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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: 41629

FusionGeneSummary for VPS53_RTN4RL1

check button Fusion gene summary
Fusion gene informationFusion gene name: VPS53_RTN4RL1
Fusion gene ID: 41629
HgeneTgene
Gene symbol

VPS53

RTN4RL1

Gene ID

55275

146760

Gene nameVPS53, GARP complex subunitreticulon 4 receptor like 1
SynonymsHCCS1|PCH2E|hVps53L|pp13624NGRH2|NgR3
Cytomap

17p13.3

17p13.3

Type of geneprotein-codingprotein-coding
Descriptionvacuolar protein sorting-associated protein 53 homologreticulon-4 receptor-like 1Nogo-66 receptor homolog 2Nogo-66 receptor-related protein 3nogo receptor-like 2
Modification date2018052320180523
UniProtAcc

Q5VIR6

Q86UN2

Ensembl transtripts involved in fusion geneENST00000437048, ENST00000574029, 
ENST00000576149, ENST00000446250, 
ENST00000291074, ENST00000571805, 
ENST00000401468, 
ENST00000331238, 
Fusion gene scores* DoF score10 X 5 X 10=5006 X 1 X 7=42
# samples 137
** MAII scorelog2(13/500*10)=-1.94341647163363
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/42*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: VPS53 [Title/Abstract] AND RTN4RL1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotationTumor suppressor gene involved fusion gene, retained protein feature but frameshift.
DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain.
* 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
TCGARVBRCATCGA-OL-A5RW-01AVPS53chr17

600658

-RTN4RL1chr17

1841102

-
TCGALDOVTCGA-29-1702-01AVPS53chr17

505035

-RTN4RL1chr17

1841102

-
* 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-shiftENST00000437048ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
intron-3CDSENST00000574029ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
intron-3CDSENST00000576149ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
5UTR-3CDSENST00000446250ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000291074ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000571805ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000401468ENST00000331238VPS53chr17

600658

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000437048ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-
intron-3CDSENST00000574029ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-
5UTR-3CDSENST00000576149ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-
In-frameENST00000446250ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000291074ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000571805ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-
Frame-shiftENST00000401468ENST00000331238VPS53chr17

505035

-RTN4RL1chr17

1841102

-

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FusionProtFeatures for VPS53_RTN4RL1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
VPS53

Q5VIR6

RTN4RL1

Q86UN2

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}. Cell surface receptor. Plays a functionally redundantrole in postnatal brain development and in regulating axonregeneration in the adult central nervous system. Contributes tonormal axon migration across the brain midline and normalformation of the corpus callosum. Protects motoneurons againstapoptosis; protection against apoptosis is probably mediated byMAG. Plays a role in inhibiting neurite outgrowth and axonregeneration via its binding to neuronal chondroitin sulfateproteoglycans. Binds heparin (By similarity). Like other familymembers, plays a role in restricting the number dendritic spinesand the number of synapses that are formed during braindevelopment (PubMed:22325200). Signaling mediates activation ofRho and downstream reorganization of the actin cytoskeleton(PubMed:22325200). {ECO:0000250|UniProtKB:Q8K0S5,ECO:0000269|PubMed:22325200}.

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 VPS53_RTN4RL1


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.
>In-frame_VPS53_ENST00000446250_chr17_505035_-_RTN4RL1_ENST00000331238_chr17_1841102_-_437aa
GAVWSCCCCWXLRSCPWVVAAHGTVCATRRPXRSAARRTTLQPSRRASPWTASASSCRTTASASSSPATSAPPWSPCGSTRTTSPTSTPA
PSRASCTWRSWTSATTGSCGRWHPRPSRAWXSFTPSTSTSVGSAPCRPASLAACTACSTSTCRTTTSSTSRTTSSWTWSTSATCFSTATS
CGVWARAPSGAWXTWTVFCCTRTSCSGSTTRRSTTSAGXPPSSSSTTASRSCRVSAWPRWGPWSSSASTATPGTVVVARAPCGNGCRGSG
APAPLSPVCPLGCGTARTXSCXGPRTSGTARDQRPRTRSSHTRSPPPTGPPARNTTHPTAPPGARATRTAPGPATGSRGRTAPTPGTAIR


