RNF220

ring finger protein 220, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 1:44405194-44651723

Previous symbols: [ "C1orf164" ]

Links

ENSG00000187147 ∙ NCBI:55182 ∙ OMIM:616136 ∙ HGNC:25552 ∙ Uniprot:Q5VTB9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathy (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathy	AR	Cardiovascular	Among other features, the condition may include cardiomyopathy, and awareness may allow early management of this issue	Audiologic/Otolaryngologic; Cardiovascular; Gastrointestinal; Neurologic	33964137

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF220 gene.

• Leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF220 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				3		3
missense	1		24			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	24	3	0

Highest pathogenic variant AF is 0.0000197

Variants in RNF220

This is a list of pathogenic ClinVar variants found in the RNF220 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-44412191-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-44412203-C-T		not specified	Uncertain significance (Oct 14, 2023)
1-44412215-A-G		not specified	Uncertain significance (Aug 13, 2021)
1-44412311-A-G		not specified	Uncertain significance (Jul 12, 2022)
1-44412313-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-44412395-G-T		not specified	Uncertain significance (Apr 05, 2023)
1-44412396-C-T		not specified	Uncertain significance (Feb 10, 2023)
1-44412422-A-G		not specified	Uncertain significance (Jun 22, 2021)
1-44412480-A-C		not specified	Uncertain significance (Apr 04, 2024)
1-44412557-C-T		not specified	Uncertain significance (Apr 15, 2024)
1-44412576-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-44412624-C-T		not specified	Uncertain significance (Nov 13, 2023)
1-44412710-C-T		not specified	Uncertain significance (Mar 12, 2024)
1-44614276-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-44614295-G-C		RNF220-related condition	Likely benign (Apr 03, 2024)
1-44626312-G-A		not specified	Uncertain significance (Dec 02, 2021)
1-44635547-C-T		not specified	Uncertain significance (Apr 22, 2024)
1-44636047-G-A		not specified	Uncertain significance (Jul 11, 2023)
1-44636069-A-G		not specified	Uncertain significance (Dec 19, 2022)
1-44636091-G-A		not specified	Uncertain significance (Feb 16, 2023)
1-44636105-G-A		not specified	Uncertain significance (Feb 12, 2024)
1-44636124-G-A		Leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathy	Pathogenic (Apr 06, 2023)
1-44636130-G-A		Leukodystrophy, hypomyelinating, 23, with ataxia, deafness, liver dysfunction, and dilated cardiomyopathy	Pathogenic (Mar 29, 2024)
1-44636160-G-A		not specified	Uncertain significance (Dec 03, 2021)
1-44644710-T-C		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF220	protein_coding	protein_coding	ENST00000355387	14	246531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000425	125737	0	9	125746	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.22	234	351	0.666	0.0000214	3696
Missense in Polyphen		70	134.08	0.52207		1318
Synonymous	0.0200	137	137	0.998	0.00000840	1128
Loss of Function	4.84	2	31.1	0.0643	0.00000160	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000697	0.000695
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of SIN3B (By similarity). Independently of its E3 ligase activity, acts as a CTNNB1 stabilizer through USP7-mediated deubiquitination of CTNNB1 promoting Wnt signaling (PubMed:25266658). {ECO:0000250|UniProtKB:Q6PDX6, ECO:0000269|PubMed:25266658}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0531
• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.44

Haploinsufficiency Scores

• pHI: 0.743
• hipred: Y
• hipred_score: 0.783
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf220

Gene ontology

• Biological process: protein ubiquitination;protein autoubiquitination;positive regulation of canonical Wnt signaling pathway
• Cellular component: cytoplasm
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding;ubiquitin protein ligase activity