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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: 31611

FusionGeneSummary for RNFT1_VMP1

check button Fusion gene summary
Fusion gene informationFusion gene name: RNFT1_VMP1
Fusion gene ID: 31611
HgeneTgene
Gene symbol

RNFT1

VMP1

Gene ID

51136

81671

Gene namering finger protein, transmembrane 1vacuole membrane protein 1
SynonymsPTD016EPG3|TANGO5|TMEM49
Cytomap

17q23.1

17q23.1

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNFT1RING finger and transmembrane domain-containing protein 1vacuole membrane protein 1ectopic P-granules autophagy protein 3 homologtransmembrane protein 49transport and golgi organization 5 homolog
Modification date2018051920180523
UniProtAcc

Q5M7Z0

Q96GC9

Ensembl transtripts involved in fusion geneENST00000305783, ENST00000442346, 
ENST00000262291, ENST00000537567, 
ENST00000539763, ENST00000536180, 
ENST00000545362, ENST00000588617, 
Fusion gene scores* DoF score2 X 2 X 2=824 X 11 X 12=3168
# samples 227
** MAII scorelog2(2/8*10)=1.32192809488736log2(27/3168*10)=-3.55254102302878
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNFT1 [Title/Abstract] AND VMP1 [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
TCGALDKIRCTCGA-BP-4790-01ARNFT1chr17

58039901

-VMP1chr17

57917129

+
* 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-shitENST00000305783ENST00000262291RNFT1chr17

58039901

-VMP1chr17

57917129

+
Frame-shitENST00000305783ENST00000537567RNFT1chr17

58039901

-VMP1chr17

57917129

+
Frame-shitENST00000305783ENST00000539763RNFT1chr17

58039901

-VMP1chr17

57917129

+
Frame-shitENST00000305783ENST00000536180RNFT1chr17

58039901

-VMP1chr17

57917129

+
In-frameENST00000305783ENST00000545362RNFT1chr17

58039901

-VMP1chr17

57917129

+
5CDS-3UTRENST00000305783ENST00000588617RNFT1chr17

58039901

-VMP1chr17

57917129

+
intron-3CDSENST00000442346ENST00000262291RNFT1chr17

58039901

-VMP1chr17

57917129

+
intron-3CDSENST00000442346ENST00000537567RNFT1chr17

58039901

-VMP1chr17

57917129

+
intron-3CDSENST00000442346ENST00000539763RNFT1chr17

58039901

-VMP1chr17

57917129

+
intron-3CDSENST00000442346ENST00000536180RNFT1chr17

58039901

-VMP1chr17

57917129

+
intron-3CDSENST00000442346ENST00000545362RNFT1chr17

58039901

-VMP1chr17

57917129

+
intron-3UTRENST00000442346ENST00000588617RNFT1chr17

58039901

-VMP1chr17

57917129

+

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FusionProtFeatures for RNFT1_VMP1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RNFT1

Q5M7Z0

VMP1

Q96GC9

E3 ubiquitin-protein ligase that acts in the endoplasmicreticulum (ER)-associated degradation (ERAD) pathway, whichtargets misfolded proteins that accumulate in the endoplasmicreticulum (ER) for ubiquitination and subsequent proteasome-mediated degradation. Protects cells from ER stress-inducedapoptosis. {ECO:0000269|PubMed:27485036}. Stress-induced protein that, when overexpressed,promotes formation of intracellular vacuoles followed by celldeath. May be involved in the cytoplasmic vacuolization of acinarcells during the early stage of acute pancreatitis. Plays a rolein the initial stages of the autophagic process through itsinteraction with BECN1 (By similarity). Involved in cell-celladhesion. Plays an essential role in formation of cell junctions.{ECO:0000250, ECO:0000269|PubMed:17724469}.

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 RNFT1_VMP1


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_RNFT1_ENST00000305783_chr17_58039901_-_VMP1_ENST00000545362_chr17_57917129_+_245aa
MPLFLLSLPTPPSASGHERRQRPEAKTSGSEKKTLRAMQANRSQLHSPPGTGSSEDASTPQCVHTRLTGEGSCPHSGDVHIQINSIPKEC
AENASSRNIRSGVHSCAHGCVHSRLRGHSHSEARLTDDTAAESGDHGSSSFSEFRTLFKWLQKSLPTILILSVKLVMQHITGISLGIGLL


