RNF4
Basic information
Region (hg38): 4:2462219-2515857
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
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) | ||
4-2462457-A-C | not specified | Uncertain significance (Aug 17, 2022) | ||
4-2462465-G-A | not specified | Uncertain significance (Feb 28, 2023) | ||
4-2462540-G-A | not specified | Uncertain significance (Jul 08, 2022) | ||
4-2462540-G-C | not specified | Uncertain significance (Feb 22, 2023) | ||
4-2462544-G-A | not specified | Uncertain significance (May 01, 2024) | ||
4-2462546-A-G | not specified | Uncertain significance (Feb 15, 2023) | ||
4-2462583-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
4-2462603-C-G | not specified | Uncertain significance (Sep 14, 2023) | ||
4-2462837-G-A | not specified | Uncertain significance (Jan 27, 2022) | ||
4-2462871-C-T | not specified | Uncertain significance (Apr 01, 2024) | ||
4-2462880-A-C | not specified | Uncertain significance (Jun 06, 2023) | ||
4-2462898-G-A | not specified | Uncertain significance (Jun 03, 2024) | ||
4-2462918-G-A | not specified | Uncertain significance (Jun 29, 2023) | ||
4-2497044-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
4-2497067-A-C | not specified | Uncertain significance (Apr 04, 2023) | ||
4-2497071-C-T | not specified | Uncertain significance (Aug 02, 2022) | ||
4-2497088-T-G | not specified | Uncertain significance (May 06, 2024) | ||
4-2512457-G-T | not specified | Uncertain significance (Jul 13, 2021) | ||
4-2512512-G-A | not specified | Uncertain significance (Apr 15, 2024) | ||
4-2512519-A-T | not specified | Uncertain significance (Jul 14, 2023) | ||
4-2512528-G-A | not specified | Uncertain significance (Jul 19, 2022) | ||
4-2512566-A-C | not specified | Uncertain significance (Nov 03, 2022) | ||
4-2512588-C-T | not specified | Uncertain significance (Jun 01, 2023) | ||
4-2513752-A-G | not specified | Uncertain significance (May 01, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNF4 | protein_coding | protein_coding | ENST00000511600 | 7 | 163101 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.800 | 0.199 | 124589 | 0 | 1 | 124590 | 0.00000401 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.07 | 83 | 115 | 0.719 | 0.00000691 | 1234 |
Missense in Polyphen | 11 | 29.134 | 0.37756 | 345 | ||
Synonymous | 0.105 | 40 | 40.9 | 0.979 | 0.00000243 | 363 |
Loss of Function | 2.58 | 1 | 9.68 | 0.103 | 4.08e-7 | 128 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000885 | 0.00000885 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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