RPL23
ribosomal protein L23, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 17:38847859-38853764
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (13 variants)
- not specified (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 RPL23 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 5 | 1 | 6 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 5 | 1 | 6 | |||
| Total | 0 | 0 | 5 | 7 | 2 |
Variants in RPL23
This is a list of pathogenic ClinVar variants found in the RPL23 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-38850161-T-C | Uncertain significance (Aug 25, 2022) | |||
| 17-38850189-T-C | Likely benign (Jul 14, 2022) | |||
| 17-38850224-AAAAAT-A | not specified | Likely benign (Oct 10, 2022) | ||
| 17-38850224-AAAAATAAAAT-A | Likely benign (Sep 22, 2022) | |||
| 17-38850224-A-AAAAAT | Likely benign (Sep 23, 2022) | |||
| 17-38850367-A-G | Uncertain significance (Mar 28, 2022) | |||
| 17-38850422-C-T | not specified • Inborn genetic diseases | Conflicting interpretations of pathogenicity (Apr 18, 2022) | ||
| 17-38850436-C-T | Inborn genetic diseases | Uncertain significance (Nov 03, 2022) | ||
| 17-38850487-A-G | Benign (Sep 15, 2022) | |||
| 17-38852715-T-C | Uncertain significance (Oct 07, 2022) | |||
| 17-38852741-G-A | Likely benign (Apr 30, 2022) | |||
| 17-38853014-G-C | Benign (Jul 23, 2022) | |||
| 17-38853039-T-C | Uncertain significance (May 10, 2022) | |||
| 17-38853115-T-C | Likely benign (Jul 14, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPL23 | protein_coding | protein_coding | ENST00000479035 | 5 | 5979 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.330 | 0.656 | 125234 | 0 | 1 | 125235 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.95 | 33 | 82.9 | 0.398 | 0.00000429 | 887 |
| Missense in Polyphen | 1 | 18.973 | 0.052706 | 242 | ||
| Synonymous | 0.525 | 27 | 30.7 | 0.879 | 0.00000155 | 291 |
| Loss of Function | 2.07 | 2 | 8.54 | 0.234 | 5.24e-7 | 92 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000109 | 0.0000545 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.000109 | 0.0000545 |
| 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;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;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.363
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.891
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.662
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Rpl23
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;ribosomal protein import into nucleus;SRP-dependent cotranslational protein targeting to membrane;positive regulation of cell population proliferation;positive regulation of gene expression;protein-DNA complex disassembly;protein stabilization;negative regulation of cell cycle arrest;positive regulation of cell cycle arrest;cellular response to actinomycin D;positive regulation of signal transduction by p53 class mediator;negative regulation of ubiquitin protein ligase activity;negative regulation of ubiquitin-dependent protein catabolic process
- Cellular component
- nucleoplasm;nucleolus;cytoplasm;cytosol;ribosome;focal adhesion;postsynaptic density;membrane;cytosolic large ribosomal subunit;protein-containing complex;extracellular exosome
- Molecular function
- transcription coactivator binding;RNA binding;structural constituent of ribosome;protein binding;ubiquitin protein ligase binding;large ribosomal subunit rRNA binding;ubiquitin ligase inhibitor activity