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GeneBe

RNF11

ring finger protein 11, the group of Ring finger proteins

Basic information

Region (hg38): 1:51236272-51273447

Links

ENSG00000123091NCBI:26994OMIM:612598HGNC:10056Uniprot:Q9Y3C5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF11 gene.

  • Inborn genetic diseases (3 variants)

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
clinvar
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 Inborn genetic diseases Uncertain significance (Jan 10, 2023)2461305
1-51236807-C-G Inborn genetic diseases Uncertain significance (Dec 19, 2022)2337258
1-51271179-T-C Inborn genetic diseases Uncertain significance (Dec 01, 2022)2330766

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF11protein_codingprotein_codingENST00000242719 337185
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5790.412124290021242920.00000805
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.484886.70.5540.000004231001
Missense in Polyphen218.2650.1095222
Synonymous0.3193133.30.9300.00000165301
Loss of Function2.0816.870.1463.57e-777

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.000009300.00000899
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

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