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RFWD3 ring finger and WD repeat domain 3 [ Homo sapiens (human) ]

Gene ID: 55159, updated on 5-Mar-2024

Summary

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Official Symbol
RFWD3provided by HGNC
Official Full Name
ring finger and WD repeat domain 3provided by HGNC
Primary source
HGNC:HGNC:25539
See related
Ensembl:ENSG00000168411 MIM:614151; AllianceGenome:HGNC:25539
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FANCW; RNF201
Summary
Enables MDM2/MDM4 family protein binding activity; p53 binding activity; and ubiquitin protein ligase activity. Involved in several processes, including DNA metabolic process; regulation of cell cycle phase transition; and response to ionizing radiation. Located in nucleoplasm and site of DNA damage. Colocalizes with site of double-strand break. Implicated in Fanconi anemia. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in testis (RPKM 15.0), bone marrow (RPKM 14.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q23.1
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (74621399..74666877, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (80668129..80713619, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (74655297..74700775, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene golgi glycoprotein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74586439-74586940 Neighboring gene MPRA-validated peak2638 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74599495-74599996 Neighboring gene ribosomal protein S10 pseudogene 23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:74601639-74602138 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7698 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:74654659-74655158 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7699 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:74715965-74716163 Neighboring gene thymopoietin pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:74728193-74728362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11108 Neighboring gene mixed lineage kinase domain like pseudokinase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Systematic analysis on expression quantitative trait loci identifies a novel regulatory variant in ring finger and WD repeat domain 3 associated with prognosis of pancreatic cancer. Zhu Y, et al. Chin Med J (Engl), 2022 Jun 5. PMID 35830250, Free PMC Article
  2. The ubiquitin ligase RFWD3 is required for translesion DNA synthesis. Gallina I, et al. Mol Cell, 2021 Feb 4. PMID 33321094, Free PMC Article
  3. Down-regulation of RFWD3 inhibits cancer cells proliferation and migration in gastric carcinoma. Jia J, et al. Gen Physiol Biophys, 2020 Jul. PMID 32902405
  4. Identification of an E3 ligase-encoding gene RFWD3 in non-small cell lung cancer. Zhang Y, et al. Front Med, 2020 Jun. PMID 31571161
  5. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks. Moore CE, et al. J Cell Biol, 2023 May 1. PMID 37036693, Free PMC Article

See all (52) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks.
    Title: RFWD3 promotes ZRANB3 recruitment to regulate the remodeling of stalled replication forks.
  2. Systematic analysis on expression quantitative trait loci identifies a novel regulatory variant in ring finger and WD repeat domain 3 associated with prognosis of pancreatic cancer.
    Title: Systematic analysis on expression quantitative trait loci identifies a novel regulatory variant in ring finger and WD repeat domain 3 associated with prognosis of pancreatic cancer.
  3. The E3 ligase RFWD3 stabilizes ORC in a p53-dependent manner.
    Title: The E3 ligase RFWD3 stabilizes ORC in a p53-dependent manner.
  4. E3 ligase RFWD3 is a novel modulator of stalled fork stability in BRCA2-deficient cells.
    Title: E3 ligase RFWD3 is a novel modulator of stalled fork stability in BRCA2-deficient cells.
  5. Identification of an E3 ligase-encoding gene RFWD3 in non-small cell lung cancer.
    Title: Identification of an E3 ligase-encoding gene RFWD3 in non-small cell lung cancer.
  6. The ubiquitin ligase RFWD3 is required for translesion DNA synthesis.
    Title: The ubiquitin ligase RFWD3 is required for translesion DNA synthesis.
  7. Down-regulation of RFWD3 inhibits cancer cells proliferation and migration in gastric carcinoma.
    Title: Down-regulation of RFWD3 inhibits cancer cells proliferation and migration in gastric carcinoma.
  8. The results suggest that RPA phosphorylation enhances the recruitment of PRP19 to RPA-ssDNA and stimulates RPA ubiquitylation through a process requiring both PRP19 and RFWD3, thereby triggering a phosphorylation-ubiquitylation circuitry that promotes ATR activation and homologous recombination.
    Title: A phosphorylation-and-ubiquitylation circuitry driving ATR activation and homologous recombination.
  9. E3 ligase RFWD3 functions in timely removal and degradation of RPA and RAD51 to allow homologous recombination progression to subsequent steps following mitomycin C damage.
    Title: RFWD3-Mediated Ubiquitination Promotes Timely Removal of Both RPA and RAD51 from DNA Damage Sites to Facilitate Homologous Recombination.
  10. Single point mutations in the RPA32 subunit of RPA that abolish interaction with RFWD3 also inhibit interstrand crossling repair, demonstrating that RPA-mediated RFWD3 recruitment to stalled replication forks is important for ICL repair.
    Title: RPA-Mediated Recruitment of the E3 Ligase RFWD3 Is Vital for Interstrand Crosslink Repair and Human Health.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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
Fanconi anemia, complementation group W
MedGen: C4521564 OMIM: 617784 GeneReviews: Fanconi Anemia
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EBI GWAS Catalog

Description
Meta-analysis identifies four new loci associated with testicular germ cell tumor.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10520

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables MDM2/MDM4 family protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables p53 binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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
  