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_RNFT1_ENST00000305783_chr17_58039901_-_VMP1_ENST00000545362_chr17_57917129_+_735nt
ATGCCGCTGTTCTTGCTGTCGCTCCCGACACCTCCGTCCGCTTCTGGTCATGAGAGGAGACAGAGGCCTGAAGCAAAGACATCTGGGTCA
GAGAAAAAGTATTTAAGGGCCATGCAAGCCAATCGTAGCCAACTGCACAGTCCTCCAGGAACTGGAAGCAGTGAGGATGCCTCAACCCCT
CAGTGTGTCCACACAAGATTGACAGGAGAGGGTTCTTGCCCTCATTCTGGAGATGTTCATATCCAGATAAACTCCATACCTAAAGAATGT
GCAGAAAATGCAAGCTCCAGAAATATAAGGTCAGGTGTCCATAGCTGTGCCCATGGATGTGTACACAGTCGCTTACGGGGTCACTCCCAC
AGTGAAGCAAGGCTGACTGATGATACTGCCGCAGAATCTGGAGATCATGGTAGTAGCTCCTTCTCAGAATTCCGCTATCTCTTCAAGTGG
CTGCAAAAAAGTCTTCCATATATTTTGATTCTGAGCGTCAAACTTGTTATGCAGCATATAACAGGAATTTCTCTTGGAATTGGGCTGCTA
ACAACTTTTATGTATGCAAACAAAAGCATTGTAAATCAGGTTTTTCTAAGAGGAGAAAACTGGTTGTCCTGGATGTTTGAAAAGTTGGTC
GTTGTCATGGTGTGTTACTTCATCCTATCTATCATTAACTCCATGGCACAAAGTTATGCCAAACGAATCCAGCAGCGGTTGAACTCAGAG


* Fusion transcript sequences (Full-length transcript).
>In-frame_RNFT1_ENST00000305783_chr17_58039901_-_VMP1_ENST00000545362_chr17_57917129_+_1043nt
GAAGAGCTTGCGGGGTTTGCGGTTGATGGCCCCGACTGAAGGGCTGGAGGCGGTGTATGCCGCTGTTCTTGCTGTCGCTCCCGACACCTC
CGTCCGCTTCTGGTCATGAGAGGAGACAGAGGCCTGAAGCAAAGACATCTGGGTCAGAGAAAAAGTATTTAAGGGCCATGCAAGCCAATC
GTAGCCAACTGCACAGTCCTCCAGGAACTGGAAGCAGTGAGGATGCCTCAACCCCTCAGTGTGTCCACACAAGATTGACAGGAGAGGGTT
CTTGCCCTCATTCTGGAGATGTTCATATCCAGATAAACTCCATACCTAAAGAATGTGCAGAAAATGCAAGCTCCAGAAATATAAGGTCAG
GTGTCCATAGCTGTGCCCATGGATGTGTACACAGTCGCTTACGGGGTCACTCCCACAGTGAAGCAAGGCTGACTGATGATACTGCCGCAG
AATCTGGAGATCATGGTAGTAGCTCCTTCTCAGAATTCCGCTATCTCTTCAAGTGGCTGCAAAAAAGTCTTCCATATATTTTGATTCTGA
GCGTCAAACTTGTTATGCAGCATATAACAGGAATTTCTCTTGGAATTGGGCTGCTAACAACTTTTATGTATGCAAACAAAAGCATTGTAA
ATCAGGTTTTTCTAAGAGGAGAAAACTGGTTGTCCTGGATGTTTGAAAAGTTGGTCGTTGTCATGGTGTGTTACTTCATCCTATCTATCA
TTAACTCCATGGCACAAAGTTATGCCAAACGAATCCAGCAGCGGTTGAACTCAGAGGAGAAAACTAAATAAGTAGAGAAAGTTTTAAACT
GCAGAAATTGGAGTGGATGGGTTCTGCCTTAAATTGGGAGGACTCCAAGCCGGGAAGGAAAATTCCCTTTTCCAACCTGTATCAATTTTT
ACAACTTTTTTCCTGAAAGCAGTTTAGTCCATACTTTGCACTGACATACTTTTTCCTTCTGTGCTAAGGTAAGGTATCCACCCTCGATGC


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FusionGenePPI for RNFT1_VMP1


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
RNFT1UBE2U, NXF1, KRAS, IL17RB, REEP5VMP1HGS, ELAVL1, TJP1, KLK11, LPAR6, ERGIC3, FAF2, KRAS, TCTN2, TCTN3, TMEM216, DPEP1, CDH13, MAS1, LMNA


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 RNFT1_VMP1


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 RNFT1_VMP1


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