RNF6

ring finger protein 6, the group of Ring finger proteins

Basic information

Region (hg38): 13:26132114-26222314

Links

ENSG00000127870 ∙ NCBI:6049 ∙ OMIM:604242 ∙ HGNC:10069 ∙ Uniprot:Q9Y252 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

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	2
missense			26	4	1	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)
13-26214123-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)
13-26214218-G-T		not specified	Uncertain significance (Nov 30, 2021)
13-26214257-G-T			Likely benign (Apr 11, 2018)
13-26214380-T-C		not specified	Uncertain significance (Jun 22, 2023)
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)
13-26214641-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)
13-26214925-A-C		not specified	Uncertain significance (Mar 14, 2023)
13-26214959-T-C		not specified	Likely benign (Aug 26, 2022)
13-26215017-C-T		not specified	Uncertain significance (May 30, 2023)
13-26215062-G-A		not specified	Uncertain significance (Jul 13, 2022)
13-26215127-C-T		not specified	Likely benign (Aug 30, 2021)
13-26215151-C-T		Esophageal squamous cell carcinoma, somatic	Pathogenic (Aug 01, 2002)

GnomAD

Source: gnomAD

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: 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

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

Mouse Genome Informatics

• Gene name: Rnf6

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