RNF169

ring finger protein 169, the group of Ring finger proteins

Basic information

Region (hg38): 11:74748849-74842413

Links

ENSG00000166439 ∙ NCBI:254225 ∙ OMIM:618650 ∙ HGNC:26961 ∙ Uniprot:Q8NCN4 ∙ 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 RNF169 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF169 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			39	2		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	2	0

Variants in RNF169

This is a list of pathogenic ClinVar variants found in the RNF169 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-74748914-T-G		not specified	Uncertain significance (May 03, 2023)
11-74748918-C-T		not specified	Uncertain significance (Jan 26, 2022)
11-74748921-C-T		not specified	Uncertain significance (Mar 21, 2024)
11-74748932-G-T		not specified	Uncertain significance (Sep 22, 2023)
11-74749032-C-T		not specified	Uncertain significance (Jul 19, 2023)
11-74749099-G-C		not specified	Uncertain significance (Dec 15, 2022)
11-74749100-C-T		not specified	Uncertain significance (Nov 21, 2023)
11-74749146-G-A		not specified	Uncertain significance (Apr 12, 2022)
11-74749146-G-C		not specified	Uncertain significance (May 13, 2024)
11-74749159-A-T		not specified	Uncertain significance (May 13, 2024)
11-74749223-C-T		not specified	Uncertain significance (Oct 12, 2022)
11-74749224-G-A		not specified	Uncertain significance (May 24, 2024)
11-74749236-G-A		not specified	Uncertain significance (Jun 09, 2022)
11-74749249-G-C		not specified	Uncertain significance (Jun 27, 2023)
11-74749281-G-T		not specified	Uncertain significance (Mar 07, 2024)
11-74749319-G-C		not specified	Uncertain significance (Sep 22, 2023)
11-74749338-G-T		not specified	Uncertain significance (Mar 25, 2024)
11-74749353-A-T		not specified	Uncertain significance (Nov 21, 2023)
11-74749370-C-T		not specified	Uncertain significance (Dec 15, 2022)
11-74789677-A-G		not specified	Uncertain significance (Mar 07, 2024)
11-74789679-G-A		not specified	Uncertain significance (Aug 17, 2021)
11-74789680-A-G		not specified	Uncertain significance (Jan 03, 2024)
11-74810328-C-T		not specified	Uncertain significance (May 01, 2022)
11-74810329-G-A		not specified	Likely benign (Feb 28, 2024)
11-74817603-C-T		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF169	protein_coding	protein_coding	ENST00000299563	6	93546

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0395	0.960	124768	0	35	124803	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.358	303	321	0.944	0.0000183	4499
Missense in Polyphen		104	126.73	0.82067		1659
Synonymous	-1.89	149	122	1.22	0.00000612	1508
Loss of Function	3.20	7	23.9	0.293	0.00000150	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000463	0.000463
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000112	0.000111
South Asian	0.0000981	0.0000980
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable E3 ubiquitin-protein ligase that acts as a negative regulator of double-strand breaks (DSBs) repair following DNA damage. Recruited to DSB repair sites by recognizing and binding ubiquitin catalyzed by RNF168 and competes with TP53BP1 and BRCA1 for association with RNF168-modified chromatin, thereby acting as a negative regulator of DSBs repair. E3 ubiquitin- protein ligase activity is not required for regulation of DSBs repair. {ECO:0000269|PubMed:22492721, ECO:0000269|PubMed:22733822, ECO:0000269|PubMed:22742833}.

Intolerance Scores

• loftool: 0.577
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.73

Haploinsufficiency Scores

• pHI: 0.421
• hipred: N
• hipred_score: 0.372
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf169
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: cellular response to DNA damage stimulus;protein ubiquitination;negative regulation of double-strand break repair
• Cellular component: nucleus;nucleoplasm;nuclear speck;site of double-strand break
• Molecular function: transferase activity;nucleosome binding;metal ion binding;K63-linked polyubiquitin modification-dependent protein binding