RNF11
Basic information
Region (hg38): 1:51236273-51273447
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 RNF11 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 | 3 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 3 | 0 | 0 |
Variants in RNF11
This is a list of pathogenic ClinVar variants found in the RNF11 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-51236779-C-T | not specified | Uncertain significance (Jan 10, 2023) | ||
1-51236807-C-G | not specified | Uncertain significance (Dec 19, 2022) | ||
1-51270109-G-A | not specified | Uncertain significance (May 08, 2024) | ||
1-51271179-T-C | not specified | Uncertain significance (Dec 01, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNF11 | protein_coding | protein_coding | ENST00000242719 | 3 | 37185 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.579 | 0.412 | 124290 | 0 | 2 | 124292 | 0.00000805 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.48 | 48 | 86.7 | 0.554 | 0.00000423 | 1001 |
Missense in Polyphen | 2 | 18.265 | 0.1095 | 222 | ||
Synonymous | 0.319 | 31 | 33.3 | 0.930 | 0.00000165 | 301 |
Loss of Function | 2.08 | 1 | 6.87 | 0.146 | 3.57e-7 | 77 |
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 | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.00000930 | 0.00000899 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential component of a ubiquitin-editing protein complex, comprising also TNFAIP3, ITCH and TAX1BP1, that ensures the transient nature of inflammatory signaling pathways. Promotes the association of TNFAIP3 to RIPK1 after TNF stimulation. TNFAIP3 deubiquitinates 'Lys-63' polyubiquitin chains on RIPK1 and catalyzes the formation of 'Lys-48'-polyubiquitin chains. This leads to RIPK1 proteasomal degradation and consequently termination of the TNF- or LPS-mediated activation of NF-kappa-B. Recruits STAMBP to the E3 ubiquitin-ligase SMURF2 for ubiquitination, leading to its degradation by the 26S proteasome. {ECO:0000269|PubMed:14755250}.;
- Pathway
- TNFalpha
(Consensus)
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- loftool
- 0.222
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.203
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.647
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Low | Low | Low |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rnf11
- Phenotype
Zebrafish Information Network
- Gene name
- rnf11b
- Affected structure
- somite
- Phenotype tag
- abnormal
- Phenotype quality
- apoptotic
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein autoubiquitination
- Cellular component
- ubiquitin ligase complex;nucleus;early endosome;recycling endosome;extracellular exosome
- Molecular function
- DNA binding;ubiquitin-protein transferase activity;protein binding;zinc ion binding