RPS19
ribosomal protein S19, the group of S ribosomal proteins|MicroRNA protein coding host genes
Basic information
Region (hg38): 19:41860255-41872925
Previous symbols: [ "LOH19CR1" ]
Links
Phenotypes
GenCC
Source:
- Diamond-Blackfan anemia 1 (Definitive), mode of inheritance: AD
- Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
- Diamond-Blackfan anemia 1 (Definitive), mode of inheritance: AD
- Diamond-Blackfan anemia 1 (Strong), mode of inheritance: AD
- Diamond-Blackfan anemia (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Diamond-Blackfan anemia 1 | 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; Craniofacial; Hematologic; Musculoskeletal; Neurologic; Oncologic; Ophthalmologic; Renal | 13722603; 16317735; 276838; 273451; 1958491; 8826887; 9988267; 10541318; 10590074; 16741228; 19061985; 20301769; 23812780; 23812780 |
ClinVar
This is a list of variants' phenotypes submitted to
- Diamond-Blackfan_anemia (184 variants)
- Diamond-Blackfan_anemia_1 (77 variants)
- not_provided (42 variants)
- not_specified (14 variants)
- RPS19-related_disorder (7 variants)
- Landsteiner-Wiener_phenotype (1 variants)
- Hepatoblastoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001022.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 39 | 42 | ||||
| missense | 18 | 56 | 82 | |||
| nonsense | 13 | 16 | ||||
| start loss | 4 | 1 | 5 | |||
| frameshift | 23 | 32 | ||||
| splice donor/acceptor (+/-2bp) | 12 | |||||
| Total | 51 | 31 | 66 | 41 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS19 | protein_coding | protein_coding | ENST00000598742 | 5 | 13007 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.921 | 0.0785 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.45 | 53 | 92.2 | 0.575 | 0.00000596 | 926 |
| Missense in Polyphen | 2 | 14.212 | 0.14073 | 185 | ||
| Synonymous | -2.13 | 54 | 37.4 | 1.44 | 0.00000238 | 297 |
| Loss of Function | 2.64 | 0 | 8.14 | 0.00 | 3.90e-7 | 88 |
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:
- Function
- FUNCTION: Required for pre-rRNA processing and maturation of 40S ribosomal subunits. {ECO:0000269|PubMed:16990592}.;
- Pathway
- Ribosome - Homo sapiens (human);Human Complement System;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
- 0.400
Intolerance Scores
- loftool
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.676
- hipred
- Y
- hipred_score
- 0.771
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.960
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rps19
- Phenotype
- limbs/digits/tail phenotype; pigmentation phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- rps19
- Affected structure
- erythroid lineage cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);monocyte chemotaxis;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;nucleolus organization;response to extracellular stimulus;erythrocyte differentiation;maturation of SSU-rRNA;killing of cells of other organism;ribosomal small subunit biogenesis;defense response to Gram-negative bacterium;protein tetramerization;positive regulation of cellular component movement;positive regulation of respiratory burst involved in inflammatory response;negative regulation of respiratory burst involved in inflammatory response;antimicrobial humoral immune response mediated by antimicrobial peptide
- Cellular component
- nucleoplasm;nucleolus;cytoplasm;cytosol;ribosome;focal adhesion;postsynaptic density;membrane;cytosolic small ribosomal subunit;extracellular exosome
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding;fibroblast growth factor binding;protein kinase binding;protein homodimerization activity