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GeneBe

RPS5

ribosomal protein S5, the group of S ribosomal proteins

Basic information

Region (hg38): 19:58386399-58394806

Links

ENSG00000083845NCBI:6193OMIM:603630HGNC:10426Uniprot:P46782AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS5 gene.

  • Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS5 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
0
missense
5
clinvar
5
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 5 0 0

Variants in RPS5

This is a list of pathogenic ClinVar variants found in the RPS5 region.

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

Position Type Phenotype Significance ClinVar
19-58388169-T-G Inborn genetic diseases Uncertain significance (Jun 22, 2021)2352243
19-58393141-A-G Inborn genetic diseases Uncertain significance (Aug 28, 2023)2621989
19-58394524-C-A Inborn genetic diseases Uncertain significance (Aug 10, 2021)2392831
19-58394525-G-A Inborn genetic diseases Uncertain significance (Jun 21, 2021)2365514
19-58394555-T-C Inborn genetic diseases Uncertain significance (Mar 27, 2023)2530187

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS5protein_codingprotein_codingENST00000596046 58407
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9480.052200000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.79471400.3360.000009861330
Missense in Polyphen1136.8130.29881386
Synonymous-1.376451.51.240.00000339417
Loss of Function2.8309.300.004.96e-795

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)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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)

Recessive Scores

pRec
0.315

Intolerance Scores

loftool
rvis_EVS
-0.25
rvis_percentile_EVS
35.42

Haploinsufficiency Scores

pHI
0.963
hipred
Y
hipred_score
0.840
ghis
0.634

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.912

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps5
Phenotype

Zebrafish Information Network

Gene name
rps5
Affected structure
trunk
Phenotype tag
abnormal
Phenotype quality
decreased thickness

Gene ontology

Biological process
ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;regulation of translational fidelity;SRP-dependent cotranslational protein targeting to membrane
Cellular component
nucleoplasm;cytosol;focal adhesion;membrane;cytosolic small ribosomal subunit;extracellular exosome;ribonucleoprotein complex
Molecular function
RNA binding;mRNA binding;structural constituent of ribosome;protein binding;rRNA binding