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_VPS53_ENST00000446250_chr17_505035_-_RTN4RL1_ENST00000331238_chr17_1841102_-_1313nt
GGTGCTGTGTGGAGTTGCTGCTGCTGTTGGTAGCTGCGGAGCTGCCCCTGGGTGGTGGCTGCCCACGGGACTGTGTGTGCTACCCGGCGC
CCATGACGGTCAGCTGCCAGGCGCACAACTTTGCAGCCATCCCGGAGGGCATCCCCGTGGACAGCGAGCGCGTCTTCCTGCAGAACAACC
GCATCGGCCTCCTCCAGCCCGGCCACTTCAGCCCCGCCATGGTCACCCTGTGGATCTACTCGAACAACATCACCTACATCCACCCCAGCA
CCTTCGAGGGCTTCGTGCACCTGGAGGAGCTGGACCTCGGCGACAACCGGCAGCTGCGGACGCTGGCACCCGAGACCTTCCAGGGCCTGG
TGAAGCTTCACGCCCTCTACCTCTACAAGTGTGGGCTCAGCGCCTTGCCGGCCGGCGTCTTTGGCGGCCTGCACAGCCTGCAGTACCTCT
ACCTGCAGGACAACCACATCGAGTACCTCCAGGACGACATCTTCGTGGACCTGGTCAACCTCAGCCACCTGTTTCTCCACGGCAACAAGC
TGTGGAGTCTGGGCCCGGGCACCTTCCGGGGCCTGGTGAACCTGGACCGTCTTTTGCTGCACGAGAACCAGCTGCAGTGGGTCCACCACA
AGGCGTTCCACGACCTCCGCAGGCTGACCACCCTCTTCCTCTTCAACAACAGCCTCTCGGAGCTGCAGGGTGAGTGCCTGGCCCCGCTGG
GGGCCCTGGAGTTCCTCCGCCTCAACGGCAACCCCTGGGACTGTGGTTGTCGCGCGCGCTCCCTGTGGGAATGGCTGCAGAGGTTCCGGG
GCTCCAGCTCCGCTGTCCCCTGTGTGTCCCCTGGGCTGCGGCACGGCCAGGACCTGAAGCTGCTGAGGGCCGAGGACTTCCGGAACTGCA
CGGGACCAGCGTCCCCGCACCAGATCAAGTCACACACGCTCACCACCACCGACAGGGCCGCCCGCAAGGAACACCACTCACCCCACGGCC
CCACCAGGAGCAAGGGCCACCCGCACGGCCCCCGGCCCGGCCACAGGAAGCCGGGGAAGAACTGCACCAACCCCAGGAACCGCAATCAGA
TCTCTAAGGCGGGCGCCGGGAAACAGGCCCCCGAGCTGCCAGACTATGCCCCAGACTACCAGCACAAGTTCAGTTTTGACATCATGCCTA
CGGCCCGGCCCAAGAGGAAGGGCAAGTGTGCCCGCAGGACCCCCATCCGTGCCCCCAGCGGGGTGCAGCAGGCCTCCTCGGCCAGTTCCC


