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Aliases for ZNRF3 Gene

Aliases for ZNRF3 Gene

  • Zinc And Ring Finger 3 2 3 5
  • RING-Type E3 Ubiquitin Transferase ZNRF3 3 4
  • E3 Ubiquitin-Protein Ligase ZNRF3 3 4
  • Zinc/RING Finger Protein 3 3 4
  • RING Finger Protein 203 3 4
  • RNF203 3 4
  • Novel C3HC4 Type Zinc Finger (Ring Finger) 3
  • CTA-292E10.6 3
  • EC 2.3.2.27 4
  • BK747E2.3 3
  • KIAA1133 4

External Ids for ZNRF3 Gene

Previous GeneCards Identifiers for ZNRF3 Gene

  • GC22P027605
  • GC22P029279
  • GC22P012347
  • GC22P028883

Summaries for ZNRF3 Gene

GeneCards Summary for ZNRF3 Gene

ZNRF3 (Zinc And Ring Finger 3) is a Protein Coding gene. Diseases associated with ZNRF3 include Primary Angle-Closure Glaucoma and Osteoblastoma. Among its related pathways are Regulation of FZD by ubiquitination and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include ligase activity and frizzled binding. An important paralog of this gene is RNF43.

UniProtKB/Swiss-Prot for ZNRF3 Gene

  • E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components Frizzled and LRP6. Acts on both canonical and non-canonical Wnt signaling pathway. Acts as a tumor suppressor in the intestinal stem cell zone by inhibiting the Wnt signaling pathway, thereby resticting the size of the intestinal stem cell zone (PubMed:22575959). Along with RSPO2 and RNF43, constitutes a master switch that governs limb specification (By similarity).

Additional gene information for ZNRF3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZNRF3 Gene

Genomics for ZNRF3 Gene

GeneHancer (GH) Regulatory Elements for ZNRF3 Gene

Promoters and enhancers for ZNRF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J028798 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 609.3 -0.3 -267 7.6 MTA3 ZNF652 ZFX SP1 ELF3 MNT NKRF POLR2A MLLT1 ZNF121 ZNRF3 XBP1 ENSG00000226471 EWSR1 CCDC117 ENSG00000272858 TTC28 CHEK2 TTC28-AS1 HSCB
GH22J028882 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 611.6 +84.0 84047 4.6 SP1 MNT ZNF148 NKRF POLR2A ZNF121 ZNF384 ZNF687 TFE3 ZBTB7A ZNRF3 C22orf31 CCDC117 CHEK2 HSCB LOC646408 ZNRF3-IT1
GH22J028914 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 23 +120.1 120146 11.2 ZNF652 SP1 ELF3 MNT ZNF121 CEBPG RERE ZNF687 AHR ZNF24 ZNRF3 C22orf31 CCDC117 HSCB CHEK2 ZNRF3-IT1 LOC646408
GH22J028910 Enhancer 1.3 Ensembl ENCODE dbSUPER 23 +111.8 111847 4.6 ELF3 CEBPG SP7 SP1 PKNOX1 RXRA PRDM10 CEBPA GATAD2A RXRB ZNRF3 C22orf31 CHEK2 HSCB LOC646408 ZNRF3-IT1
GH22J029381 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.7 +584.8 584750 8.1 SP1 ZNF652 ZFX ELF3 MNT NKRF POLR2A ZNF121 CEBPG ZNF687 AP1B1 RASL10A SNORD125 ZNRF3 GAS2L1 RHBDD3 ENSG00000285697 ENSG00000280968
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ZNRF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZNRF3 gene promoter:
  • AML1a
  • c-Myb
  • Evi-1
  • FOXL1
  • HNF-3beta
  • p300
  • RORalpha1

Genomic Locations for ZNRF3 Gene

Genomic Locations for ZNRF3 Gene
chr22:28,800,654-29,057,488
(GRCh38/hg38)
Size:
256,835 bases
Orientation:
Plus strand
chr22:29,279,580-29,453,476
(GRCh37/hg19)
Size:
173,897 bases
Orientation:
Plus strand

Genomic View for ZNRF3 Gene

Genes around ZNRF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZNRF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZNRF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZNRF3 Gene

