RNF34

ring finger protein 34, the group of Ring finger proteins

Basic information

Region (hg38): 12:121400082-121430623

Links

ENSG00000170633 ∙ NCBI:80196 ∙ OMIM:608299 ∙ HGNC:17297 ∙ Uniprot:Q969K3 ∙ 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 RNF34 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF34 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			8	2	1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	1

Variants in RNF34

This is a list of pathogenic ClinVar variants found in the RNF34 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121416174-A-G		not specified	Uncertain significance (Feb 21, 2024)
12-121416312-G-A		not specified	Uncertain significance (Jan 29, 2024)
12-121416336-T-G		not specified	Uncertain significance (Jun 06, 2023)
12-121417567-C-T		not specified	Uncertain significance (Sep 06, 2022)
12-121417690-C-T		not specified	Uncertain significance (Nov 18, 2022)
12-121417707-G-T		not specified	Uncertain significance (Jul 11, 2023)
12-121417724-G-A		not specified	Uncertain significance (Dec 16, 2021)
12-121417808-G-A			Benign (Jun 02, 2018)
12-121417811-C-T		not specified	Uncertain significance (Sep 21, 2023)
12-121417894-T-C		not specified	Uncertain significance (May 27, 2022)
12-121420295-T-G		not specified	Uncertain significance (Sep 26, 2023)
12-121420301-T-G		not specified	Likely benign (Feb 09, 2022)
12-121420313-A-T		not specified	Likely benign (Aug 12, 2021)
12-121420679-G-T		not specified	Uncertain significance (Jan 26, 2023)
12-121420683-G-A		not specified	Uncertain significance (Jul 05, 2023)
12-121420743-G-A		not specified	Uncertain significance (Jan 20, 2023)
12-121423391-G-A		not specified	Uncertain significance (Mar 01, 2024)
12-121430113-G-A		KDM2B-related disorder	Likely benign (Apr 11, 2019)
12-121430121-C-T		KDM2B-related disorder	Uncertain significance (Jan 31, 2023)
12-121430125-C-T		KDM2B-related disorder	Likely benign (Feb 04, 2020)
12-121430138-G-A		KDM2B-related disorder	Uncertain significance (Feb 05, 2024)
12-121430362-G-A			Uncertain significance (Aug 25, 2022)
12-121430436-A-G			Uncertain significance (Dec 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF34	protein_coding	protein_coding	ENST00000392465	6	30546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.611	0.389	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	159	219	0.726	0.0000133	2434
Missense in Polyphen		60	103.8	0.57802		1089
Synonymous	0.751	78	86.9	0.897	0.00000570	719
Loss of Function	3.01	3	16.0	0.188	7.61e-7	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000682	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that regulates several biological processes through the ubiquitin-mediated proteasomal degradation of various target proteins. Ubiquitinates the caspases CASP8 and CASP10, promoting their proteasomal degradation, to negatively regulate cell death downstream of death domain receptors in the extrinsic pathway of apoptosis (PubMed:15069192). May mediate 'Lys-48'-linked polyubiquitination of RIPK1 and its subsequent proteasomal degradation thereby indirectly regulating the tumor necrosis factor-mediated signaling pathway (Ref.13). Negatively regulates p53/TP53 through its direct ubiquitination and targeting to proteasomal degradation (PubMed:17121812). Indirectly, may also negatively regulate p53/TP53 through ubiquitination and degradation of SFN (PubMed:18382127). Mediates PPARGC1A proteasomal degradation probably through ubiquitination thereby indirectly regulating the metabolism of brown fat cells (PubMed:22064484). Possibly involved in innate immunity, through 'Lys-48'-linked polyubiquitination of NOD1 and its subsequent proteasomal degradation (PubMed:25012219). {ECO:0000269|PubMed:12118383, ECO:0000269|PubMed:15069192, ECO:0000269|PubMed:15897238, ECO:0000269|PubMed:17121812, ECO:0000269|PubMed:22064484, ECO:0000269|PubMed:25012219, ECO:0000269|Ref.13, ECO:0000303|PubMed:18382127}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.160

Intolerance Scores

• loftool: 0.642
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.477
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.627

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf34

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;apoptotic process;protein ubiquitination;nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway;proteasome-mediated ubiquitin-dependent protein catabolic process;cellular response to cold;protein K48-linked ubiquitination;negative regulation of signal transduction by p53 class mediator;negative regulation of extrinsic apoptotic signaling pathway via death domain receptors;regulation of oxygen metabolic process;negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;endomembrane system;nuclear body;nuclear speck
• Molecular function: p53 binding;protein binding;ubiquitin protein ligase binding;metal ion binding;ubiquitin protein ligase activity;phosphatidylinositol phosphate binding