RNF43 Gene (Protein Coding)

Ring Finger Protein 43

GC17M058352
GIFtS:
40
The protein encoded by this gene is a RING-type E3 ubiquitin ligase and is predicted to contain a transmembrane domain, a protease-associated domain, an ectodomain, and a cytoplasmic RING domain. This protein is thought to negatively regulate Wnt signaling, and expression of this gene results in an increase in ubiquitination of frizzled receptors, an alteration in their subcell... See more...

Aliases for RNF43 Gene

Aliases for RNF43 Gene

  • Ring Finger Protein 43 2 3 5
  • RING-Type E3 Ubiquitin Transferase RNF43 3 4
  • E3 Ubiquitin-Protein Ligase RNF43 3 4
  • RING Finger Protein 43 4
  • EC 2.3.2.27 4
  • RNF124 3
  • SSPCS 3
  • URCC 3

External Ids for RNF43 Gene

Previous GeneCards Identifiers for RNF43 Gene

  • GC17U990330
  • GC17M053787
  • GC17M056429
  • GC17M051791

Summaries for RNF43 Gene

Entrez Gene Summary for RNF43 Gene

  • The protein encoded by this gene is a RING-type E3 ubiquitin ligase and is predicted to contain a transmembrane domain, a protease-associated domain, an ectodomain, and a cytoplasmic RING domain. This protein is thought to negatively regulate Wnt signaling, and expression of this gene results in an increase in ubiquitination of frizzled receptors, an alteration in their subcellular distribution, resulting in reduced surface levels of these receptors. Mutations in this gene have been reported in multiple tumor cells, including colorectal and endometrial cancers. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]

GeneCards Summary for RNF43 Gene

RNF43 (Ring Finger Protein 43) is a Protein Coding gene. Diseases associated with RNF43 include Sessile Serrated Polyposis Cancer Syndrome and Hyperplastic Polyposis Syndrome. Among its related pathways are Wnt Signaling Pathways: beta-Catenin-dependent Wnt Signaling and HIV Life Cycle. Gene Ontology (GO) annotations related to this gene include ligase activity and obsolete signal transducer activity. An important paralog of this gene is ENSG00000285897.

UniProtKB/Swiss-Prot Summary for RNF43 Gene

  • E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination, endocytosis and subsequent degradation of Wnt receptor complex components Frizzled. Acts on both canonical and non-canonical Wnt signaling pathway (PubMed:18313049, PubMed:22575959, PubMed:22895187). Along with RSPO2 and ZNRF3, constitutes a master switch that governs limb specification (By similarity).

Additional gene information for RNF43 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RNF43 Gene

Genomics for RNF43 Gene

GeneHancer (GH) Regulatory Elements for RNF43 Gene

Promoters and enhancers for RNF43 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNF43 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNF43 gene promoter:
  • AhR
  • AP-1
  • Arnt
  • c-Fos
  • c-Jun
  • FOXL1
  • FOXO4
  • PPAR-gamma1
  • PPAR-gamma2
  • SREBP-1a

Genomic Locations for RNF43 Gene

Genomic Locations for RNF43 Gene
chr17:58,352,500-58,417,620
(GRCh38/hg38)
Size:
65,121 bases
Orientation:
Minus strand
chr17:56,429,861-56,494,956
(GRCh37/hg19)
Size:
65,096 bases
Orientation:
Minus strand

Genomic View for RNF43 Gene

Genes around RNF43 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNF43 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNF43 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RNF43 Gene

Proteins for RNF43 Gene

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  • Protein details for RNF43 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q68DV7-RNF43_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase RNF43
    Protein Accession:
    Q68DV7
    Secondary Accessions:
    • A8K4R2
    • B7Z443
    • B7Z5D5
    • B7Z5J5
    • Q65ZA4
    • Q6AI04
    • Q9NXD0

    Protein attributes for RNF43 Gene

    Size:
    783 amino acids
    Molecular mass:
    85722 Da
    Quaternary structure:
    • Interacts with AKAP8L, NONO and SFPQ (PubMed:18313049, PubMed:18655028). Interacts with FZD5 (PubMed:22895187). Identified in a complex composed of RNF43, LGR5 and RSPO1 (PubMed:23756651). Interacts with RSPO2 (PubMed:29769720).
    Miscellaneous:
    • Acts as a cytotoxic T-lymphocyte tumor antigen, suggesting that it may be used as a target for cancer immunotherapy.
    SequenceCaution:
    • Sequence=BAH12871.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RNF43 Gene

    Alternative splice isoforms for RNF43 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RNF43 Gene

Post-translational modifications for RNF43 Gene

Other Protein References for RNF43 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RNF43 Gene

