RPS25
ribosomal protein S25, the group of S ribosomal proteins
Basic information
Region (hg38): 11:119015711-119018691
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (11 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 RPS25 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | 1 | ||||
missense | 1 | 1 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 10 | 10 | ||||
Total | 0 | 0 | 1 | 0 | 11 |
Variants in RPS25
This is a list of pathogenic ClinVar variants found in the RPS25 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-119015870-G-C | Inborn genetic diseases | Uncertain significance (Jul 13, 2021) | ||
11-119015893-G-A | Benign (Jun 21, 2018) | |||
11-119018306-G-A | Benign (May 26, 2021) | |||
11-119018318-G-A | Benign (May 16, 2021) | |||
11-119018363-G-T | Benign (May 15, 2021) | |||
11-119018404-A-G | Benign (May 15, 2021) | |||
11-119018422-A-G | Benign (May 15, 2021) | |||
11-119018475-T-C | Benign (May 15, 2021) | |||
11-119018537-A-AG | Benign (May 15, 2021) | |||
11-119018668-G-A | Benign (May 15, 2021) | |||
11-119018686-G-GAGA | Benign (May 30, 2021) | |||
11-119018686-G-GAGGAGA | Benign (May 15, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPS25 | protein_coding | protein_coding | ENST00000527673 | 4 | 2980 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.863 | 0.135 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.83 | 23 | 64.2 | 0.358 | 0.00000277 | 807 |
Missense in Polyphen | 7 | 15.045 | 0.46526 | 224 | ||
Synonymous | -1.16 | 32 | 24.7 | 1.30 | 0.00000108 | 244 |
Loss of Function | 2.37 | 0 | 6.52 | 0.00 | 3.15e-7 | 91 |
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
- 0.171
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.943
- hipred
- Y
- hipred_score
- 0.526
- ghis
- 0.659
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 | Medium | Low | Medium |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rps25
- Phenotype
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytosol;ribosome;postsynaptic density;small ribosomal subunit;cytosolic small ribosomal subunit;extracellular exosome
- Molecular function
- RNA binding;protein binding