RPS29
ribosomal protein S29, the group of S ribosomal proteins
Basic information
Region (hg38): 14:49570983-49599164
Links
Phenotypes
GenCC
Source:
- Diamond-Blackfan anemia 13 (Moderate), mode of inheritance: AD
- Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Diamond-Blackfan anemia 13 | AD | Cardiovascular; Hematologic; Oncologic | Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may allow early detection and management; Individuals with DBA may manifest a variety of congenital malformations (eg, cardiac anomalies), and awareness may allow prompt detection and management | Cardiovascular; Hematologic; Oncologic | 24829207 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (32 variants)
- Diamond-Blackfan anemia 13 (4 variants)
- Inborn genetic diseases (2 variants)
- not specified (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS29 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | 8 | ||||
| missense | 1 | 2 | 8 | 1 | 12 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 3 | 2 | 1 | 7 | |
| non coding | 7 | 1 | 8 | |||
| Total | 1 | 3 | 11 | 18 | 2 |
Variants in RPS29
This is a list of pathogenic ClinVar variants found in the RPS29 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-49577674-T-C | Benign (Jun 29, 2018) | |||
| 14-49583678-GA-G | Diamond-Blackfan anemia 13 | Benign/Likely benign (Sep 24, 2022) | ||
| 14-49583678-G-GA | Benign (May 12, 2022) | |||
| 14-49583688-A-C | Likely benign (May 25, 2021) | |||
| 14-49583692-A-G | Likely benign (Aug 09, 2022) | |||
| 14-49583693-G-A | Likely benign (Sep 27, 2022) | |||
| 14-49583732-C-T | Benign (Jun 05, 2019) | |||
| 14-49585933-C-G | Likely benign (Jun 26, 2021) | |||
| 14-49585934-G-A | Uncertain significance (Aug 27, 2021) | |||
| 14-49585946-C-A | Uncertain significance (Sep 08, 2020) | |||
| 14-49585947-T-C | Uncertain significance (Jun 20, 2022) | |||
| 14-49585955-T-C | Uncertain significance (Oct 24, 2022) | |||
| 14-49585963-A-G | Diamond-Blackfan anemia 13 | Likely pathogenic (Jun 26, 2019) | ||
| 14-49585973-C-A | Inborn genetic diseases | Uncertain significance (Nov 12, 2021) | ||
| 14-49585986-A-G | Likely benign (Oct 17, 2022) | |||
| 14-49585995-G-A | Likely benign (Apr 25, 2021) | |||
| 14-49586010-A-G | Likely benign (Sep 07, 2022) | |||
| 14-49586021-T-A | Diamond-Blackfan anemia 13 | Pathogenic (Jul 03, 2014) | ||
| 14-49586036-T-G | Uncertain significance (Aug 30, 2021) | |||
| 14-49586037-T-G | Likely benign (Nov 23, 2021) | |||
| 14-49586039-A-G | Likely pathogenic (Jun 30, 2016) | |||
| 14-49586046-A-G | Likely benign (Sep 19, 2022) | |||
| 14-49586048-G-T | Uncertain significance (Apr 22, 2022) | |||
| 14-49586052-G-T | Likely pathogenic (Oct 03, 2017) | |||
| 14-49586055-A-C | Diamond-Blackfan anemia 13 | Uncertain significance (Aug 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS29 | protein_coding | protein_coding | ENST00000396020 | 3 | 22019 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.291 | 0.634 | 102073 | 0 | 1 | 102074 | 0.00000490 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.02 | 21 | 38.9 | 0.540 | 0.00000176 | 435 |
| Missense in Polyphen | 5 | 20.364 | 0.24553 | 200 | ||
| Synonymous | -0.126 | 15 | 14.4 | 1.04 | 6.49e-7 | 116 |
| Loss of Function | 1.35 | 1 | 3.87 | 0.258 | 1.64e-7 | 41 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000352 | 0.0000352 |
| 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:
- Disease
- DISEASE: Diamond-Blackfan anemia 13 (DBA13) [MIM:615909]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:24829207}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- 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
- 0.0852
Intolerance Scores
- loftool
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.25
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.801
- ghis
- 0.587
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rps29
- Phenotype
Zebrafish Information Network
- Gene name
- rps29
- Affected structure
- nucleate erythrocyte
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
- Cellular component
- nucleoplasm;cytosol;focal adhesion;small ribosomal subunit;cytosolic small ribosomal subunit;polysomal ribosome;extracellular exosome;cytoplasmic side of rough endoplasmic reticulum membrane
- Molecular function
- structural constituent of ribosome;zinc ion binding