RPS9

ribosomal protein S9, the group of S ribosomal proteins

Basic information

Region (hg38): 19:54200809-54249003

Links

ENSG00000170889 ∙ NCBI:6203 ∙ OMIM:603631 ∙ HGNC:10442 ∙ Uniprot:P46781 ∙ 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 RPS9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS9 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					2	2
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	2

Variants in RPS9

This is a list of pathogenic ClinVar variants found in the RPS9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-54201535-C-T		not specified	Uncertain significance (Feb 27, 2024)
19-54206305-A-G		not specified	Uncertain significance (May 24, 2024)
19-54206364-G-A		RPS9-related disorder	Benign (Jun 28, 2019)
19-54206381-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-54207459-A-G		not specified	Uncertain significance (Aug 28, 2023)
19-54207461-C-T		RPS9-related disorder	Benign (Nov 12, 2019)
19-54207462-G-A		not specified	Uncertain significance (Dec 16, 2022)
19-54207474-C-T		not specified	Uncertain significance (Jun 16, 2024)
19-54217101-T-C		not specified	Uncertain significance (Dec 12, 2023)
19-54217143-C-T		not specified	Uncertain significance (Sep 29, 2023)
19-54217175-C-G		not specified	Uncertain significance (Apr 20, 2023)
19-54217323-G-C		not specified	Uncertain significance (Aug 04, 2023)
19-54217324-T-C		not specified	Uncertain significance (Aug 02, 2021)
19-54218362-T-C		not specified	Uncertain significance (Dec 05, 2022)
19-54218365-C-G		not specified	Uncertain significance (Dec 05, 2022)
19-54218372-G-T		not specified	Uncertain significance (Dec 05, 2022)
19-54218382-G-C		not specified	Likely benign (Feb 21, 2024)
19-54218663-C-T		not specified	Likely benign (Apr 13, 2022)
19-54218669-C-G		not specified	Uncertain significance (Dec 08, 2023)
19-54218815-G-A		not specified	Uncertain significance (May 26, 2022)
19-54218829-T-G		not specified	Uncertain significance (Sep 14, 2022)
19-54219161-A-T		not specified	Uncertain significance (Jun 05, 2023)
19-54219198-C-T		not specified	Likely benign (Feb 06, 2024)
19-54219209-G-A		not specified	Uncertain significance (May 25, 2022)
19-54220564-A-T		not specified	Uncertain significance (Jun 24, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS9	protein_coding	protein_coding	ENST00000302907	4	48253

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.880	0.119	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.73	46	136	0.339	0.00000874	1240
Missense in Polyphen		13	32.097	0.40502		290
Synonymous	0.245	52	54.3	0.958	0.00000318	418
Loss of Function	2.43	0	6.90	0.00	2.91e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;rRNA processing;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;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol;Cap-dependent Translation Initiation (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.939
• hipred: Y
• hipred_score: 0.807
• ghis: 0.501

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps9

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;positive regulation of cell population proliferation;positive regulation of translational fidelity
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;ribosome;focal adhesion;membrane;cytosolic small ribosomal subunit;synapse;extracellular exosome;ribonucleoprotein complex
• Molecular function: RNA binding;structural constituent of ribosome;protein binding;rRNA binding;translation regulator activity;5.8S rRNA binding