RPS2
Basic information
Region (hg38): 16:1962057-1964841
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
missense | 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) | ||
16-1964603-G-A | not specified | Uncertain significance (May 13, 2024) | ||
16-1964604-C-G | not specified | Uncertain significance (May 13, 2024) |
GnomAD
Source:
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:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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