RPS20

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

Basic information

Region (hg38): 8:56067254-56074510

Links

ENSG00000008988 ∙ NCBI:6224 ∙ OMIM:603682 ∙ HGNC:10405 ∙ Uniprot:P60866 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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
• Lynch syndrome (Limited), mode of inheritance: AD

ClinVar

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

• 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				69	1	70
missense	2		51			53
nonsense			1			1
start loss			1			1
frameshift			6			6
inframe indel			3			3
splice donor/acceptor (+/-2bp)			2			2
splice region			7	8		15
non coding			12	46	20	78
Total	2	0	76	115	21

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)
8-56069483-G-A			Benign (Jun 15, 2019)
8-56069525-C-G			Benign (Jun 15, 2019)
8-56069695-A-T		not specified	Likely benign (Feb 06, 2024)
8-56069703-C-T		not specified	Benign (Aug 15, 2023)
8-56069704-T-G		not specified	Uncertain significance (Jul 31, 2024)
8-56069724-G-A		not specified	Benign/Likely benign (Aug 15, 2023)
8-56069746-G-C		RPS20-related disorder	Likely benign (Feb 02, 2024)
8-56069757-G-A			Uncertain significance (-)
8-56069817-T-A		not specified	Uncertain significance (Aug 15, 2023)
8-56069824-A-G		not specified	Benign (Aug 15, 2023)
8-56069842-C-G		not specified	Likely benign (Jul 31, 2024)
8-56069854-GA-G		not specified	Likely benign (Aug 15, 2023)
8-56069854-GAAAA-G		not specified	Likely benign (Feb 06, 2024)
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	Uncertain significance (Aug 15, 2023)
8-56073096-A-G		not specified	Likely benign (Jul 05, 2022)
8-56073099-T-C		not specified	Likely benign (Jul 10, 2023)
8-56073102-A-G		not specified	Likely benign (Jun 03, 2023)
8-56073105-G-A		not specified	Likely benign (Mar 23, 2024)
8-56073117-C-A			Uncertain significance (Oct 15, 2023)

GnomAD

Source: gnomAD

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: 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

• 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