RNF111

ring finger protein 111, the group of Ring finger proteins

Basic information

Region (hg38): 15:58865174-59097419

Links

ENSG00000157450 ∙ NCBI:54778 ∙ OMIM:605840 ∙ HGNC:17384 ∙ Uniprot:Q6ZNA4 ∙ 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 RNF111 gene.

• Inborn genetic diseases (43 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF111 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			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	0

Variants in RNF111

This is a list of pathogenic ClinVar variants found in the RNF111 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-58883674-C-T		not specified	Uncertain significance (Sep 14, 2023)
15-58883692-C-G		not specified	Uncertain significance (Mar 01, 2023)
15-58883759-C-G		not specified	Uncertain significance (Dec 06, 2023)
15-58887040-C-T		not specified	Uncertain significance (Sep 26, 2022)
15-58887061-G-C		not specified	Uncertain significance (Aug 17, 2022)
15-58887063-G-A		not specified	Uncertain significance (Feb 09, 2023)
15-58887236-G-A		not specified	Uncertain significance (Mar 20, 2023)
15-58887250-A-G		not specified	Uncertain significance (Oct 05, 2023)
15-58887278-G-T		not specified	Uncertain significance (Jul 14, 2021)
15-58887289-T-C		not specified	Uncertain significance (Nov 08, 2022)
15-58887316-G-T		Jeune thoracic dystrophy	Likely pathogenic (-)
15-58887323-T-G		not specified	Uncertain significance (Jan 08, 2024)
15-58887338-C-G		not specified	Uncertain significance (Jan 30, 2024)
15-58887358-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-58887376-C-T		not specified	Uncertain significance (Jan 16, 2024)
15-58887478-T-C		not specified	Uncertain significance (Jan 09, 2024)
15-58888454-T-C		not specified	Uncertain significance (Jan 09, 2024)
15-58888490-T-C		not specified	Uncertain significance (May 24, 2023)
15-58888520-A-G		not specified	Uncertain significance (Jun 29, 2023)
15-58889511-T-G		not specified	Uncertain significance (Nov 04, 2023)
15-58890363-C-A		not specified	Uncertain significance (Dec 22, 2023)
15-58890366-T-G		not specified	Uncertain significance (Jun 06, 2023)
15-58890385-G-A		not specified	Uncertain significance (Jan 04, 2024)
15-58890403-C-T		not specified	Uncertain significance (Jan 04, 2022)
15-58893841-C-A		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF111	protein_coding	protein_coding	ENST00000559209	13	232245

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000134	125735	0	13	125748	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.320	520	541	0.961	0.0000276	6514
Missense in Polyphen		234	263.92	0.88664		3112
Synonymous	-1.10	207	188	1.10	0.00000956	1971
Loss of Function	5.51	4	43.0	0.0930	0.00000238	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000682	0.0000682
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000948	0.0000924
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase (PubMed:26656854). Required for mesoderm patterning during embryonic development (By similarity). Acts as an enhancer of the transcriptional responses of the SMAD2/SMAD3 effectors, which are activated downstream of BMP (PubMed:14657019, PubMed:16601693). Acts by mediating ubiquitination and degradation of SMAD inhibitors such as SMAD7, inducing their proteasomal degradation and thereby enhancing the transcriptional activity of TGF-beta and BMP (PubMed:14657019, PubMed:16601693). In addition to enhance transcription of SMAD2/SMAD3 effectors, also regulates their turnover by mediating their ubiquitination and subsequent degradation, coupling their activation with degradation, thereby ensuring that only effectors 'in use' are degraded (By similarity). Activates SMAD3/SMAD4- dependent transcription by triggering signal-induced degradation of SNON isoform of SKIL (PubMed:17591695). Associates with UBE2D2 as an E2 enzyme (PubMed:22411132). Specifically binds polysumoylated chains via SUMO interaction motifs (SIMs) and mediates ubiquitination of sumoylated substrates (PubMed:23751493). Catalyzes 'Lys-63'-linked ubiquitination of sumoylated XPC in response to UV irradiation, promoting nucleotide excision repair (PubMed:23751493). Mediates ubiquitination and degradation of sumoylated PML (By similarity). The regulation of the BMP-SMAD signaling is however independent of sumoylation and is not dependent of SUMO interaction motifs (SIMs) (By similarity). {ECO:0000250|UniProtKB:Q99ML9, ECO:0000269|PubMed:14657019, ECO:0000269|PubMed:16601693, ECO:0000269|PubMed:17591695, ECO:0000269|PubMed:22411132, ECO:0000269|PubMed:23751493, ECO:0000269|PubMed:26656854}.
• Pathway: TGF-Ncore;TGF-beta Signaling Pathway;DNA Repair;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Immune System;Adaptive Immune System;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Downregulation of SMAD2/3:SMAD4 transcriptional activity;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Signaling by TGF-beta Receptor Complex;Formation of Incision Complex in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Signaling by TGF-beta family members;TGF-beta receptor signaling;Nucleotide Excision Repair (Consensus)

Recessive Scores

• pRec: 0.175

Intolerance Scores

• loftool: 0.402
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.75

Haploinsufficiency Scores

• pHI: 0.321
• hipred: Y
• hipred_score: 0.814
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rnf111
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Zebrafish Information Network

• Gene name: rnf111
• Affected structure: blastoderm
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;pattern specification process;protein ubiquitination;positive regulation of transforming growth factor beta receptor signaling pathway;ubiquitin-dependent SMAD protein catabolic process;positive regulation of protein ubiquitination;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;global genome nucleotide-excision repair
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;PML body;protein-containing complex
• Molecular function: protein binding;SUMO polymer binding;SMAD binding;metal ion binding;ubiquitin protein ligase activity