: 30001

FusionGeneSummary for RAB3GAP1_LRP1B

check button Fusion gene summary
Fusion gene informationFusion gene name: RAB3GAP1_LRP1B
Fusion gene ID: 30001
HgeneTgene
Gene symbol

RAB3GAP1

LRP1B

Gene ID

22930

53353

Gene nameRAB3 GTPase activating protein catalytic subunit 1LDL receptor related protein 1B
SynonymsP130|RAB3GAP|RAB3GAP130|WARBM1LRP-1B|LRP-DIT|LRPDIT
Cytomap

2q21.3

2q22.1-q22.2

Type of geneprotein-codingprotein-coding
Descriptionrab3 GTPase-activating protein catalytic subunitRAB3 GTPase activating protein subunit 1 (catalytic)RAB3 GTPase-activating protein 130 kDa subunitrab3-GAP p130low-density lipoprotein receptor-related protein 1BLRP-deleted in tumorslow density lipoprotein receptor related protein-deleted in tumorlow density lipoprotein receptor-related protein 1Blow density lipoprotein-related protein 1B (deleted in tumors)
Modification date2018052320180519
UniProtAcc

Q15042

Q9NZR2

Ensembl transtripts involved in fusion geneENST00000264158, ENST00000539493, 
ENST00000442034, ENST00000487003, 
ENST00000425393, 
ENST00000389484, 
ENST00000486364, 
Fusion gene scores* DoF score8 X 8 X 6=3845 X 5 X 4=100
# samples 115
** MAII scorelog2(11/384*10)=-1.8036027871965
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: RAB3GAP1 [Title/Abstract] AND LRP1B [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
HgeneRAB3GAP1

GO:0043087

regulation of GTPase activity

10859313


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
TCGARVKIRPTCGA-BQ-5878-01ARAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
* 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-shiftENST00000264158ENST00000389484RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
5CDS-intronENST00000264158ENST00000486364RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
Frame-shiftENST00000539493ENST00000389484RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
5CDS-intronENST00000539493ENST00000486364RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
Frame-shiftENST00000442034ENST00000389484RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
5CDS-intronENST00000442034ENST00000486364RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
3UTR-3CDSENST00000487003ENST00000389484RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
3UTR-intronENST00000487003ENST00000486364RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
intron-3CDSENST00000425393ENST00000389484RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-
intron-intronENST00000425393ENST00000486364RAB3GAP1chr2

135851263

+LRP1Bchr2

141739845

-

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FusionProtFeatures for RAB3GAP1_LRP1B


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RAB3GAP1

Q15042

LRP1B

Q9NZR2

Probable catalytic subunit of a GTPase activatingprotein that has specificity for Rab3 subfamily (RAB3A, RAB3B,RAB3C and RAB3D). Rab3 proteins are involved in regulatedexocytosis of neurotransmitters and hormones. Specificallyconverts active Rab3-GTP to the inactive form Rab3-GDP. Requiredfor normal eye and brain development. May participate inneurodevelopmental processes such as proliferation, migration anddifferentiation before synapse formation, and non-synapticvesicular release of neurotransmitters.{ECO:0000269|PubMed:10859313, ECO:0000269|PubMed:9030515}. Potential cell surface proteins that bind andinternalize ligands in the process of receptor-mediatedendocytosis.

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 RAB3GAP1_LRP1B


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 RAB3GAP1_LRP1B


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
RAB3GAP1RPH3AL, WDR7, DMXL2, MAP1LC3A, FEZ1, FEZ2, RAB22A, RAB39A, RAB39B, LMAN1, PAXIP1, VCP, GABPA, GNE, NCOA7, RAB3GAP2, TSEN34, VAPB, VAPA, BCAT1, BTN2A1, SIRT2, DCAF15, NTRK1, NPHP1, BRAF, ALOX5, C6orf141, DOCK5, RCCD1, PSMC4, TRIM25, TESLRP1BARRB1, CUL4B, TAZ, RSPO1, SFRP4, PTPRK, FOXD4L6, ZFP41, EWSR1, LRPAP1, ZNF408, ZNF224, ZNF331, FAM19A3, ZNF563, ZNF517, ZNF169, SCGB1D1, DNAJC10, CHRDL1, OLFM3, EGFL6, 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 RAB3GAP1_LRP1B


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 RAB3GAP1_LRP1B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneLRP1BC0007134Renal Cell Carcinoma1CTD_human
TgeneLRP1BC0025202melanoma1CTD_human