Proteins for ZNRF3 Gene

  • Protein details for ZNRF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9ULT6-ZNRF3_HUMAN
    Recommended name:
    E3 ubiquitin-protein ligase ZNRF3
    Protein Accession:
    Q9ULT6
    Secondary Accessions:
    • B3KU18
    • Q6ICH1
    • Q6NTF8
    • Q8WU18

    Protein attributes for ZNRF3 Gene

    Size:
    936 amino acids
    Molecular mass:
    100574 Da
    Quaternary structure:
    • Interacts with LRP6, FZD4, FZD5, FZD6 and FZD8 (PubMed:22575959). Interacts with RSPO1; interaction promotes indirect interaction with LGR4 and membrane clearance of ZNRF3 (PubMed:22575959). Also interacts with RSPO2 (PubMed:29769720).
    SequenceCaution:
    • Sequence=CAG30283.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for ZNRF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ZNRF3 Gene

Post-translational modifications for ZNRF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZNRF3 Gene

Domains & Families for ZNRF3 Gene

Gene Families for ZNRF3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Protein Domains for ZNRF3 Gene

Suggested Antigen Peptide Sequences for ZNRF3 Gene

GenScript: Design optimal peptide antigens:
  • ZNRF3 protein (Q96GS9_HUMAN)
  • RING finger protein 203 (ZNRF3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9ULT6

UniProtKB/Swiss-Prot:

ZNRF3_HUMAN :
  • Belongs to the ZNRF3 family.
Family:
  • Belongs to the ZNRF3 family.
genes like me logo Genes that share domains with ZNRF3: view

Function for ZNRF3 Gene

Molecular function for ZNRF3 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase that acts as a negative regulator of the Wnt signaling pathway by mediating the ubiquitination and subsequent degradation of Wnt receptor complex components Frizzled and LRP6. Acts on both canonical and non-canonical Wnt signaling pathway. Acts as a tumor suppressor in the intestinal stem cell zone by inhibiting the Wnt signaling pathway, thereby resticting the size of the intestinal stem cell zone (PubMed:22575959). Along with RSPO2 and RNF43, 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;.
UniProtKB/Swiss-Prot EnzymeRegulation:
Negatively regulated by R-spondin proteins such as RSPO1: interaction with RSPO1 induces the indirect association between ZNRF3 and LGR4, promoting membrane clearance of ZNRF3.

Enzyme Numbers (IUBMB) for ZNRF3 Gene

Phenotypes From GWAS Catalog for ZNRF3 Gene

Gene Ontology (GO) - Molecular Function for ZNRF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IDA 22575959
GO:0005109 frizzled binding IPI 22575959
GO:0005515 protein binding IPI 22575959
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZNRF3: view
genes like me logo Genes that share phenotypes with ZNRF3: view

Animal Models for ZNRF3 Gene

MGI Knock Outs for ZNRF3:

Animal Model Products

CRISPR Products

miRNA for ZNRF3 Gene

miRTarBase miRNAs that target ZNRF3

Clone Products

  • Applied Biological Materials (abm): Clones for ZNRF3 - Now 50% OFF >
  • * ZNRF3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * ZNRF3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ZNRF3 Gene

Localization for ZNRF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZNRF3 Gene

Cell membrane; Single-pass type I membrane protein.

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 ZNRF3 gene
Compartment Confidence
plasma membrane 5
nucleus 1
cytosol 1
endoplasmic reticulum 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ZNRF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IBA,IDA 22575959
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ZNRF3: view

Pathways & Interactions for ZNRF3 Gene

genes like me logo Genes that share pathways with ZNRF3: view

Pathways by source for ZNRF3 Gene

UniProtKB/Swiss-Prot Q9ULT6-ZNRF3_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

SIGNOR curated interactions for ZNRF3 Gene

Inactivates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for ZNRF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006511 ubiquitin-dependent protein catabolic process IBA,IMP 22575959
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 IEA --
genes like me logo Genes that share ontologies with ZNRF3: view

Drugs & Compounds for ZNRF3 Gene

No Compound Related Data Available

Transcripts for ZNRF3 Gene

mRNA/cDNA for ZNRF3 Gene

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

Unigene Clusters for ZNRF3 Gene

Zinc and ring finger 3:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for ZNRF3 - Now 50% OFF >
  • * ZNRF3 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * ZNRF3 tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for ZNRF3 Gene

