RNF11

ring finger protein 11, the group of Ring finger proteins

Basic information

Region (hg38): 1:51236273-51273447

Links

ENSG00000123091

∙ NCBI:26994 ∙ OMIM:612598 ∙ HGNC:10056 ∙ Uniprot:Q9Y3C5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (14 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. These statistics are base on transcript: NM_000014372.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			14 clinvar			14
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: 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

	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