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RPS3

ribosomal protein S3, the group of S ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 11:75399514-75422280

Links

ENSG00000149273NCBI:6188OMIM:600454HGNC:10420Uniprot:P23396AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS3 gene.

  • not provided (1 variants)
  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS3 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
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 1 0 0

Variants in RPS3

This is a list of pathogenic ClinVar variants found in the RPS3 region.

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

Position Type Phenotype Significance ClinVar
11-75401637-C-T Benign (Jun 04, 2018)769802
11-75404831-C-T Inborn genetic diseases Uncertain significance (Jun 28, 2023)2591662

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS3protein_codingprotein_codingENST00000278572 622795
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9200.0799125721021257230.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.78571540.3700.000008401654
Missense in Polyphen124.6430.040579299
Synonymous-1.296956.71.220.00000298553
Loss of Function3.01112.50.08006.57e-7146

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)0.00001760.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in translation as a component of the 40S small ribosomal subunit (PubMed:8706699). Has endonuclease activity and plays a role in repair of damaged DNA (PubMed:7775413). Cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA (PubMed:15707971). Displays high binding affinity for 7,8-dihydro-8-oxoguanine (8-oxoG), a common DNA lesion caused by reactive oxygen species (ROS) (PubMed:14706345). Has also been shown to bind with similar affinity to intact and damaged DNA (PubMed:18610840). Stimulates the N-glycosylase activity of the base excision protein OGG1 (PubMed:15518571). Enhances the uracil excision activity of UNG1 (PubMed:18973764). Also stimulates the cleavage of the phosphodiester backbone by APEX1 (PubMed:18973764). When located in the mitochondrion, reduces cellular ROS levels and mitochondrial DNA damage (PubMed:23911537). Has also been shown to negatively regulate DNA repair in cells exposed to hydrogen peroxide (PubMed:17049931). Plays a role in regulating transcription as part of the NF-kappa-B p65-p50 complex where it binds to the RELA/p65 subunit, enhances binding of the complex to DNA and promotes transcription of target genes (PubMed:18045535). Represses its own translation by binding to its cognate mRNA (PubMed:20217897). Binds to and protects TP53/p53 from MDM2-mediated ubiquitination (PubMed:19656744). Involved in spindle formation and chromosome movement during mitosis by regulating microtubule polymerization (PubMed:23131551). Involved in induction of apoptosis through its role in activation of CASP8 (PubMed:14988002). Induces neuronal apoptosis by interacting with the E2F1 transcription factor and acting synergistically with it to up-regulate pro-apoptotic proteins BCL2L11/BIM and HRK/Dp5 (PubMed:20605787). Interacts with TRADD following exposure to UV radiation and induces apoptosis by caspase-dependent JNK activation (PubMed:22510408). {ECO:0000269|PubMed:14706345, ECO:0000269|PubMed:14988002, ECO:0000269|PubMed:15518571, ECO:0000269|PubMed:15707971, ECO:0000269|PubMed:17049931, ECO:0000269|PubMed:18045535, ECO:0000269|PubMed:18610840, ECO:0000269|PubMed:18973764, ECO:0000269|PubMed:19656744, ECO:0000269|PubMed:20217897, ECO:0000269|PubMed:20605787, ECO:0000269|PubMed:22510408, ECO:0000269|PubMed:23131551, ECO:0000269|PubMed:23911537, ECO:0000269|PubMed:7775413, ECO:0000269|PubMed:8706699}.;
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
0.453

Intolerance Scores

loftool
rvis_EVS
0.33
rvis_percentile_EVS
73.11

Haploinsufficiency Scores

pHI
0.986
hipred
Y
hipred_score
0.783
ghis

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.781

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps3
Phenotype

Zebrafish Information Network

Gene name
rps3
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;DNA repair;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;apoptotic process;cellular response to DNA damage stimulus;response to oxidative stress;chromosome segregation;positive regulation of gene expression;negative regulation of translation;positive regulation of microtubule polymerization;positive regulation of protein complex assembly;negative regulation of protein ubiquitination;positive regulation of endodeoxyribonuclease activity;positive regulation of interleukin-2 production;positive regulation of activated T cell proliferation;DNA damage response, detection of DNA damage;regulation of apoptotic process;positive regulation of JUN kinase activity;negative regulation of DNA repair;positive regulation of DNA repair;positive regulation of T cell receptor signaling pathway;positive regulation of NF-kappaB transcription factor activity;spindle assembly;cell division;response to TNF agonist;cellular response to hydrogen peroxide;cellular response to tumor necrosis factor;positive regulation of NIK/NF-kappaB signaling;positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage;positive regulation of DNA N-glycosylase activity;positive regulation of base-excision repair;positive regulation of apoptotic signaling pathway;positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis
Cellular component
nucleus;nucleoplasm;nucleolus;cytoplasm;mitochondrial inner membrane;mitochondrial matrix;endoplasmic reticulum;cytosol;ribosome;polysome;plasma membrane;focal adhesion;postsynaptic density;membrane;cytosolic small ribosomal subunit;ruffle membrane;extracellular exosome;NF-kappaB complex;mitotic spindle;ribonucleoprotein complex
Molecular function
RNA polymerase II regulatory region sequence-specific DNA binding;DNA binding;damaged DNA binding;RNA binding;mRNA binding;structural constituent of ribosome;DNA-(apurinic or apyrimidinic site) endonuclease activity;endodeoxyribonuclease activity;protein binding;microtubule binding;transcription factor binding;oxidized purine nucleobase lesion DNA N-glycosylase activity;tubulin binding;DNA N-glycosylase activity;enzyme binding;kinase binding;protein kinase binding;Hsp70 protein binding;oxidized purine DNA binding;oxidized pyrimidine DNA binding;ubiquitin-like protein conjugating enzyme binding;protein-containing complex binding;protein kinase A binding;iron-sulfur cluster binding;Hsp90 protein binding;small ribosomal subunit rRNA binding;supercoiled DNA binding;class I DNA-(apurinic or apyrimidinic site) endonuclease activity