RNF25

ring finger protein 25, the group of Ring finger proteins

Basic information

Region (hg38): 2:218663892-218672002

Links

ENSG00000163481 ∙ NCBI:64320 ∙ OMIM:616014 ∙ HGNC:14662 ∙ Uniprot:Q96BH1 ∙ 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 RNF25 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF25 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	1	0

Variants in RNF25

This is a list of pathogenic ClinVar variants found in the RNF25 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-218664009-C-T		not specified	Uncertain significance (Jul 15, 2021)
2-218664027-C-T		not specified	Uncertain significance (Jun 16, 2024)
2-218664082-G-A		not specified	Uncertain significance (May 12, 2024)
2-218664094-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-218664102-C-T		not specified	Uncertain significance (Apr 27, 2024)
2-218664114-C-A		not specified	Uncertain significance (Nov 12, 2021)
2-218664130-G-T		not specified	Uncertain significance (Oct 26, 2022)
2-218664213-G-A		not specified	Uncertain significance (Jun 24, 2022)
2-218664237-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-218664238-G-A		not specified	Uncertain significance (Dec 21, 2023)
2-218664240-G-C		not specified	Uncertain significance (Dec 14, 2021)
2-218664282-C-T		not specified	Uncertain significance (Apr 11, 2023)
2-218664283-G-A		not specified	Uncertain significance (Sep 14, 2022)
2-218664283-G-C		not specified	Uncertain significance (Apr 11, 2023)
2-218664318-G-T		not specified	Uncertain significance (Oct 03, 2022)
2-218664346-C-T		not specified	Uncertain significance (Oct 03, 2023)
2-218664417-G-A		not specified	Uncertain significance (Oct 05, 2023)
2-218664439-C-T		not specified	Uncertain significance (May 31, 2023)
2-218664465-G-C		not specified	Uncertain significance (Apr 26, 2024)
2-218664522-G-A		not specified	Likely benign (Feb 28, 2024)
2-218664797-C-G		not specified	Uncertain significance (May 18, 2022)
2-218664821-C-T		not specified	Uncertain significance (Mar 01, 2023)
2-218664828-G-A		not specified	Uncertain significance (Jul 09, 2021)
2-218664869-A-G		not specified	Uncertain significance (Aug 17, 2021)
2-218665226-G-T		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF25	protein_coding	protein_coding	ENST00000295704	10	8548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0176	0.982	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	240	269	0.892	0.0000153	2918
Missense in Polyphen		75	94.66	0.79231		1107
Synonymous	1.27	85	101	0.839	0.00000522	952
Loss of Function	3.61	9	30.5	0.295	0.00000183	296

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00102	0.00102
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.0000968	0.0000967
Middle Eastern	0.0000544	0.0000544
South Asian	0.000198	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of NKD2 (By similarity). Stimulates transcription mediated by NF-kappa-B. {ECO:0000250, ECO:0000269|PubMed:12748188}.
• Pathway: Tryptophan metabolism;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Tryptophan degradation;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.798
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.8

Haploinsufficiency Scores

• pHI: 0.401
• hipred: N
• hipred_score: 0.372
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.665

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf25
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: rnf25
• Affected structure: caudal fin
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: protein ubiquitination;positive regulation of NF-kappaB transcription factor activity
• Cellular component: nucleus;cytosol
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding;NF-kappaB binding;ubiquitin protein ligase activity