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.

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			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: 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

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