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GeneBe

RNF6

ring finger protein 6, the group of Ring finger proteins

Basic information

Region (hg38): 13:26132114-26222314

Links

ENSG00000127870NCBI:6049OMIM:604242HGNC:10069Uniprot:Q9Y252AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • esophageal cancer (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF6 gene.

  • Inborn genetic diseases (19 variants)
  • not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF6 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
2
clinvar
2
missense
18
clinvar
3
clinvar
1
clinvar
22
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 18 3 3

Variants in RNF6

This is a list of pathogenic ClinVar variants found in the RNF6 region.

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

Position Type Phenotype Significance ClinVar
13-26213841-T-G not specified Uncertain significance (Jan 03, 2024)3155465
13-26214123-G-A not specified Uncertain significance (Jun 12, 2023)2559453
13-26214126-G-C not specified Uncertain significance (Dec 07, 2021)3155464
13-26214167-C-T Benign (Aug 15, 2018)714576
13-26214183-C-T not specified Uncertain significance (Jul 07, 2022)2396878
13-26214200-C-T not specified Uncertain significance (Dec 13, 2023)3155463
13-26214218-G-T not specified Uncertain significance (Nov 30, 2021)2379140
13-26214257-G-T Likely benign (Apr 11, 2018)728784
13-26214380-T-C not specified Uncertain significance (Jun 22, 2023)2605306
13-26214507-T-C not specified Uncertain significance (Oct 05, 2022)2317223
13-26214521-C-T not specified Uncertain significance (Nov 08, 2022)2324181
13-26214554-C-T not specified Uncertain significance (Dec 21, 2022)2294872
13-26214641-C-G not specified Uncertain significance (Sep 22, 2023)3155462
13-26214641-C-T not specified Uncertain significance (Feb 28, 2024)3155461
13-26214743-T-C not specified Uncertain significance (Jul 13, 2022)2227807
13-26214793-T-C Benign (Apr 18, 2018)730413
13-26214861-C-G not specified Uncertain significance (Oct 12, 2021)2349845
13-26214920-G-C not specified Uncertain significance (Jun 06, 2023)2557577
13-26214923-C-T not specified Uncertain significance (Jan 09, 2024)3155469
13-26214925-A-C not specified Uncertain significance (Mar 14, 2023)2468309
13-26214959-T-C not specified Likely benign (Aug 26, 2022)3155468
13-26215017-C-T not specified Uncertain significance (May 30, 2023)2552760
13-26215062-G-A not specified Uncertain significance (Jul 13, 2022)2301807
13-26215127-C-T not specified Likely benign (Aug 30, 2021)2247224
13-26215151-C-T Esophageal squamous cell carcinoma, somatic Pathogenic (Aug 01, 2002)5702

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF6protein_codingprotein_codingENST00000381588 390539
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01390.9861257270201257470.0000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.253103780.8190.00002194469
Missense in Polyphen73110.820.658751357
Synonymous0.3651251300.9590.000006491377
Loss of Function3.54929.80.3020.00000244294

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001480.000148
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.00007960.0000791
Middle Eastern0.0001090.000109
South Asian0.0001310.000131
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: E3 ubiquitin-protein ligase mediating 'Lys-48'-linked polyubiquitination of LIMK1 and its subsequent targeting to the proteasome for degradation. Negatively regulates axonal outgrowth through regulation of the LIMK1 turnover. Mediates 'Lys-6' and 'Lys-27'-linked polyubiquitination of AR/androgen receptor thereby modulating its transcriptional activity. May also bind DNA and function as a transcriptional regulator. {ECO:0000269|PubMed:19345326}.;
Disease
DISEASE: Esophageal cancer (ESCR) [MIM:133239]: A malignancy of the esophagus. The most common types are esophageal squamous cell carcinoma and adenocarcinoma. Cancer of the esophagus remains a devastating disease because it is usually not detected until it has progressed to an advanced incurable stage. {ECO:0000269|PubMed:12154016}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
Pathway
Androgen receptor signaling pathway;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;AndrogenReceptor (Consensus)

Recessive Scores

pRec
0.0930

Intolerance Scores

loftool
0.766
rvis_EVS
0.16
rvis_percentile_EVS
64.85

Haploinsufficiency Scores

pHI
0.118
hipred
N
hipred_score
0.344
ghis
0.573

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.992

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rnf6
Phenotype

Gene ontology

Biological process
regulation of transcription, DNA-templated;ubiquitin-dependent protein catabolic process;negative regulation of axon extension;protein K27-linked ubiquitination;positive regulation of transcription, DNA-templated;regulation of androgen receptor signaling pathway;protein K48-linked ubiquitination;protein K6-linked ubiquitination
Cellular component
nucleus;nucleoplasm;cytoplasm;PML body;axon;nuclear membrane;intracellular membrane-bounded organelle
Molecular function
DNA binding;ubiquitin-protein transferase activity;protein binding;metal ion binding;androgen receptor binding;ubiquitin protein ligase activity