RPS5
Basic information
Region (hg38): 19:58386400-58394806
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 RPS5 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in RPS5
This is a list of pathogenic ClinVar variants found in the RPS5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-58388169-T-G | not specified | Uncertain significance (Jun 22, 2021) | ||
| 19-58393141-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
| 19-58394524-C-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 19-58394525-G-A | not specified | Uncertain significance (Jun 21, 2021) | ||
| 19-58394555-T-C | not specified | Uncertain significance (Mar 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS5 | protein_coding | protein_coding | ENST00000596046 | 5 | 8407 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.948 | 0.0522 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.79 | 47 | 140 | 0.336 | 0.00000986 | 1330 |
| Missense in Polyphen | 11 | 36.813 | 0.29881 | 386 | ||
| Synonymous | -1.37 | 64 | 51.5 | 1.24 | 0.00000339 | 417 |
| Loss of Function | 2.83 | 0 | 9.30 | 0.00 | 4.96e-7 | 95 |
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
- 0.315
Intolerance Scores
- loftool
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.963
- hipred
- Y
- hipred_score
- 0.840
- ghis
- 0.634
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.912
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rps5
- Phenotype
Zebrafish Information Network
- Gene name
- rps5
- Affected structure
- trunk
- Phenotype tag
- abnormal
- Phenotype quality
- decreased thickness
Gene ontology
- Biological process
- ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;regulation of translational fidelity;SRP-dependent cotranslational protein targeting to membrane
- Cellular component
- nucleoplasm;cytosol;focal adhesion;membrane;cytosolic small ribosomal subunit;extracellular exosome;ribonucleoprotein complex
- Molecular function
- RNA binding;mRNA binding;structural constituent of ribosome;protein binding;rRNA binding