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GeneBe

RPS20

ribosomal protein S20, the group of Small nucleolar RNA protein coding host genes|S ribosomal proteins

Basic information

Region (hg38): 8:56067253-56074510

Links

ENSG00000008988NCBI:6224OMIM:603682HGNC:10405Uniprot:P60866AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
  • familial colorectal cancer type X (Supportive), mode of inheritance: AD
  • hereditary nonpolyposis colon cancer (Limited), mode of inheritance: AD
  • hereditary nonpolyposis colon cancer (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS20 gene.

  • not provided (127 variants)
  • Hereditary cancer-predisposing syndrome (99 variants)
  • not specified (28 variants)
  • Hereditary nonpolyposis colon cancer (5 variants)
  • Diamond-Blackfan anemia (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS20 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
67
clinvar
1
clinvar
68
missense
2
clinvar
45
clinvar
47
nonsense
0
start loss
1
clinvar
1
frameshift
5
clinvar
5
inframe indel
3
clinvar
3
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
7
9
16
non coding
12
clinvar
42
clinvar
19
clinvar
73
Total 2 0 68 109 20

Variants in RPS20

This is a list of pathogenic ClinVar variants found in the RPS20 region.

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

Position Type Phenotype Significance ClinVar
8-56069456-A-G Benign (Jun 14, 2019)1223975
8-56069483-G-A Benign (Jun 15, 2019)1272383
8-56069525-C-G Benign (Jun 15, 2019)1246771
8-56069695-A-T not specified Likely benign (Feb 06, 2024)2692138
8-56069703-C-T not specified Benign (Aug 15, 2023)1279207
8-56069724-G-A not specified Benign/Likely benign (Aug 15, 2023)1321491
8-56069746-G-C RPS20-related condition Likely benign (Feb 02, 2024)3046237
8-56069757-G-A Uncertain significance (-)1049806
8-56069817-T-A not specified Uncertain significance (Aug 15, 2023)2576432
8-56069824-A-G Hereditary cancer-predisposing syndrome • not specified Benign (Aug 15, 2023)1232012
8-56069854-GA-G not specified Likely benign (Aug 15, 2023)2576434
8-56069854-GAAAA-G not specified Likely benign (Feb 06, 2024)2692139
8-56069865-G-C not specified Likely benign (Aug 15, 2023)1802761
8-56070020-C-T Benign (Jun 15, 2019)1270961
8-56072854-C-G Benign (Jun 15, 2019)1278075
8-56073068-TC-T not specified Benign (Aug 15, 2023)1802762
8-56073093-A-G Likely benign (Sep 07, 2022)2147299
8-56073094-G-C not specified • Hereditary cancer-predisposing syndrome Uncertain significance (Aug 15, 2023)1802763
8-56073096-A-G Hereditary cancer-predisposing syndrome Likely benign (Jul 05, 2022)1732584
8-56073099-T-C Hereditary cancer-predisposing syndrome Likely benign (Jul 10, 2023)757864
8-56073102-A-G Hereditary cancer-predisposing syndrome Likely benign (Jun 03, 2023)1113798
8-56073117-C-A Uncertain significance (Oct 15, 2023)2768769
8-56073117-C-T Hereditary cancer-predisposing syndrome Likely benign (Jul 16, 2023)716532
8-56073141-G-A Hereditary cancer-predisposing syndrome Likely benign (Jun 20, 2022)1727560
8-56073142-G-T Hereditary cancer-predisposing syndrome Uncertain significance (Aug 09, 2022)1727430

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS20protein_codingprotein_codingENST00000519807 57216
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.02070.912125271031252740.0000120
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.055176.90.6630.00000384914
Missense in Polyphen38.28320.36218127
Synonymous-2.474427.51.600.00000155271
Loss of Function1.5649.060.4414.90e-7102

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006180.0000616
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008870.00000879
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Pathway
Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;Eukaryotic Translation Initiation;Eukaryotic Translation Termination;Translation;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;Cap-dependent Translation Initiation (Consensus)

Intolerance Scores

loftool
rvis_EVS
0.21
rvis_percentile_EVS
67.72

Haploinsufficiency Scores

pHI
0.955
hipred
Y
hipred_score
0.825
ghis
0.454

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
H
gene_indispensability_pred
E
gene_indispensability_score
0.982

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps20
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation 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); limbs/digits/tail phenotype;

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
Cellular component
nucleoplasm;cytosol;membrane;cytosolic small ribosomal subunit;synapse;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding