RNF4
ring finger protein 4, the group of Ring finger proteins
Basic information
Region (hg38): 4:2462219-2515857
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 5 | 5 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 1 | 1 | ||||
| Total | 0 | 0 | 6 | 0 | 0 |
Variants in RNF4
This is a list of pathogenic ClinVar variants found in the RNF4 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-2462456-A-G | Inborn genetic diseases | Uncertain significance (Aug 17, 2022) | ||
| 4-2462457-A-C | Inborn genetic diseases | Uncertain significance (Aug 17, 2022) | ||
| 4-2462465-G-A | Inborn genetic diseases | Uncertain significance (Feb 28, 2023) | ||
| 4-2462540-G-A | Inborn genetic diseases | Uncertain significance (Jul 08, 2022) | ||
| 4-2462540-G-C | Inborn genetic diseases | Uncertain significance (Feb 22, 2023) | ||
| 4-2462546-A-G | Inborn genetic diseases | Uncertain significance (Feb 15, 2023) | ||
| 4-2462583-G-A | Inborn genetic diseases | Uncertain significance (Dec 19, 2022) | ||
| 4-2462603-C-G | Inborn genetic diseases | Uncertain significance (Sep 14, 2023) | ||
| 4-2462837-G-A | Inborn genetic diseases | Uncertain significance (Jan 27, 2022) | ||
| 4-2462880-A-C | Inborn genetic diseases | Uncertain significance (Jun 06, 2023) | ||
| 4-2462918-G-A | Inborn genetic diseases | Uncertain significance (Jun 29, 2023) | ||
| 4-2497044-C-T | Inborn genetic diseases | Uncertain significance (Jul 14, 2021) | ||
| 4-2497067-A-C | Inborn genetic diseases | Uncertain significance (Apr 04, 2023) | ||
| 4-2497071-C-T | Inborn genetic diseases | Uncertain significance (Aug 02, 2022) | ||
| 4-2512457-G-T | Inborn genetic diseases | Uncertain significance (Jul 13, 2021) | ||
| 4-2512519-A-T | Inborn genetic diseases | Uncertain significance (Jul 14, 2023) | ||
| 4-2512528-G-A | Inborn genetic diseases | Uncertain significance (Jul 19, 2022) | ||
| 4-2512566-A-C | Inborn genetic diseases | Uncertain significance (Nov 03, 2022) | ||
| 4-2512588-C-T | Inborn genetic diseases | Uncertain significance (Jun 01, 2023) |
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