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GeneBe

RNF20

ring finger protein 20, the group of Ring finger proteins

Basic information

Region (hg38): 9:101533852-101563344

Links

ENSG00000155827NCBI:56254OMIM:607699HGNC:10062Uniprot:Q5VTR2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF20 gene.

  • Inborn genetic diseases (29 variants)
  • not provided (6 variants)

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
clinvar
1
clinvar
2
missense
29
clinvar
2
clinvar
31
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 29 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)2208982
9-101535464-G-C not specified Uncertain significance (Dec 14, 2022)2397500
9-101540225-T-G not specified Uncertain significance (Jun 24, 2022)2297604
9-101540295-G-C not specified Uncertain significance (Jan 06, 2023)3155256
9-101540320-C-T not provided (-)135634
9-101540497-A-G not specified Uncertain significance (Dec 31, 2023)3155257
9-101540502-A-G not specified Uncertain significance (Sep 16, 2021)2367356
9-101540891-C-T not specified Uncertain significance (Aug 01, 2022)2345814
9-101540895-G-A not specified Uncertain significance (Jan 10, 2023)2471204
9-101540948-C-T not specified Uncertain significance (Jan 31, 2022)2274752
9-101544785-A-C not specified Uncertain significance (May 27, 2022)3155258
9-101544814-G-A Likely benign (Jun 04, 2018)743589
9-101544844-A-C not specified Uncertain significance (Jul 14, 2021)2408106
9-101544868-C-T not specified Uncertain significance (Nov 03, 2023)3155259
9-101546824-C-G not specified Uncertain significance (Jun 13, 2023)2517861
9-101546878-C-T not specified Uncertain significance (Dec 27, 2023)3155260
9-101546955-G-T not specified Uncertain significance (Oct 02, 2023)3155261
9-101547435-G-C not specified Uncertain significance (Feb 28, 2023)2491496
9-101547475-G-A not specified Uncertain significance (Aug 12, 2021)2390191
9-101550609-G-A not specified Uncertain significance (Jul 25, 2023)2613486
9-101550624-G-T not specified Uncertain significance (Dec 07, 2021)2408125
9-101550636-G-A not specified Uncertain significance (Feb 16, 2023)2468145
9-101551715-G-C not specified Uncertain significance (Jun 16, 2023)2603991
9-101551742-C-T not specified Uncertain significance (Dec 07, 2021)2272928
9-101552260-A-G not specified Uncertain significance (Mar 14, 2023)2455008

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF20protein_codingprotein_codingENST00000389120 1929490
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.75e-101.001256800681257480.000270
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.113435480.6260.00003236453
Missense in Polyphen2368.0240.33811683
Synonymous0.7031761880.9350.000009001776
Loss of Function3.992760.50.4460.00000398657

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007640.000764
Ashkenazi Jewish0.0002980.000298
East Asian0.0002730.000272
Finnish0.0001390.000139
European (Non-Finnish)0.0002920.000281
Middle Eastern0.0002730.000272
South Asian0.0002290.000229
Other0.0006540.000652

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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