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GeneBe

RNF4

ring finger protein 4, the group of Ring finger proteins

Basic information

Region (hg38): 4:2462219-2515857

Links

ENSG00000063978NCBI:6047OMIM:602850HGNC:10067Uniprot:P78317AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF4 gene.

  • Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF4 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
8
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 8 0 0

Variants in RNF4

This is a list of pathogenic ClinVar variants found in the RNF4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
4-2462456-A-G not specified Uncertain significance (Aug 17, 2022)2382642
4-2462457-A-C not specified Uncertain significance (Aug 17, 2022)2382643
4-2462465-G-A not specified Uncertain significance (Feb 28, 2023)2491182
4-2462540-G-A not specified Uncertain significance (Jul 08, 2022)2300094
4-2462540-G-C not specified Uncertain significance (Feb 22, 2023)2469663
4-2462546-A-G not specified Uncertain significance (Feb 15, 2023)2484015
4-2462583-G-A not specified Uncertain significance (Dec 19, 2022)2336817
4-2462603-C-G not specified Uncertain significance (Sep 14, 2023)2591244
4-2462837-G-A not specified Uncertain significance (Jan 27, 2022)2342498
4-2462880-A-C not specified Uncertain significance (Jun 06, 2023)2557925
4-2462898-G-A not specified Uncertain significance (Dec 20, 2021)3143761
4-2462918-G-A not specified Uncertain significance (Jun 29, 2023)2607422
4-2497044-C-T not specified Uncertain significance (Jul 14, 2021)2237295
4-2497067-A-C not specified Uncertain significance (Apr 04, 2023)2532671
4-2497071-C-T not specified Uncertain significance (Aug 02, 2022)2384278
4-2512457-G-T not specified Uncertain significance (Jul 13, 2021)2362553
4-2512519-A-T not specified Uncertain significance (Jul 14, 2023)2611894
4-2512528-G-A not specified Uncertain significance (Jul 19, 2022)2383230
4-2512566-A-C not specified Uncertain significance (Nov 03, 2022)2322181
4-2512588-C-T not specified Uncertain significance (Jun 01, 2023)2554886

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF4protein_codingprotein_codingENST00000511600 7163101
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8000.199124589011245900.00000401
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.07831150.7190.000006911234
Missense in Polyphen1129.1340.37756345
Synonymous0.1054040.90.9790.00000243363
Loss of Function2.5819.680.1034.08e-7128

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008850.00000885
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor- mediated transcriptional activation. {ECO:0000269|PubMed:12885770, ECO:0000269|PubMed:18408734, ECO:0000269|PubMed:19307308, ECO:0000269|PubMed:20026589, ECO:0000269|PubMed:20212317, ECO:0000269|PubMed:20943951}.;
Pathway
Androgen receptor signaling pathway;HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;Homology Directed Repair;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;AndrogenReceptor;Processing of DNA double-strand break ends (Consensus)

Recessive Scores

pRec
0.123

Intolerance Scores

loftool
0.167
rvis_EVS
0.55
rvis_percentile_EVS
81.22

Haploinsufficiency Scores

pHI
0.155
hipred
Y
hipred_score
0.798
ghis
0.608

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.920

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rnf4
Phenotype
cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
androgen receptor signaling pathway;proteasome-mediated ubiquitin-dependent protein catabolic process;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;response to arsenic-containing substance;protein autoubiquitination;protein K63-linked ubiquitination;protein K48-linked ubiquitination;protein K11-linked ubiquitination;protein K6-linked ubiquitination;regulation of spindle assembly;regulation of kinetochore assembly
Cellular component
nucleus;nucleoplasm;cytoplasm;PML body
Molecular function
DNA binding;transcription coactivator activity;ubiquitin-protein transferase activity;protein binding;transcription factor binding;zinc ion binding;nuclear receptor transcription coactivator activity;nucleosome binding;SUMO polymer binding;identical protein binding;androgen receptor binding;ubiquitin protein ligase activity