RNF180

ring finger protein 180, the group of Ring finger proteins

Basic information

Region (hg38): 5:64165843-64372869

Links

ENSG00000164197 ∙ NCBI:285671 ∙ OMIM:616015 ∙ HGNC:27752 ∙ Uniprot:Q86T96 ∙ 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 RNF180 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF180 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			26	6		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	6	0

Variants in RNF180

This is a list of pathogenic ClinVar variants found in the RNF180 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-64200847-C-A		not specified	Uncertain significance (Mar 18, 2024)
5-64200916-G-A		not specified	Likely benign (Feb 15, 2023)
5-64200931-C-G		not specified	Uncertain significance (Aug 30, 2021)
5-64212125-G-A		not specified	Uncertain significance (Feb 02, 2024)
5-64213604-G-A		not specified	Uncertain significance (Nov 30, 2022)
5-64213637-A-C		not specified	Uncertain significance (Jul 11, 2023)
5-64213786-A-G		not specified	Uncertain significance (Apr 08, 2022)
5-64213835-G-A		not specified	Likely benign (Nov 15, 2021)
5-64213847-A-G		not specified	Likely benign (Jan 04, 2024)
5-64213886-G-A		not specified	Uncertain significance (Jan 24, 2024)
5-64213905-G-A		not specified	Uncertain significance (Jun 24, 2022)
5-64213919-T-C		not specified	Uncertain significance (Dec 21, 2021)
5-64214072-A-G		not specified	Uncertain significance (Apr 15, 2024)
5-64214116-A-T		not specified	Uncertain significance (Jun 11, 2021)
5-64214146-A-G		not specified	Uncertain significance (Nov 08, 2022)
5-64214157-C-G		not specified	Uncertain significance (Aug 10, 2023)
5-64214159-A-G		not specified	Likely benign (Nov 04, 2023)
5-64214256-T-A		not specified	Uncertain significance (May 03, 2023)
5-64214267-T-C		not specified	Uncertain significance (Mar 01, 2024)
5-64214296-A-G		not specified	Likely benign (Jun 27, 2022)
5-64214308-A-G		not specified	Uncertain significance (Sep 06, 2022)
5-64214329-C-G		not specified	Uncertain significance (May 14, 2024)
5-64214390-T-C		not specified	Uncertain significance (Aug 22, 2023)
5-64214495-G-A		not specified	Likely benign (Aug 16, 2021)
5-64325200-G-C		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF180	protein_coding	protein_coding	ENST00000389100	7	207026

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000276	0.983	125708	0	37	125745	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.624	257	287	0.896	0.0000141	3922
Missense in Polyphen		16	20.687	0.77345		262
Synonymous	0.0902	100	101	0.989	0.00000478	1080
Loss of Function	2.18	13	24.7	0.526	0.00000132	337

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000393	0.000391
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000272	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000272	0.000217
South Asian	0.000327	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which promotes polyubiquitination and degradation by the proteasome pathway of ZIC2. {ECO:0000250|UniProtKB:Q3U827}.

Recessive Scores

• pRec: 0.0769

Intolerance Scores

• loftool: 0.268
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.413
• hipred: N
• hipred_score: 0.170
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.626

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf180
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: protein polyubiquitination;adult behavior;positive regulation of protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;norepinephrine metabolic process;serotonin metabolic process;regulation of catalytic activity
• Cellular component: nuclear envelope;integral component of membrane;intrinsic component of endoplasmic reticulum membrane
• Molecular function: ubiquitin conjugating enzyme binding;metal ion binding;ubiquitin protein ligase activity