RNF6
Basic information
Region (hg38): 13:26132114-26222314
Links
Phenotypes
GenCC
Source:
- esophageal cancer (No Known Disease Relationship), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 26 | 31 | ||||
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 | 26 | 4 | 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) | ||
13-26214071-C-T | not specified | Uncertain significance (Mar 30, 2024) | ||
13-26214122-C-T | not specified | Uncertain significance (Apr 20, 2024) | ||
13-26214123-G-A | not specified | Uncertain significance (Jun 12, 2023) | ||
13-26214126-G-C | not specified | Uncertain significance (Dec 07, 2021) | ||
13-26214167-C-T | Benign (Aug 15, 2018) | |||
13-26214183-C-T | not specified | Uncertain significance (Jul 07, 2022) | ||
13-26214200-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
13-26214210-G-A | not specified | Uncertain significance (Apr 16, 2024) | ||
13-26214218-G-T | not specified | Uncertain significance (Nov 30, 2021) | ||
13-26214257-G-T | Likely benign (Apr 11, 2018) | |||
13-26214295-C-G | not specified | Uncertain significance (May 29, 2024) | ||
13-26214380-T-C | not specified | Uncertain significance (Jun 22, 2023) | ||
13-26214504-T-C | not specified | Uncertain significance (Mar 25, 2024) | ||
13-26214507-T-C | not specified | Uncertain significance (Oct 05, 2022) | ||
13-26214521-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
13-26214554-C-T | not specified | Uncertain significance (Dec 21, 2022) | ||
13-26214635-C-G | not specified | Uncertain significance (May 13, 2024) | ||
13-26214641-C-G | not specified | Uncertain significance (Sep 22, 2023) | ||
13-26214641-C-T | not specified | Uncertain significance (Feb 28, 2024) | ||
13-26214743-T-C | not specified | Uncertain significance (Jul 13, 2022) | ||
13-26214793-T-C | Benign (Apr 18, 2018) | |||
13-26214861-C-G | not specified | Uncertain significance (Oct 12, 2021) | ||
13-26214920-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
13-26214923-C-T | not specified | Uncertain significance (Jan 09, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNF6 | protein_coding | protein_coding | ENST00000381588 | 3 | 90539 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0139 | 0.986 | 125727 | 0 | 20 | 125747 | 0.0000795 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.25 | 310 | 378 | 0.819 | 0.0000219 | 4469 |
Missense in Polyphen | 73 | 110.82 | 0.65875 | 1357 | ||
Synonymous | 0.365 | 125 | 130 | 0.959 | 0.00000649 | 1377 |
Loss of Function | 3.54 | 9 | 29.8 | 0.302 | 0.00000244 | 294 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000148 | 0.000148 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000796 | 0.0000791 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.000131 | 0.000131 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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