Domains & Families for RNF43 Gene

Gene Families for RNF43 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted membrane proteins

Protein Domains for RNF43 Gene

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RNF43 Gene

GenScript: Design optimal peptide antigens:
  • RING finger protein 43 (RNF43_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q68DV7

UniProtKB/Swiss-Prot:

RNF43_HUMAN :
  • Belongs to the ZNRF3 family.
Family:
  • Belongs to the ZNRF3 family.
genes like me logo Genes that share domains with RNF43: view

Function for RNF43 Gene

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Molecular function for RNF43 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination, endocytosis and subsequent degradation of Wnt receptor complex components Frizzled. Acts on both canonical and non-canonical Wnt signaling pathway (PubMed:18313049, PubMed:22575959, PubMed:22895187). Along with RSPO2 and ZNRF3, constitutes a master switch that governs limb specification (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.; EC=2.3.2.27;.

Enzyme Numbers (IUBMB) for RNF43 Gene

Phenotypes From GWAS Catalog for RNF43 Gene

Gene Ontology (GO) - Molecular Function for RNF43 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IDA 22575959
GO:0005109 frizzled binding IPI 22895187
GO:0005515 protein binding IPI 18313049
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RNF43: view
genes like me logo Genes that share phenotypes with RNF43: view

Human Phenotype Ontology for RNF43 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

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miRNA for RNF43 Gene

miRTarBase miRNAs that target RNF43

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for RNF43 Gene

Localization for RNF43 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNF43 Gene

Cell membrane; Single-pass type I membrane protein. Endoplasmic reticulum membrane; Single-pass type I membrane protein. Nucleus envelope. Note=According to a report, may be secreted. {ECO:0000269 PubMed:15492824}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RNF43 gene
Compartment Confidence
plasma membrane 5
nucleus 5
endoplasmic reticulum 5
extracellular 1
mitochondrion 1
peroxisome 1
cytosol 1
cytoskeleton 0

Gene Ontology (GO) - Cellular Components for RNF43 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005635 nuclear envelope IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with RNF43: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RNF43 Gene

Pathways & Interactions for RNF43 Gene

genes like me logo Genes that share pathways with RNF43: view

UniProtKB/Swiss-Prot Q68DV7-RNF43_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for RNF43 Gene

Activates:

Gene Ontology (GO) - Biological Process for RNF43 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process IBA,IDA 22895187
GO:0007275 multicellular organism development IEA --
GO:0016055 Wnt signaling pathway IEA --
GO:0016567 protein ubiquitination IEA --
GO:0030178 negative regulation of Wnt signaling pathway IMP 22575959
genes like me logo Genes that share ontologies with RNF43: view

Drugs & Compounds for RNF43 Gene

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(7) Drugs for RNF43 Gene - From: ClinicalTrials

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
leucovorin Approved Pharma 3801,1351
Levoleucovorin Approved, Investigational Pharma 856
Tegafur Approved, Investigational Pharma 121
Antimetabolites Pharma 13688
Antimetabolites, Antineoplastic Pharma 8498
genes like me logo Genes that share compounds with RNF43: view

Transcripts for RNF43 Gene

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mRNA/cDNA for RNF43 Gene

(3) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(568) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNF43 Gene

No ASD Table

Relevant External Links for RNF43 Gene

GeneLoc Exon Structure for
RNF43
ECgene alternative splicing isoforms for
RNF43

Expression for RNF43 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNF43 Gene

mRNA expression in normal human tissues for RNF43 Gene
mRNA expression by BioGPS for RNF43 GenemRNA expression by GTEx for RNF43 Gene

mRNA differential expression in normal tissues according to GTEx for RNF43 Gene

This gene is overexpressed in Colon - Transverse (x4.3).

NURSA nuclear receptor signaling pathways regulating expression of RNF43 Gene:

RNF43

SOURCE GeneReport for Unigene cluster for RNF43 Gene:

Hs.584916

mRNA Expression by UniProt/SwissProt for RNF43 Gene:

Q68DV7-RNF43_HUMAN
Tissue specificity: Expressed in fetal kidney, fetal lung, in colon cancer tissues, hepatocellular carcinomas and lung adenocarcinomas. Overexpressed in colorectal cancer cell lines.

Evidence on tissue expression from TISSUES for RNF43 Gene

  • Intestine(3.5)
  • Pancreas(2.2)
genes like me logo Genes that share expression patterns with RNF43: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNF43 Gene

Orthologs for RNF43 Gene

This gene was present in the common ancestor of animals.

Orthologs for RNF43 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia RNF43 33 32
  • 99.36 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia RNF43 33 32
  • 89.12 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia RNF43 33 32
  • 86.04 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Rnf43 32
  • 84.53 (n)
mouse
(Mus musculus)
 Mammalia Rnf43 17 33 32
  • 84.23 (n)
oppossum
(Monodelphis domestica)
 Mammalia RNF43 33
  • 72 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia RNF43 33
  • 59 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves RNF43 33 32
  • 63.62 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia RNF43 33
  • 37 (a)
 OneToOne
worm
(Caenorhabditis elegans)
 Secernentea Y47D3B.11 33
  • 21 (a)
 OneToMany
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.8714 33
  • 25 (a)
 OneToMany
Species where no ortholog for RNF43 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for RNF43 Gene

ENSEMBL:
Gene Tree for RNF43 (if available)
TreeFam:
Gene Tree for RNF43 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RNF43: view image

Paralogs for RNF43 Gene

Paralogs for RNF43 Gene

(1) SIMAP similar genes for RNF43 Gene using alignment to 2 proteins:

  • RNF43_HUMAN
  • J3KSE3_HUMAN
genes like me logo Genes that share paralogs with RNF43: view

Variants for RNF43 Gene

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Sequence variations from dbSNP and Humsavar for RNF43 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1567880628 pathogenic, Sessile serrated polyposis cancer syndrome 58,370,949(-) G/A 5_prime_UTR_variant, coding_sequence_variant, stop_gained
rs2526374 benign, not specified, - 58,358,524(-) G/T coding_sequence_variant, missense_variant
rs3744093 benign, not specified, - 58,415,439(-) T/C coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, missense_variant
rs786205215 pathogenic, Colon Serrated Polyposis, Sessile serrated polyposis cancer syndrome 58,363,582(-) G/A coding_sequence_variant, stop_gained
rs2158460 benign, not specified 58,355,001(-) C/G/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RNF43 Gene

Variant ID Type Subtype PubMed ID
esv3554602 CNV deletion 23714750
nsv473283 CNV novel sequence insertion 20440878
nsv517229 CNV gain+loss 19592680
nsv575800 CNV gain 21841781

Variation tolerance for RNF43 Gene

Residual Variation Intolerance Score: 84.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 20.27; 99.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNF43 Gene

Human Gene Mutation Database (HGMD)
RNF43
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNF43

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNF43 Gene

Disorders for RNF43 Gene

MalaCards: The human disease database

(9) MalaCards diseases for RNF43 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
sessile serrated polyposis cancer syndrome
  • sspcs
hyperplastic polyposis syndrome
  • serrated polyposis
pancreatic intraductal papillary-mucinous neoplasm
tumor of exocrine pancreas
  • malignant neoplasm of the exocrine pancreas
appendiceal neoplasm
  • appendix neoplasm
- elite association - COSMIC cancer census association via MalaCards
Search RNF43 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RNF43_HUMAN
  • Sessile serrated polyposis cancer syndrome (SSPCS) [MIM:617108]: A rare disease characterized by multiple and/or large serrated polyps developing in the colon, and an increased personal and familial risk of colorectal cancer. A patient is diagnosed with SSPCS if at least one of the following criteria is met: the presence of at least five sessile serrated polyps proximal to the sigmoid colon, two of which are greater than 10 mm in diameter; the presence of any number of serrated polyps occurring proximal to the sigmoid colon in an individual who has a first-degree relative with serrated polyposis; the presence of more than 20 serrated polyps of any size distributed throughout the colon. Sessile serrated polyps are also known as sessile serrated adenomas (SSA) and are estimated to be responsible for 20 to 35% of all colon cancers. Individuals with SSPCS may have a strong personal or family history of extracolonic cancers. {ECO:0000269 PubMed:24512911, ECO:0000269 PubMed:27081527}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.

Additional Disease Information for RNF43

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with RNF43: view

No data available for Genatlas for RNF43 Gene

Publications for RNF43 Gene

  1. Ring finger protein 43 as a new target for cancer immunotherapy. (PMID: 15623641) Uchida N … Tahara H (Clinical cancer research : an official journal of the American Association for Cancer Research 2004) 3 4 23 56
  2. A novel oncoprotein RNF43 functions in an autocrine manner in colorectal cancer. (PMID: 15492824) Yagyu R … Nakamura Y (International journal of oncology 2004) 3 4 23 56
  3. RSPO2 inhibition of RNF43 and ZNRF3 governs limb development independently of LGR4/5/6. (PMID: 29769720) Szenker-Ravi E … Reversade B (Nature 2018) 3 4 56
  4. The structural basis of R-spondin recognition by LGR5 and RNF43. (PMID: 23756651) Chen PH … He X (Genes & development 2013) 3 4 56
  5. ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner. (PMID: 22575959) Hao HX … Cong F (Nature 2012) 3 4 56

ExternalLinks

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