RNF20

ring finger protein 20, the group of Ring finger proteins

Basic information

Region (hg38): 9:101533852-101563344

Links

ENSG00000155827 ∙ NCBI:56254 ∙ OMIM:607699 ∙ HGNC:10062 ∙ Uniprot:Q5VTR2 ∙ 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 RNF20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF20 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				1	1	2
missense			38	2		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	38	4	1

Variants in RNF20

This is a list of pathogenic ClinVar variants found in the RNF20 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-101535461-C-T		not specified	Uncertain significance (Sep 27, 2021)
9-101535464-G-C		not specified	Uncertain significance (Dec 14, 2022)
9-101540225-T-G		not specified	Uncertain significance (Jun 24, 2022)
9-101540295-G-C		not specified	Uncertain significance (Jan 06, 2023)
9-101540320-C-T			not provided (-)
9-101540497-A-G		not specified	Uncertain significance (Dec 31, 2023)
9-101540502-A-G		not specified	Uncertain significance (Sep 16, 2021)
9-101540891-C-T		not specified	Uncertain significance (Aug 01, 2022)
9-101540895-G-A		not specified	Uncertain significance (Jan 10, 2023)
9-101540948-C-T		not specified	Uncertain significance (Jan 31, 2022)
9-101544785-A-C		not specified	Uncertain significance (May 27, 2022)
9-101544814-G-A			Likely benign (Jun 04, 2018)
9-101544844-A-C		not specified	Uncertain significance (Jul 14, 2021)
9-101544868-C-T		not specified	Uncertain significance (Nov 03, 2023)
9-101546824-C-G		not specified	Uncertain significance (Jun 13, 2023)
9-101546878-C-T		not specified	Uncertain significance (Dec 27, 2023)
9-101546955-G-T		not specified	Uncertain significance (Oct 02, 2023)
9-101547435-G-C		not specified	Uncertain significance (Feb 28, 2023)
9-101547475-G-A		not specified	Uncertain significance (Aug 12, 2021)
9-101550609-G-A		not specified	Uncertain significance (Jul 25, 2023)
9-101550624-G-T		not specified	Uncertain significance (Dec 07, 2021)
9-101550636-G-A		not specified	Uncertain significance (Feb 16, 2023)
9-101551715-G-C		not specified	Uncertain significance (Jun 16, 2023)
9-101551742-C-T		not specified	Uncertain significance (Apr 01, 2024)
9-101552260-A-G		not specified	Uncertain significance (Mar 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF20	protein_coding	protein_coding	ENST00000389120	19	29490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-10	1.00	125680	0	68	125748	0.000270

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.11	343	548	0.626	0.0000323	6453
Missense in Polyphen		23	68.024	0.33811		683
Synonymous	0.703	176	188	0.935	0.00000900	1776
Loss of Function	3.99	27	60.5	0.446	0.00000398	657

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000764	0.000764
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000273	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000292	0.000281
Middle Eastern	0.000273	0.000272
South Asian	0.000229	0.000229
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the RNF20/40 E3 ubiquitin-protein ligase complex that mediates monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1). H2BK120ub1 gives a specific tag for epigenetic transcriptional activation and is also prerequisite for histone H3 'Lys-4' and 'Lys-79' methylation (H3K4me and H3K79me, respectively). It thereby plays a central role inb histone code and gene regulation. The RNF20/40 complex forms a H2B ubiquitin ligase complex in cooperation with the E2 enzyme UBE2A or UBE2B; reports about the cooperation with UBE2E1/UBCH are contradictory. Required for transcriptional activation of Hox genes. Recruited to the MDM2 promoter, probably by being recruited by p53/TP53, and thereby acts as a transcriptional coactivator. Mediates the polyubiquitination of isoform 2 of PA2G4 in cancer cells leading to its proteasome-mediated degradation. {ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16337599, ECO:0000269|PubMed:19037095, ECO:0000269|PubMed:19410543}.
• Pathway: ATM Signaling Network in Development and Disease;Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.764
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.14

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.706
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.912

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf20
• Phenotype: growth/size/body region phenotype; embryo phenotype; vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: protein polyubiquitination;regulation of transcription, DNA-templated;ubiquitin-dependent protein catabolic process;regulation of mitotic cell cycle;histone monoubiquitination;protein ubiquitination;negative regulation of cell migration;positive regulation of histone methylation;histone H2B ubiquitination;positive regulation of transcription, DNA-templated;negative regulation of mRNA polyadenylation;positive regulation of histone H2B ubiquitination
• Cellular component: ubiquitin ligase complex;nucleus;nucleoplasm;nucleolus;HULC complex
• Molecular function: p53 binding;chromatin binding;transcription coactivator activity;mRNA 3'-UTR binding;ubiquitin-protein transferase activity;protein binding;ubiquitin protein ligase binding;histone binding;metal ion binding