RPS28
ribosomal protein S28, the group of S ribosomal proteins
Basic information
Region (hg38): 19:8321157-8323340
Links
Phenotypes
GenCC
Source:
- Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (Moderate), mode of inheritance: AD
- Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
- Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Diamond-Blackfan anemia 15 with mandibulofacial dysostosis | AD | Audiologic/Otolaryngologic; Hematologic; Oncologic | Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; surveillance for and early treatment of malignancy may be beneficial; Individuals with DBA may manifest a variety of congenital malformations, and awareness may allow prompt detection and management | Audiologic/Otolaryngologic; Craniofacial; Hematologic; Musculoskeletal; Oncologic | 11424144; 24942156 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (14 variants)
- Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (2 variants)
- Inborn genetic diseases (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS28 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 0 | |||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 2 | 2 | ||||
| non coding | 2 | 9 | 11 | |||
| Total | 1 | 0 | 2 | 5 | 9 |
Variants in RPS28
This is a list of pathogenic ClinVar variants found in the RPS28 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-8321172-G-C | Benign (Jun 20, 2021) | |||
| 19-8321175-T-G | Benign (Jun 20, 2021) | |||
| 19-8321354-G-A | Inborn genetic diseases | Uncertain significance (Dec 13, 2022) | ||
| 19-8321422-G-A | Benign (May 14, 2021) | |||
| 19-8321483-C-T | Benign (Aug 27, 2019) | |||
| 19-8321531-A-G | Diamond-Blackfan anemia 15 with mandibulofacial dysostosis | Pathogenic (Jun 08, 2022) | ||
| 19-8321536-C-T | Likely benign (Sep 05, 2022) | |||
| 19-8321542-C-T | Likely benign (Aug 22, 2022) | |||
| 19-8321589-T-G | Benign (Oct 04, 2022) | |||
| 19-8321649-C-T | Likely benign (Sep 26, 2022) | |||
| 19-8321709-C-T | Likely benign (May 25, 2018) | |||
| 19-8321778-T-C | Benign (May 16, 2021) | |||
| 19-8321817-G-A | Benign (May 14, 2021) | |||
| 19-8322067-T-C | Likely benign (Sep 01, 2022) | |||
| 19-8322069-G-A | Likely benign (Sep 13, 2022) | |||
| 19-8322114-T-C | Diamond-Blackfan anemia 15 with mandibulofacial dysostosis | Benign (Nov 07, 2021) | ||
| 19-8322323-G-A | Benign (Nov 12, 2018) | |||
| 19-8322919-C-T | Inborn genetic diseases | Uncertain significance (Jan 05, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS28 | protein_coding | protein_coding | ENST00000600659 | 3 | 2183 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.683 | 0.300 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 12 | 38.4 | 0.313 | 0.00000176 | 425 |
| Missense in Polyphen | 0 | 6.442 | 0 | 108 | ||
| Synonymous | -0.912 | 20 | 15.4 | 1.30 | 6.88e-7 | 140 |
| Loss of Function | 1.79 | 0 | 3.75 | 0.00 | 1.63e-7 | 43 |
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:
- Disease
- DISEASE: Diamond-Blackfan anemia 15, with mandibulofacial dysostosis (DBA15) [MIM:606164]: 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:24942156}. 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)
Intolerance Scores
- loftool
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.04
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.528
- ghis
- 0.428
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.833
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rps28
- Phenotype
- normal phenotype;
Zebrafish Information Network
- Gene name
- rps28
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;maturation of SSU-rRNA;ribosome biogenesis;ribosomal small subunit biogenesis
- Cellular component
- nucleoplasm;cytosol;small ribosomal subunit;cytosolic small ribosomal subunit;polysomal ribosome;extracellular exosome;cytoplasmic side of rough endoplasmic reticulum membrane
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding