RPS15A
ribosomal protein S15a, the group of S ribosomal proteins
Basic information
Region (hg38): 16:18781294-18790383
Links
Phenotypes
GenCC
Source:
- Diamond-Blackfan anemia 20 (Limited), mode of inheritance: AD
- Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
- Diamond-Blackfan anemia 20 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Diamond-Blackfan anemia 20 | AD | Hematologic; Oncologic | Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may be beneficial | Hematologic; Oncologic | 28280134 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (8 variants)
- Diamond-Blackfan anemia 20 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS15A gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | 3 | ||||
missense | 1 | 1 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 1 | 1 | 2 | |||
non coding | 1 | 2 | 3 | |||
Total | 1 | 0 | 1 | 5 | 2 |
Variants in RPS15A
This is a list of pathogenic ClinVar variants found in the RPS15A region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-18784831-A-G | Likely benign (Sep 21, 2022) | |||
16-18784832-T-TAAC | Likely benign (May 11, 2022) | |||
16-18788063-C-T | Diamond-Blackfan anemia 20 | Pathogenic (Apr 06, 2021) | ||
16-18788093-A-T | Likely benign (Apr 06, 2022) | |||
16-18788132-G-A | Likely benign (Oct 11, 2022) | |||
16-18788293-C-A | Benign (May 14, 2021) | |||
16-18789063-G-T | Likely benign (Aug 03, 2022) | |||
16-18789100-T-C | Uncertain significance (May 13, 2022) | |||
16-18789316-G-C | Benign (May 16, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPS15A | protein_coding | protein_coding | ENST00000322989 | 4 | 9089 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.802 | 0.193 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.24 | 20 | 74.2 | 0.270 | 0.00000392 | 859 |
Missense in Polyphen | 1 | 6.9854 | 0.14316 | 113 | ||
Synonymous | -0.744 | 33 | 28.0 | 1.18 | 0.00000156 | 246 |
Loss of Function | 2.14 | 0 | 5.36 | 0.00 | 2.26e-7 | 66 |
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
- 0.230
Intolerance Scores
- loftool
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.373
- hipred
- Y
- hipred_score
- 0.748
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Low | Low | Low |
Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rps15a
- Phenotype
Zebrafish Information Network
- Gene name
- rps15a
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;positive regulation of cell population proliferation;response to virus;positive regulation of cell cycle
- Cellular component
- nucleoplasm;cytoplasm;cytosol;membrane;cytosolic small ribosomal subunit;extracellular exosome
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding