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RNF5

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

Basic information

Region (hg38): 6:32178404-32180793

Links

ENSG00000204308NCBI:6048OMIM:602677HGNC:10068Uniprot:Q99942AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF5 gene.

  • Inborn genetic diseases (3 variants)

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
2
clinvar
1
clinvar
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 2 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)2273728
6-32178588-A-G not specified Uncertain significance (Jul 14, 2021)2368558
6-32178647-T-C not specified Uncertain significance (Nov 18, 2022)2327792
6-32180049-C-T not specified Uncertain significance (Feb 05, 2024)3155460

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF5protein_codingprotein_codingENST00000375094 65800
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00003700.6171257300181257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.790821050.7830.000005991164
Missense in Polyphen2029.1470.68617299
Synonymous0.03494040.30.9930.00000214355
Loss of Function0.797810.80.7395.52e-7116

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001490.000149
Ashkenazi Jewish0.000.00
East Asian0.00005460.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.00007980.0000791
Middle Eastern0.00005460.0000544
South Asian0.00009820.0000980
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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