RNF41
ring finger protein 41, the group of Ring finger proteins
Basic information
Region (hg38): 12:56202179-56221933
Links
Phenotypes
GenCC
Source:
No genCC data.
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 RNF41 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 | 2 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 6 | |||||
| Total | 0 | 0 | 7 | 1 | 8 |
Variants in RNF41
This is a list of pathogenic ClinVar variants found in the RNF41 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-56206668-C-T | not specified | Uncertain significance (Mar 28, 2023) | ||
| 12-56206681-A-G | Likely benign (Jun 13, 2018) | |||
| 12-56206683-C-G | not specified | Uncertain significance (Jun 16, 2022) | ||
| 12-56207453-A-G | Benign (May 14, 2021) | |||
| 12-56207666-A-C | not specified | Uncertain significance (Aug 08, 2022) | ||
| 12-56207955-G-T | Benign (May 14, 2021) | |||
| 12-56208214-G-A | Benign (Jun 26, 2018) | |||
| 12-56208253-C-G | Benign (Aug 21, 2018) | |||
| 12-56210306-T-C | not specified | Uncertain significance (Jan 04, 2022) | ||
| 12-56210382-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
| 12-56210565-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 12-56210632-GAT-G | Benign (May 14, 2021) | |||
| 12-56210689-C-T | Benign (May 22, 2021) | |||
| 12-56210705-T-C | Benign (May 22, 2021) | |||
| 12-56214017-C-T | not specified | Uncertain significance (Jun 10, 2024) | ||
| 12-56214032-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
| 12-56214143-C-T | Benign (May 14, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RNF41 | protein_coding | protein_coding | ENST00000345093 | 5 | 17433 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.968 | 0.0315 | 125741 | 0 | 2 | 125743 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.00 | 85 | 206 | 0.413 | 0.0000132 | 2098 |
| Missense in Polyphen | 10 | 47.527 | 0.21041 | 523 | ||
| Synonymous | -0.0813 | 76 | 75.1 | 1.01 | 0.00000484 | 615 |
| Loss of Function | 3.36 | 1 | 15.1 | 0.0661 | 8.18e-7 | 153 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as E3 ubiquitin-protein ligase and regulates the degradation of target proteins. Polyubiquitinates MYD88. Negatively regulates MYD88-dependent production of proinflammatory cytokines. Can promote TRIF-dependent production of type I interferon and inhibits infection with vesicular stomatitis virus (By similarity). Promotes also activation of TBK1 and IRF3. Involved in the ubiquitination of erythropoietin (EPO) and interleukin-3 (IL-3) receptors. Thus, through maintaining basal levels of cytokine receptors, RNF41 is involved in the control of hematopoietic progenitor cell differentiation into myeloerythroid lineages (By similarity). Contributes to the maintenance of steady-state ERBB3 levels by mediating its growth factor- independent degradation. Involved in the degradation of the inhibitor of apoptosis BIRC6 and thus is an important regulator of cell death by promoting apoptosis. Acts also as a PRKN modifier that accelerates its degradation, resulting in a reduction of PRKN activity, influencing the balance of intracellular redox state. The RNF41-PRKN pathway regulates autophagosome-lysosome fusion during late mitophagy. Mitophagy is a selective form of autophagy necessary for mitochondrial quality control (PubMed:24949970). {ECO:0000250, ECO:0000250|UniProtKB:Q8BH75, ECO:0000269|PubMed:12411582, ECO:0000269|PubMed:14765125, ECO:0000269|PubMed:15632191, ECO:0000269|PubMed:17210635, ECO:0000269|PubMed:18541373, ECO:0000269|PubMed:19483718, ECO:0000269|PubMed:24949970}.;
- Pathway
- Endocytosis - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Signal Transduction;neuroregulin receptor degredation protein-1 controls erbb3 receptor recycling;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Downregulation of ERBB2:ERBB3 signaling;Downregulation of ERBB2 signaling;Signaling by ERBB2;Signaling by Receptor Tyrosine Kinases;ErbB2/ErbB3 signaling events
(Consensus)
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- loftool
- 0.148
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.64
Haploinsufficiency Scores
- pHI
- 0.770
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnf41
- Phenotype
- reproductive system phenotype;
Zebrafish Information Network
- Gene name
- rnf41
- Affected structure
- melanocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein polyubiquitination;autophagy;negative regulation of cell population proliferation;proteasomal protein catabolic process;negative regulation of cell migration;regulation of MAPK cascade;regulation of lymphocyte differentiation;regulation of myeloid cell differentiation;positive regulation of protein catabolic process;positive regulation of DNA-binding transcription factor activity;protein autoubiquitination;regulation of protein kinase B signaling;extrinsic apoptotic signaling pathway;negative regulation of mitophagy;regulation of establishment of cell polarity;regulation of reactive oxygen species metabolic process;positive regulation of reactive oxygen species metabolic process
- Cellular component
- cytosol;perinuclear region of cytoplasm;endoplasmic reticulum tubular network
- Molecular function
- ubiquitin-protein transferase activity;erythropoietin receptor binding;interleukin-3 receptor binding;protein binding;zinc ion binding;Ral GTPase binding;protein domain specific binding;receptor tyrosine kinase binding;ubiquitin protein ligase activity