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
Phenotypes
GenCC
Source:
- 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
- not provided (115 variants)
- Hereditary cancer-predisposing syndrome (84 variants)
- not specified (13 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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 53 | 53 | ||||
| missense | 2 | 36 | 5 | 2 | 45 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 5 | 5 | ||||
| inframe indel | 1 | 1 | ||||
| splice variant | 13 | 14 | 3 | 30 | ||
| non coding | 2 | 20 | 20 | 42 | ||
| Total | 2 | 0 | 59 | 92 | 25 |
Variants in RPS20
This is a list of pathogenic ClinVar variants found in the RPS20 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 8-56069456-A-G | Benign (Jun 14, 2019) | |||
| 8-56069483-G-A | Benign (Jun 15, 2019) | |||
| 8-56069525-C-G | Benign (Jun 15, 2019) | |||
| 8-56069703-C-T | not specified | Benign (Aug 15, 2023) | ||
| 8-56069724-G-A | not specified | Benign/Likely benign (Aug 15, 2023) | ||
| 8-56069757-G-A | Uncertain significance (-) | |||
| 8-56069817-T-A | not specified | Uncertain significance (Aug 15, 2023) | ||
| 8-56069824-A-G | Hereditary cancer-predisposing syndrome • not specified | Benign (Aug 15, 2023) | ||
| 8-56069854-GA-G | not specified | Likely benign (Aug 15, 2023) | ||
| 8-56069865-G-C | not specified | Likely benign (Aug 15, 2023) | ||
| 8-56070020-C-T | Benign (Jun 15, 2019) | |||
| 8-56072854-C-G | Benign (Jun 15, 2019) | |||
| 8-56073068-TC-T | not specified | Benign (Aug 15, 2023) | ||
| 8-56073093-A-G | Likely benign (Sep 07, 2022) | |||
| 8-56073094-G-C | not specified • Hereditary cancer-predisposing syndrome | Uncertain significance (Aug 15, 2023) | ||
| 8-56073096-A-G | Hereditary cancer-predisposing syndrome | Likely benign (Jul 05, 2022) | ||
| 8-56073099-T-C | Hereditary cancer-predisposing syndrome | Likely benign (Sep 21, 2022) | ||
| 8-56073102-A-G | Hereditary cancer-predisposing syndrome | Likely benign (Apr 19, 2022) | ||
| 8-56073117-C-T | Hereditary cancer-predisposing syndrome | Likely benign (Oct 17, 2022) | ||
| 8-56073141-G-A | Hereditary cancer-predisposing syndrome | Likely benign (Jun 20, 2022) | ||
| 8-56073142-G-T | Hereditary cancer-predisposing syndrome | Uncertain significance (Aug 09, 2022) | ||
| 8-56073144-A-C | Hereditary cancer-predisposing syndrome | Likely benign (Aug 05, 2022) | ||
| 8-56073144-A-G | Hereditary cancer-predisposing syndrome | Likely benign (Apr 04, 2022) | ||
| 8-56073150-C-T | Hereditary cancer-predisposing syndrome | Likely benign (Sep 09, 2020) | ||
| 8-56073153-C-T | Hereditary cancer-predisposing syndrome | Likely benign (Apr 02, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS20 | protein_coding | protein_coding | ENST00000519807 | 5 | 7216 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0207 | 0.912 | 125271 | 0 | 3 | 125274 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 51 | 76.9 | 0.663 | 0.00000384 | 914 |
| Missense in Polyphen | 3 | 8.2832 | 0.36218 | 127 | ||
| Synonymous | -2.47 | 44 | 27.5 | 1.60 | 0.00000155 | 271 |
| Loss of Function | 1.56 | 4 | 9.06 | 0.441 | 4.90e-7 | 102 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000618 | 0.0000616 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000887 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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