RNF43 ring finger protein 43 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RNF43provided by HGNC
Official Full Name: ring finger protein 43provided by HGNC
Primary source: HGNC:HGNC:18505
See related: Ensembl:ENSG00000108375 MIM:612482; AllianceGenome:HGNC:18505
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: URCC; SSPCS; RNF124
Summary: 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]
Expression: Broad expression in duodenum (RPKM 7.1), colon (RPKM 6.1) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q22

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (58352500..58417534, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (59220375..59285394, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (56429861..56494895, complement)

Chromosome 17 - NC_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exome sequencing revealed comparable frequencies of RNF43 and BRAF mutations in Middle Eastern colorectal cancer.
Title: Exome sequencing revealed comparable frequencies of RNF43 and BRAF mutations in Middle Eastern colorectal cancer.
Characterization of RNF43 frameshift mutations that drive Wnt ligand- and R-spondin-dependent colon cancer.
Title: Characterization of RNF43 frameshift mutations that drive Wnt ligand- and R-spondin-dependent colon cancer.
RNF43 as a predictor of malignant transformation of pancreatic mucinous cystic neoplasm.
Title: RNF43 as a predictor of malignant transformation of pancreatic mucinous cystic neoplasm.
RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition.
Title: RNF43 G659fs is an oncogenic colorectal cancer mutation and sensitizes tumor cells to PI3K/mTOR inhibition.
RNF43 R117fs mutant positively regulates Wnt/beta-catenin signaling by failing to internalize FZD expressed on the cell surface.
Title: RNF43 R117fs mutant positively regulates Wnt/β-catenin signaling by failing to internalize FZD expressed on the cell surface.
Comprehensive Analysis of R-Spondin Fusions and RNF43 Mutations Implicate Novel Therapeutic Options in Colorectal Cancer.
Title: Comprehensive Analysis of R-Spondin Fusions and RNF43 Mutations Implicate Novel Therapeutic Options in Colorectal Cancer.
RNF43 pathogenic Germline variant in a family with colorectal cancer.
Title: RNF43 pathogenic Germline variant in a family with colorectal cancer.
Loss of RNF43 Function Contributes to Gastric Carcinogenesis by Impairing DNA Damage Response.
Title: Loss of RNF43 Function Contributes to Gastric Carcinogenesis by Impairing DNA Damage Response.
RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.
Title: RNF43/ZNRF3 loss predisposes to hepatocellular-carcinoma by impairing liver regeneration and altering the liver lipid metabolic ground-state.
RNF43 mutation analysis in serrated polyposis, sporadic serrated polyps and Lynch syndrome polyps.
Title: RNF43 mutation analysis in serrated polyposis, sporadic serrated polyps and Lynch syndrome polyps.

Submit: New GeneRIF Correction See all GeneRIFs (52)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Sessile serrated polyposis cancer syndrome MedGen: C4310714 OMIM: 617108 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide and gene-centric analyses of circulating myeloperoxidase levels in the charge and care consortia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of pancreatic cancer in Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-11652 (e-PCR)
- UniSTS:81424

SHGC-34835 (e-PCR)
- UniSTS:29457

RH36262 (e-PCR)
- UniSTS:72479

G42609 (e-PCR)
- UniSTS:94510

RH45569 (e-PCR)
- UniSTS:70968

STS-H72889 (e-PCR)
- UniSTS:74849

G42215 (e-PCR)
- UniSTS:93318

G42244 (e-PCR)
- UniSTS:93347

STS-H82846 (e-PCR)
- UniSTS:52432

RH93017 (e-PCR)
- UniSTS:87791

RH123800 (e-PCR)
- UniSTS:136177

Homology

Homologs of the RNF43 gene: The RNF43 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, and chicken.
Orthologs from Annotation Pipeline: 435 organisms have orthologs with human gene RNF43
Orthologs

Clone Names

FLJ20315, FLJ77466, FLJ99338, MGC125630, DKFZp781H0392, DKFZp781H02126

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables frizzled binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables frizzled binding	IPI Inferred from Physical Interaction more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables ubiquitin protein ligase activity	TAS Traceable Author Statement more info	PubMed
enables ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in Wnt receptor catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in Wnt receptor catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in Wnt receptor catabolic process	TAS Traceable Author Statement more info	PubMed
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of Wnt signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in stem cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
is_active_in integral component of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in integral component of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear envelope	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase RNF43

