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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 1 |
Variants in RPS3
This is a list of pathogenic ClinVar variants found in the RPS3 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-75401637-C-T | Benign (Jun 04, 2018) | |||
| 11-75404831-C-T | Inborn genetic diseases | Uncertain significance (Jun 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS3 | protein_coding | protein_coding | ENST00000278572 | 6 | 22795 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.920 | 0.0799 | 125721 | 0 | 2 | 125723 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.78 | 57 | 154 | 0.370 | 0.00000840 | 1654 |
| Missense in Polyphen | 1 | 24.643 | 0.040579 | 299 | ||
| Synonymous | -1.29 | 69 | 56.7 | 1.22 | 0.00000298 | 553 |
| Loss of Function | 3.01 | 1 | 12.5 | 0.0800 | 6.57e-7 | 146 |
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) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
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