RPS15
ribosomal protein S15, the group of S ribosomal proteins
Basic information
Region (hg38): 19:1438357-1440495
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (3 variants)
- not specified (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS15 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | 2 | ||||
missense | 1 | 1 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 0 | 0 | 3 |
Variants in RPS15
This is a list of pathogenic ClinVar variants found in the RPS15 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-1438866-C-T | not specified | Benign (May 04, 2021) | ||
19-1440069-G-C | not specified | Benign (May 04, 2021) | ||
19-1440087-A-C | Inborn genetic diseases | Uncertain significance (Jan 18, 2023) | ||
19-1440375-C-T | Benign (Jul 04, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPS15 | protein_coding | protein_coding | ENST00000586686 | 4 | 2226 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.833 | 0.164 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.78 | 46 | 94.8 | 0.485 | 0.00000707 | 916 |
Missense in Polyphen | 3 | 10.411 | 0.28814 | 149 | ||
Synonymous | -3.10 | 66 | 40.8 | 1.62 | 0.00000289 | 283 |
Loss of Function | 2.25 | 0 | 5.89 | 0.00 | 2.54e-7 | 74 |
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) | 0.00 | 0.00 |
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;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
- 0.185
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- N
- hipred_score
- 0.483
- ghis
- 0.623
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.824
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Low | Low | Low |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rps15
- Phenotype
Zebrafish Information Network
- Gene name
- rps15
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- ribosomal small subunit assembly;ribosomal small subunit export from nucleus;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;osteoblast differentiation;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;ribosomal small subunit biogenesis
- Cellular component
- nucleus;nucleoplasm;cytosol;focal adhesion;membrane;cytosolic small ribosomal subunit
- Molecular function
- DNA binding;RNA binding;structural constituent of ribosome;protein binding