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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: 31592

FusionGeneSummary for RNF43_LIMCH1

check button Fusion gene summary
Fusion gene informationFusion gene name: RNF43_LIMCH1
Fusion gene ID: 31592
HgeneTgene
Gene symbol

RNF43

LIMCH1

Gene ID

54894

22998

Gene namering finger protein 43LIM and calponin homology domains 1
SynonymsRNF124|SSPCS|URCCLIMCH1A|LMO7B
Cytomap

17q22

4p13

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase RNF43RING-type E3 ubiquitin transferase RNF43LIM and calponin homology domains-containing protein 1
Modification date2018052320180519
UniProtAcc

Q68DV7

Q9UPQ0

Ensembl transtripts involved in fusion geneENST00000500597, ENST00000407977, 
ENST00000583753, ENST00000584437, 
ENST00000577716, ENST00000581868, 
ENST00000577625, ENST00000580014, 
ENST00000513024, ENST00000509638, 
ENST00000508501, ENST00000512946, 
ENST00000313860, ENST00000512632, 
ENST00000512820, ENST00000503057, 
ENST00000511496, ENST00000514096, 
ENST00000509277, ENST00000396595, 
ENST00000381753, ENST00000509454, 
ENST00000515785, 
Fusion gene scores* DoF score7 X 5 X 6=21010 X 10 X 6=600
# samples 710
** MAII scorelog2(7/210*10)=-1.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/600*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RNF43 [Title/Abstract] AND LIMCH1 [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
HgeneRNF43

GO:0006511

ubiquitin-dependent protein catabolic process

22895187

HgeneRNF43

GO:0016567

protein ubiquitination

22575959

HgeneRNF43

GO:0038018

Wnt receptor catabolic process

22895187


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
TCGARVPAADTCGA-IB-7887-01ARNF43chr17

56492687

-LIMCH1chr4

41496553

+
* 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
5CDS-5UTRENST00000500597ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000500597ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-5UTRENST00000407977ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000407977ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-5UTRENST00000583753ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000583753ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-5UTRENST00000584437ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000584437ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-5UTRENST00000577716ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
5CDS-intronENST00000577716ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-5UTRENST00000581868ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000581868ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-5UTRENST00000577625ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000577625ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-5UTRENST00000580014ENST00000513024RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000509638RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000508501RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000512946RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000313860RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000512632RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000512820RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000503057RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000511496RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000514096RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000509277RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000396595RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000381753RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000509454RNF43chr17

56492687

-LIMCH1chr4

41496553

+
intron-intronENST00000580014ENST00000515785RNF43chr17

56492687

-LIMCH1chr4

41496553

+

Top

FusionProtFeatures for RNF43_LIMCH1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
RNF43

Q68DV7

LIMCH1

Q9UPQ0

E3 ubiquitin-protein ligase that acts as a negativeregulator of the Wnt signaling pathway by mediating theubiquitination, endocytosis and subsequent degradation of Wntreceptor complex components Frizzled. Acts on both canonical andnon-canonical Wnt signaling pathway. Acts as a tumor suppressor inthe intestinal stem cell zone by inhibiting the Wnt signalingpathway, thereby resticting the size of the intestinal stem cellzone. {ECO:0000269|PubMed:18313049, ECO:0000269|PubMed:22575959,ECO:0000269|PubMed:22895187}.

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 RNF43_LIMCH1


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 RNF43_LIMCH1


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
RNF43AKAP8L, KDM5B, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2E1, UBE2E3, UBE2N, HECW1, TP53, SFPQ, NONO, RSPO1, RNF43, DVL2, TCF7L2, FZD5, MYADM, CSNK1E, CSNK2A1LIMCH1ELAVL1, SH3KBP1, APP, HUWE1, CUTC, DIABLO, GABPA, KPNA1, NPM1, TRMT61A, RPA3, RPA2, RPA1, OTUD6B, KLHL15, RFC2, YES1, NAGK, GNB4, UNK, NTRK1, CEP120, ODF2, XPO1, CAPZA2, CDK2, MYH9, PPP1CB, IQGAP1, ANLN, MYO19, MYO18A, CDH1, 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


Top

RelatedDrugs for RNF43_LIMCH1


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 RNF43_LIMCH1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRNF43C0009404Colorectal Neoplasms1CTD_human
HgeneRNF43C0014170Endometrial Neoplasms1CTD_human
HgeneRNF43C0023897Liver Diseases, Parasitic1CTD_human
HgeneRNF43C0038356Stomach Neoplasms1CTD_human
HgeneRNF43C0206698Cholangiocarcinoma1CTD_human
TgeneLIMCH1C0236969Substance-Related Disorders1CTD_human
TgeneLIMCH1C0345967Malignant mesothelioma1CTD_human