RPS2

ribosomal protein S2, the group of S ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 16:1962057-1964841

Links

ENSG00000140988 ∙ NCBI:6187 ∙ OMIM:603624 ∙ HGNC:10404 ∙ Uniprot:P15880 ∙ 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 RPS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS2 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	2	3
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	1	2

Variants in RPS2

This is a list of pathogenic ClinVar variants found in the RPS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1962109-C-T		not specified	Uncertain significance (Feb 13, 2023)
16-1964288-G-A			Benign (Jun 21, 2018)
16-1964313-G-A		not specified	Uncertain significance (Dec 14, 2021)
16-1964488-T-C			Benign (Jun 21, 2018)
16-1964515-A-G			Likely benign (Aug 01, 2022)
16-1964528-A-C		not specified	Uncertain significance (Sep 15, 2021)
16-1964594-G-A		not specified	Uncertain significance (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS2	protein_coding	protein_coding	ENST00000343262	6	2809

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.847	0.153	125660	0	2	125662	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	112	183	0.614	0.0000107	1854
Missense in Polyphen		13	43.854	0.29644		524
Synonymous	-3.82	116	74.2	1.56	0.00000438	638
Loss of Function	2.72	1	10.5	0.0949	4.48e-7	136

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)	0.0000177	0.0000176
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;Post-translational protein modification;Selenocysteine synthesis;Metabolism of proteins;Metabolism of amino acids and derivatives;RMTs methylate histone arginines;Chromatin modifying enzymes;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;EGFR1;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);Chromatin organization;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;Protein methylation;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)

Intolerance Scores

• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

• pHI: 0.983
• hipred: Y
• hipred_score: 0.687
• ghis: 0.653

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps2

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 ubiquitin-protein transferase activity
• Cellular component: nucleus;nucleoplasm;nucleolus;cytosol;focal adhesion;membrane;cytosolic small ribosomal subunit;extracellular exosome
• Molecular function: RNA binding;mRNA binding;structural constituent of ribosome;protein binding;fibroblast growth factor binding;enzyme binding;cadherin binding