* Fusion transcript sequences (Full-length transcript).
>In-frame_VPS53_ENST00000446250_chr17_505035_-_RTN4RL1_ENST00000331238_chr17_1841102_-_4595nt
GAAGTGCCGGAGCGGCTGACAGAGCGGCTGACGGAGCCGGGCTCACCAGGTCGCTGCCGCGAGGGAGTTGCTGTGCTGGGGCCTGGGTGG
CGGCTGGAGGCCTGAGTTGGGCTCGCGGCGGGGGTCGGCAGGGGGCCGGGTGGCGGAATGATGGAGGAGGAGGAACTGGAGTTCGTGGAG
GAGCTGGAAGCCGTGCTGCAGCTCACGCCCGAGGTGCAGCTGGCCATCGAGCAGGTGTTTCCAAGCCAGGACCCTCTAGATCGAGCAGAT
TTCAATGCTGTTGAGTATATCAATACCCTGTTCCCAACCGAGCAATCTCTGGCGAACATAGACGAAGTCGTGAACAAAATTAGGCTGAAA
ATAAGGAGACTGGATGACAATATTCGAACTGTTGTAAGAGGTCAGACGAACGTGGGGCAGGATGGACGGCAAGCGCTTGAAGAGGCTCAG
AAAGCTATCCAACAACTCTTTGGCAAAATCAAAGATATCAAAGACAAAGCTGAAAAATCAGAGCAAATGGTGAAAGAAATCACCCGTGAT
ATTAAGCAATTAGATCACGCCAAACGCCACCTGACCACCTCAATCACCACACTGAACCACCTGCACATGCTGGCAGGAGGTGTCGACTCC
CTCGAAGCCATGACCAGGCGAAGACAATACGGAGAAGTTGCTAATCTCCTTCAGGGTGTGATGAATGTCCTGGAGCACTTCCACAAGTAT
ATGGGGATTCCGCAGATCCGGCAGCTTTCCGAAAGGAAACCCAAAACACTGCAGCTGCATGGATTGAACTGGACGTGATGTGAAATGAAA
TAAGCCAGACACGGGAAGACAGATTCCTCATGTTCTCACTCATAGTGAAGGCTGCACAGACTGAGTTAGGACAGCAAATCCTGGCAGATT
TTGAAGAAGCGTTTCCTTCCCAGGGCACCAAGAGACCAGGAGGACCCAGCAATGTTCTACGAGATGCATGTCTGGTTGCTAATATTCTAG
ATCCCAGGATCAAACAGGAAATCATCAAAAAGTTTATTAAACAGCATCTGTCAGAGTATCTGGTACTTTTTCAAGAAAACCAAGATGTTG
CCTGGCTGGACAAAATCGACAGACGCTATGCCTGGATAAAACGCCAGCTTGTGGACTATGAGGAGAAATACGGCCGCATGTTTCCACGTG
AGTGGTGCATGGCTGAGAGGATTGCGGTGGAATTTTGCCATGTGACAAGGGCAGAACTTGCCAAGATTATGCGTACCAGAGCGAAGGAAA
TTGAAGTGAAATTGCTTCTTTTTGCTATTCAAAGAACAACTAACTTTGAGGGGTTTCTTGCAAAACGCTTCTCCGGCTGCACCCTGACCG
ATGGGACCCTGAAAAAGCTTGAGTCTCCACCCCCATCTACCAATCCCTTCCTGGAAGATGAGCCAACACCAGAGATGGAGGAACTGGCAA
CGGAGAAAGGAGATTTAGATCAAGGTGCTGTGTGGAGTTGCTGCTGCTGTTGGTAGCTGCGGAGCTGCCCCTGGGTGGTGGCTGCCCACG
GGACTGTGTGTGCTACCCGGCGCCCATGACGGTCAGCTGCCAGGCGCACAACTTTGCAGCCATCCCGGAGGGCATCCCCGTGGACAGCGA
GCGCGTCTTCCTGCAGAACAACCGCATCGGCCTCCTCCAGCCCGGCCACTTCAGCCCCGCCATGGTCACCCTGTGGATCTACTCGAACAA
CATCACCTACATCCACCCCAGCACCTTCGAGGGCTTCGTGCACCTGGAGGAGCTGGACCTCGGCGACAACCGGCAGCTGCGGACGCTGGC
ACCCGAGACCTTCCAGGGCCTGGTGAAGCTTCACGCCCTCTACCTCTACAAGTGTGGGCTCAGCGCCTTGCCGGCCGGCGTCTTTGGCGG
CCTGCACAGCCTGCAGTACCTCTACCTGCAGGACAACCACATCGAGTACCTCCAGGACGACATCTTCGTGGACCTGGTCAACCTCAGCCA
CCTGTTTCTCCACGGCAACAAGCTGTGGAGTCTGGGCCCGGGCACCTTCCGGGGCCTGGTGAACCTGGACCGTCTTTTGCTGCACGAGAA
CCAGCTGCAGTGGGTCCACCACAAGGCGTTCCACGACCTCCGCAGGCTGACCACCCTCTTCCTCTTCAACAACAGCCTCTCGGAGCTGCA
GGGTGAGTGCCTGGCCCCGCTGGGGGCCCTGGAGTTCCTCCGCCTCAACGGCAACCCCTGGGACTGTGGTTGTCGCGCGCGCTCCCTGTG
GGAATGGCTGCAGAGGTTCCGGGGCTCCAGCTCCGCTGTCCCCTGTGTGTCCCCTGGGCTGCGGCACGGCCAGGACCTGAAGCTGCTGAG
GGCCGAGGACTTCCGGAACTGCACGGGACCAGCGTCCCCGCACCAGATCAAGTCACACACGCTCACCACCACCGACAGGGCCGCCCGCAA
GGAACACCACTCACCCCACGGCCCCACCAGGAGCAAGGGCCACCCGCACGGCCCCCGGCCCGGCCACAGGAAGCCGGGGAAGAACTGCAC