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in double-strand break repair via homologous recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in interstrand cross-link repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in interstrand cross-link repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitotic G1 DNA damage checkpoint signaling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
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 regulation of DNA damage checkpoint IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in replication fork processing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to ionizing radiation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in PML body IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
is_active_in site of DNA damage IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in site of DNA damage IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with site of double-strand break IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
E3 ubiquitin-protein ligase RFWD3
Names
RING finger and WD repeat domain-containing protein 3
RING finger protein 201
RING-type E3 ubiquitin transferase RFWD3
NP_001357463.1
NP_001357464.1
NP_001357465.1
NP_001357466.1
NP_001357468.1
NP_001357469.1
NP_001357471.1
NP_001357472.1
NP_060594.3
XP_005256079.1
XP_006721291.1
XP_011521493.1
XP_016878880.1
XP_047290279.1
XP_047290280.1
XP_054236617.1
XP_054236618.1
XP_054236619.1
XP_054236620.1
XP_054236621.1
XP_054236622.1

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.

mRNA and Protein(s)

  1. NM_001370534.1 → NP_001357463.1  E3 ubiquitin-protein ligase RFWD3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Consensus CDS
    CCDS32486.1
    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4
    Conserved Domains (3) summary
    COG2319
    Location:486 → 774
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:500 → 537
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  2. NM_001370535.1 → NP_001357464.1  E3 ubiquitin-protein ligase RFWD3 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Consensus CDS
    CCDS32486.1
    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4
    Related
    ENSP00000460049.1, ENST00000571750.5
    Conserved Domains (3) summary
    COG2319
    Location:486 → 774
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:500 → 537
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  3. NM_001370536.1 → NP_001357465.1  E3 ubiquitin-protein ligase RFWD3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Conserved Domains (2) summary
    COG2319
    Location:479 → 715
    WD40; WD40 repeat [General function prediction only]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  4. NM_001370537.1 → NP_001357466.1  E3 ubiquitin-protein ligase RFWD3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Conserved Domains (3) summary
    COG2319
    Location:208 → 496
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 302
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:5 → 65
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  5. NM_001370539.1 → NP_001357468.1  E3 ubiquitin-protein ligase RFWD3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Conserved Domains (3) summary
    COG2319
    Location:208 → 496
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 302
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:5 → 65
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  6. NM_001370540.1 → NP_001357469.1  E3 ubiquitin-protein ligase RFWD3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Conserved Domains (3) summary
    COG2319
    Location:208 → 496
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 302
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:5 → 65
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  7. NM_001370542.1 → NP_001357471.1  E3 ubiquitin-protein ligase RFWD3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Conserved Domains (3) summary
    COG2319
    Location:208 → 496
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 302
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:5 → 65
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  8. NM_001370543.1 → NP_001357472.1  E3 ubiquitin-protein ligase RFWD3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC109599
    Conserved Domains (3) summary
    COG2319
    Location:208 → 496
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 302
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:5 → 65
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  9. NM_018124.4 → NP_060594.3  E3 ubiquitin-protein ligase RFWD3 isoform 1

    See identical proteins and their annotated locations for NP_060594.3

    Status: VALIDATED

    Source sequence(s)
    BC002574, BC059371, BM467919, BP872110
    Consensus CDS
    CCDS32486.1
    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4
    Related
    ENSP00000354361.4, ENST00000361070.9
    Conserved Domains (3) summary
    COG2319
    Location:486 → 774
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:500 → 537
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    74621399..74666877 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011523191.4 → XP_011521493.1  E3 ubiquitin-protein ligase RFWD3 isoform X1

    See identical proteins and their annotated locations for XP_011521493.1

    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4
    Conserved Domains (3) summary
    COG2319
    Location:486 → 774
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:500 → 537
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  2. XM_047434323.1 → XP_047290279.1  E3 ubiquitin-protein ligase RFWD3 isoform X2

  3. XM_017023391.2 → XP_016878880.1  E3 ubiquitin-protein ligase RFWD3 isoform X1

    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4
    Conserved Domains (3) summary
    COG2319
    Location:486 → 774
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:500 → 537
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  4. XM_006721228.4 → XP_006721291.1  E3 ubiquitin-protein ligase RFWD3 isoform X2

    Conserved Domains (2) summary
    COG2319
    Location:479 → 715
    WD40; WD40 repeat [General function prediction only]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  5. XM_005256022.5 → XP_005256079.1  E3 ubiquitin-protein ligase RFWD3 isoform X1

    See identical proteins and their annotated locations for XP_005256079.1

    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4
    Conserved Domains (3) summary
    COG2319
    Location:486 → 774
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:500 → 537
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:283 → 331
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

  6. XM_047434324.1 → XP_047290280.1  E3 ubiquitin-protein ligase RFWD3 isoform X3

    Conserved Domains (3) summary
    COG2319
    Location:208 → 496
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:264 → 302
    7WD40; WD40 repeat [structural motif]
    cd16450
    Location:5 → 65
    mRING-C3HGC3_RFWD3; Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    80668129..80713619 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054380644.1 → XP_054236619.1  E3 ubiquitin-protein ligase RFWD3 isoform X2

  2. XM_054380642.1 → XP_054236617.1  E3 ubiquitin-protein ligase RFWD3 isoform X1

    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4

  3. XM_054380643.1 → XP_054236618.1  E3 ubiquitin-protein ligase RFWD3 isoform X2

  4. XM_054380646.1 → XP_054236621.1  E3 ubiquitin-protein ligase RFWD3 isoform X1

    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4

  5. XM_054380645.1 → XP_054236620.1  E3 ubiquitin-protein ligase RFWD3 isoform X1

    UniProtKB/Swiss-Prot
    A8K585, B2RE35, D3DUJ8, Q5XKR3, Q6PCD5, Q9H9Q3, Q9NVT4

  6. XM_054380647.1 → XP_054236622.1  E3 ubiquitin-protein ligase RFWD3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6PCD5.3 GenPept UniProtKB/Swiss-Prot:Q6PCD5

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