No ASD Table

Relevant External Links for ZNRF3 Gene

GeneLoc Exon Structure for
ZNRF3
ECgene alternative splicing isoforms for
ZNRF3

Expression for ZNRF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZNRF3 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ZNRF3 Gene



NURSA nuclear receptor signaling pathways regulating expression of ZNRF3 Gene:

ZNRF3

SOURCE GeneReport for Unigene cluster for ZNRF3 Gene:

Hs.655242

Evidence on tissue expression from TISSUES for ZNRF3 Gene

  • Nervous system(4.3)
  • Muscle(4.1)
  • Intestine(2)
genes like me logo Genes that share expression patterns with ZNRF3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZNRF3 Gene

Orthologs for ZNRF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZNRF3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ZNRF3 35 34
  • 99.28 (n)
OneToOne
dog
(Canis familiaris)
Mammalia ZNRF3 35 34
  • 90.1 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Znrf3 17 35 34
  • 86.26 (n)
rat
(Rattus norvegicus)
Mammalia Znrf3 34
  • 81.1 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia ZNRF3 35
  • 73 (a)
OneToOne
cow
(Bos Taurus)
Mammalia ZNRF3 35
  • 72 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia ZNRF3 35
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves ZNRF3 35 34
  • 73.11 (n)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia znrf3 34
  • 65.1 (n)
zebrafish
(Danio rerio)
Actinopterygii znrf3 35 34
  • 64.83 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea Y47D3B.11 35
  • 22 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8714 35
  • 32 (a)
OneToMany
Species where no ortholog for ZNRF3 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)
  • lizard (Anolis carolinensis)
  • 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)
  • wheat (Triticum aestivum)

Evolution for ZNRF3 Gene

ENSEMBL:
Gene Tree for ZNRF3 (if available)
TreeFam:
Gene Tree for ZNRF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ZNRF3: view image

Paralogs for ZNRF3 Gene

Paralogs for ZNRF3 Gene

genes like me logo Genes that share paralogs with ZNRF3: view

Variants for ZNRF3 Gene

Sequence variations from dbSNP and Humsavar for ZNRF3 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000004119 -- 29,015,959(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000005096 -- 28,900,704(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000010206 -- 28,951,501(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000015607 -- 28,994,863(+) G/A genic_upstream_transcript_variant, intron_variant
rs1000038285 -- 28,816,657(+) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for ZNRF3 Gene

Variant ID Type Subtype PubMed ID
esv2657238 CNV deletion 23128226
esv26777 CNV loss 19812545
esv3647523 CNV loss 21293372
nsv1064079 CNV gain 25217958
nsv1072633 CNV deletion 25765185
nsv3589 CNV deletion 18451855
nsv471980 CNV novel sequence insertion 20440878
nsv476091 CNV novel sequence insertion 20440878
nsv834169 CNV loss 17160897
nsv953066 CNV deletion 24416366

Variation tolerance for ZNRF3 Gene

Residual Variation Intolerance Score: 10.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.10; 38.27% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ZNRF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ZNRF3
Human Gene Mutation Database (HGMD)
ZNRF3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZNRF3 Gene

Disorders for ZNRF3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for ZNRF3 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
primary angle-closure glaucoma
  • primary angle closure glaucoma
osteoblastoma
gastric adenocarcinoma
  • adenocarcinoma of stomach
- elite association - COSMIC cancer census association via MalaCards
Search ZNRF3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ZNRF3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with ZNRF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ZNRF3 Gene

Publications for ZNRF3 Gene

  1. Characterization of cDNA clones selected by the GeneMark analysis from size-fractionated cDNA libraries from human brain. (PMID: 10574461) Hirosawa M … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  2. 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 58
  3. ZNRF3 promotes Wnt receptor turnover in an R-spondin-sensitive manner. (PMID: 22575959) Hao HX … Cong F (Nature 2012) 3 4 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 58
  5. Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. (PMID: 20935629) Heid IM … Lindgren CM (Nature genetics 2010) 3 45 58

Products for ZNRF3 Gene

Sources for ZNRF3 Gene

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