RPL15
ribosomal protein L15, the group of L ribosomal proteins
Basic information
Region (hg38): 3:23916590-23924374
Links
Phenotypes
GenCC
Source:
- Diamond-Blackfan anemia 12 (Strong), mode of inheritance: AD
- Diamond-Blackfan anemia 12 (Strong), 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 12 | 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; Musculoskeletal; Neurologic; Oncologic | 20301769; 23812780 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (89 variants)
- not specified (9 variants)
- Diamond-Blackfan anemia 12 (6 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL15 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 22 | 5 | 29 | ||
| missense | 1 | 36 | 1 | 38 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | 6 | 2 | 10 | |
| non coding | 2 | 7 | 8 | 17 | ||
| Total | 3 | 1 | 41 | 35 | 16 |
Variants in RPL15
This is a list of pathogenic ClinVar variants found in the RPL15 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-23917732-A-C | Likely benign (Dec 21, 2018) | |||
| 3-23917766-T-C | Likely benign (Aug 09, 2018) | |||
| 3-23917859-G-C | not specified | Uncertain significance (Jan 03, 2019) | ||
| 3-23917877-C-T | Likely benign (Dec 16, 2019) | |||
| 3-23917888-T-C | Diamond-Blackfan anemia 12 | Pathogenic (May 18, 2023) | ||
| 3-23917906-C-G | Uncertain significance (Sep 19, 2022) | |||
| 3-23917914-A-G | Uncertain significance (Jul 19, 2022) | |||
| 3-23917934-C-G | not specified | Benign (Nov 02, 2022) | ||
| 3-23917944-C-A | Uncertain significance (Jun 30, 2022) | |||
| 3-23917944-C-T | Diamond-Blackfan anemia 12 | Pathogenic (May 18, 2023) | ||
| 3-23917946-G-T | Uncertain significance (Apr 23, 2019) | |||
| 3-23917960-C-T | not specified | Uncertain significance (Jun 23, 2022) | ||
| 3-23917962-G-A | Uncertain significance (Jun 11, 2019) | |||
| 3-23917979-C-T | Likely benign (Oct 21, 2022) | |||
| 3-23917983-C-T | Uncertain significance (Mar 24, 2022) | |||
| 3-23917986-AC-A | Diamond-Blackfan anemia 12 | Pathogenic (Aug 30, 2021) | ||
| 3-23917987-C-T | Uncertain significance (Nov 19, 2021) | |||
| 3-23917997-T-G | Uncertain significance (Mar 18, 2022) | |||
| 3-23918004-C-T | Uncertain significance (Aug 24, 2021) | |||
| 3-23918015-C-T | Likely benign (Mar 12, 2022) | |||
| 3-23918025-A-G | Uncertain significance (Aug 29, 2022) | |||
| 3-23918027-G-A | Likely benign (Jul 08, 2021) | |||
| 3-23918036-G-A | Diamond-Blackfan anemia 12 | Conflicting interpretations of pathogenicity (Oct 26, 2022) | ||
| 3-23918038-G-A | Likely benign (Dec 09, 2021) | |||
| 3-23918046-G-A | Likely benign (Feb 18, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPL15 | protein_coding | protein_coding | ENST00000307839 | 3 | 7148 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.971 | 0.0285 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.83 | 70 | 129 | 0.545 | 0.00000764 | 1302 |
| Missense in Polyphen | 5 | 22.468 | 0.22254 | 311 | ||
| Synonymous | -2.00 | 58 | 41.6 | 1.39 | 0.00000192 | 425 |
| Loss of Function | 3.07 | 0 | 11.0 | 0.00 | 7.39e-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:
- Disease
- DISEASE: Diamond-Blackfan anemia 12 (DBA12) [MIM:615550]: 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:23812780}. 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;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);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
- 0.171
Intolerance Scores
- loftool
- rvis_EVS
- -0.08
- rvis_percentile_EVS
- 47.79
Haploinsufficiency Scores
- pHI
- 0.481
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.662
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.860
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpl15
- Phenotype
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
- nucleus;cytosol;ribosome;membrane;cytosolic large ribosomal subunit
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding;cadherin binding