Names: RING-type E3 ubiquitin transferase RNF43

NP_001292473.1

EC 2.3.2.27

NP_001292474.1

EC 2.3.2.27

NP_060233.3

EC 2.3.2.27

XP_011523258.1

EC 2.3.2.27

XP_016880289.1

EC 2.3.2.27

XP_047292286.1

EC 2.3.2.27

XP_047292287.1

EC 2.3.2.27

XP_047292288.1

EC 2.3.2.27

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_042894.1 RefSeqGene

Range

5001..70083

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1026

mRNA and Protein(s)

NM_001305544.2 → NP_001292473.1 E3 ubiquitin-protein ligase RNF43 isoform 1 precursor

See identical proteins and their annotated locations for NP_001292473.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in its 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AB081837, AC004687, AK000322, BC109028, CR627423

Consensus CDS

CCDS11607.1

UniProtKB/Swiss-Prot

Q68DV7, Q9NXD0

Related

ENSP00000462764.1, ENST00000577716.5

Conserved Domains (4) summary

cd16798
Location:270 → 316

RING-H2_RNF43; RING finger, H2 subclass, found in RING finger protein 43 (RNF43) and similar proteins

cl26464
Location:570 → 747

Atrophin-1; Atrophin-1 family

cl28033
Location:312 → 669

Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

cl28883
Location:87 → 186

PA; PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. ...
NM_001305545.1 → NP_001292474.1 E3 ubiquitin-protein ligase RNF43 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in a distinct 5' UTR and cause translation initiation at a downstream start codon, compared to variant 1. The encoded protein (isoform 2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AB081837, AC004687, AK000322, AK299024, BC109028

Consensus CDS

CCDS82172.1

UniProtKB/Swiss-Prot

Q68DV7

Related

ENSP00000463716.1, ENST00000577625.5

Conserved Domains (1) summary

pfam13639
Location:143 → 185

zf-RING_2; Ring finger domain
NM_017763.6 → NP_060233.3 E3 ubiquitin-protein ligase RNF43 isoform 1 precursor

See identical proteins and their annotated locations for NP_060233.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 2 encode the same protein.

Source sequence(s)

AK000322, AK291027, BC109028, CR627423

Consensus CDS

CCDS11607.1

UniProtKB/Swiss-Prot

Q68DV7, Q9NXD0

Related

ENSP00000385328.2, ENST00000407977.7

Conserved Domains (4) summary

cd16798
Location:270 → 316

RING-H2_RNF43; RING finger, H2 subclass, found in RING finger protein 43 (RNF43) and similar proteins

cl26464
Location:570 → 747

Atrophin-1; Atrophin-1 family

cl28033
Location:312 → 669

Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region

cl28883
Location:87 → 186

PA; PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

58352500..58417534 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047436332.1 → XP_047292288.1 E3 ubiquitin-protein ligase RNF43 isoform X2

UniProtKB/Swiss-Prot

Q9NXD0
XM_047436331.1 → XP_047292287.1 E3 ubiquitin-protein ligase RNF43 isoform X2

UniProtKB/Swiss-Prot

Q9NXD0

Related

ENSP00000463069.1, ENST00000584437.5
XM_017024800.3 → XP_016880289.1 E3 ubiquitin-protein ligase RNF43 isoform X1

UniProtKB/Swiss-Prot

Q68DV7

Conserved Domains (2) summary

pfam13639
Location:270 → 312

zf-RING_2; Ring finger domain

cl10459
Location:87 → 186

Peptidases_S8_S53; Peptidase domain in the S8 and S53 families
XM_047436330.1 → XP_047292286.1 E3 ubiquitin-protein ligase RNF43 isoform X1
XM_011524956.4 → XP_011523258.1 E3 ubiquitin-protein ligase RNF43 isoform X3

UniProtKB/TrEMBL

J3KSE3

Related

ENSP00000462447.1, ENST00000581868.1

Conserved Domains (1) summary

pfam13639
Location:143 → 185

zf-RING_2; Ring finger domain