CAACCCCAGGAACCGCAATCAGATCTCTAAGGCGGGCGCCGGGAAACAGGCCCCCGAGCTGCCAGACTATGCCCCAGACTACCAGCACAA
GTTCAGTTTTGACATCATGCCTACGGCCCGGCCCAAGAGGAAGGGCAAGTGTGCCCGCAGGACCCCCATCCGTGCCCCCAGCGGGGTGCA
GCAGGCCTCCTCGGCCAGTTCCCTGGGGGCCTCCCTCCTGGCCTGGACACTGGGGCTGGCGGTCACTCTCCGCTGAGGACCCAGGGCGTC
AGCACCCAGCACTGCCACATGTCCACCAAGGAACAGAATTTATTTTCTTCTTTTTTTAACAAGTGGAAGATCTGCTGGGTTTCAGGAAAA
GGCTGGTAGAGCCTTCGGCTGCTGTCTGGACGTCTGGACCCTGCCATGTGGATTATAAACCCAAAGTGTACAGCCCTAGGCGGGAGGGGG
TGGCGCTTCTCAGCCGGCTGTCCCAGCCAGCCCCGCAGAGCGCCCACGGACAGTGTCCACTCTGGCAAGGTGGGAAAAGGCACTCCAAGT
GCATCCTCCACTGGCAACAGTGGGACAATTGCCCCCGACGGCGGCACCGGGGCTCTGTGGAATCCCGATCGTTCCGAGAGGTCTGGAGGG
CCCCGTGGTTCCTGGAGAAAGCAGGACGCAGAGAAGAACAAATGAGGCTCACCCACGAGGCTGGGTGGCCAGCAGTCTGGGCACACACGA
GCAGGTGGCATCTTGGCTCTTGCCTGAGGCCAGTCACCCTGCCCTGAATTCTATCCTACTCCACCTTCAGCCCCTCCCTCGGGGGTAGCG
CCTCTCATTCCTGATGTCTCAGGCAACCCTGGCAGACCCAGGTCCAACTGCTGGGGTCCAAGAACCAATTACCAAAGGAAAGATCATCAG
AGGCTGAAATCTAGAACTTCATCCCGGGCAATGAGGTTCTCACAGAAGGTGCAGTTTTATAACTAACTACGTCCACTTATATATATTCAC
ACTCTACATATATATATATATATATATATATATATATATATATATATATACACAAATGCACAGTCCCCCTCCCACTCCGTTACCTAACTG
TACGTCTTTTCATGTTTATAAACTATACAGAAAACTGTATTTGCTGAACTAAGGATTGTATTGGTGATTTCTAGCAAAAACAAAGTGATA
GAATTTTTGTCTAGAATCCCAAACTGGCAACGATAGTCTCCAAGGGACCTGGCCTTGCCAAGGGCCTGGGGCAAGGTGTCGGCGGGACGG
TGAGGAAGGGGGAGGCAGCAAGAGTCACTTTGGGGGACCAATATTCTTAGATATTTAGAGCATCACCTTGTTTTTATATGCAACACAAGC
CTGTCTGCCACCCTGGAGCGCCCTGTCACCCCTGCTGTCGTAGCTGTTGGCTTCAGGGTGAGAAGTGAGAAGCAGCTTATTGTATATGAG
GGAGCCAGGCCCCGAGGGTGAGCGAGATGGAGAAGGGGAAGGAAGGGGCTTTGGGATCTGGAAACCAGCAGGCCAGGCAGCATCCACAGT
GTTAGTCCAAAGGGTCGGACCGTGTCGTCAGCCTAGCGTTTGGTCAGTGACGGCCTGGACGGGCCAAGGAGACTCCGGGCTTGAGCCCAG
GCCTCCCGCACGGCTCAGCTGCTGAATTTTTCCTTGAGGCTGTTTGGTGTGTGACCCAGCAAGGGCCCTGTGTGGGACAGCAGGAGGGAG
GCGTCGGGGGCCTTAGCAGAAGGGGAACAATGAGGGCATTTCATGAACCATCTCAGGCACTTCTGCATCACGGAAGACCTGGCCCTCCCA
GCCGTCCTGGGGATGCTCAGGGTGCAGGCAGAGGCTCGGGAGGCCGGACTCAGGGGTCAGAAGCAGGGACTGGGGCAGGCGAGCCCGGAC
AGGGAAGAGGGGCTCCGATCAAAGCCGGCCGTGCTGCTGGCCGGGGGCCCAGGTGGGTACAAGCTCCTTTGTGCTTTGCACAAACCTGAA
TCCCCCACCAGAGAGGATGTGTGTGAGGAGCCAGAAACGCTGAATCCAATTAAGAGAGAAAAATAATAATAACAATAAATGATCTTGGAC


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FusionGenePPI for VPS53_RTN4RL1


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
VPS53VPS52, 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, TRIM25RTN4RL1CUL3, KRTAP10-7, KRTAP10-8, KRTAP10-3, NOTCH2NL, 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 VPS53_RTN4RL1


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 VPS53_RTN4RL1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVPS53C4014488PONTOCEREBELLAR HYPOPLASIA, TYPE 2E1UNIPROT