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GeneBe

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

ENSG00000140988NCBI:6187OMIM:603624HGNC:10404Uniprot:P15880AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS2 gene.

  • Inborn genetic diseases (4 variants)
  • not provided (3 variants)

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
clinvar
2
clinvar
3
missense
4
clinvar
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 Inborn genetic diseases Uncertain significance (Feb 13, 2023)2483050
16-1964288-G-A Benign (Jun 21, 2018)781179
16-1964313-G-A Inborn genetic diseases Uncertain significance (Dec 14, 2021)2267076
16-1964488-T-C Benign (Jun 21, 2018)768738
16-1964515-A-G Likely benign (Aug 01, 2022)2645954
16-1964528-A-C Inborn genetic diseases Uncertain significance (Sep 15, 2021)2249310
16-1964594-G-A Inborn genetic diseases Uncertain significance (Dec 20, 2021)2215289

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS2protein_codingprotein_codingENST00000343262 62809
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8470.153125660021256620.00000796
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.851121830.6140.00001071854
Missense in Polyphen1343.8540.29644524
Synonymous-3.8211674.21.560.00000438638
Loss of Function2.72110.50.09494.48e-7136

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps2
Phenotype

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