RNF5

ring finger protein 5, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 6:32178404-32180793

Links

ENSG00000204308 ∙ NCBI:6048 ∙ OMIM:602677 ∙ HGNC:10068 ∙ Uniprot:Q99942 ∙ 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 RNF5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF5 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	1		4
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	1	0

Variants in RNF5

This is a list of pathogenic ClinVar variants found in the RNF5 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-32178557-C-T		not specified	Likely benign (Jan 26, 2022)
6-32178588-A-G		not specified	Uncertain significance (Jul 14, 2021)
6-32178647-T-C		not specified	Uncertain significance (Nov 18, 2022)
6-32180049-C-T		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF5	protein_coding	protein_coding	ENST00000375094	6	5800

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000370	0.617	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.790	82	105	0.783	0.00000599	1164
Missense in Polyphen		20	29.147	0.68617		299
Synonymous	0.0349	40	40.3	0.993	0.00000214	355
Loss of Function	0.797	8	10.8	0.739	5.52e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000798	0.0000791
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has E2-dependent E3 ubiquitin-protein ligase activity. May function together with E2 ubiquitin-conjugating enzymes UBE2D1/UBCH5A and UBE2D2/UBC4. Mediates ubiquitination of PXN/paxillin and Salmonella type III secreted protein sopA. May be involved in regulation of cell motility and localization of PXN/paxillin. Mediates the 'Lys-63'-linked polyubiquitination of JKAMP thereby regulating JKAMP function by decreasing its association with components of the proteasome and ERAD; the ubiquitination appears to involve E2 ubiquitin-conjugating enzyme UBE2N. Mediates the 'Lys-48'-linked polyubiquitination of TMEM173 at 'Lys-150' leading to its proteasomal degradation; the ubiquitination occurs in mitochondria after viral transfection and regulates antiviral responses. {ECO:0000269|PubMed:11329381, ECO:0000269|PubMed:12861019, ECO:0000269|PubMed:16176924, ECO:0000269|PubMed:19269966, ECO:0000269|PubMed:19285439}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Disorders of transmembrane transporters;Disease;Defective CFTR causes cystic fibrosis;ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Transport of small molecules;Asparagine N-linked glycosylation;ABC-family proteins mediated transport;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;ABC transporter disorders (Consensus)

Intolerance Scores

• loftool: 0.519
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.613
• ghis: 0.465

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf5
• Phenotype: muscle phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;response to bacterium;negative regulation of autophagy;ubiquitin-dependent ERAD pathway;protein destabilization;ERAD pathway;cellular protein catabolic process;transmembrane transport;protein K63-linked ubiquitination;protein K48-linked ubiquitination;ER-associated misfolded protein catabolic process;endoplasmic reticulum mannose trimming;regulation of autophagosome assembly
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;mitochondrial membrane;Derlin-1 retrotranslocation complex;endoplasmic reticulum quality control compartment
• Molecular function: ubiquitin-protein transferase activity;protein binding;zinc ion binding;identical protein binding;ubiquitin-like protein conjugating enzyme binding;ubiquitin protein ligase activity