RPL3
ribosomal protein L3, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes
Basic information
Region (hg38): 22:39312881-39320389
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (8 variants)
- not provided (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 RPL3 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 9 | 9 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 2 |
Variants in RPL3
This is a list of pathogenic ClinVar variants found in the RPL3 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-39312960-C-T | Inborn genetic diseases | Likely benign (Feb 10, 2023) | ||
| 22-39313286-G-A | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
| 22-39313303-A-G | Inborn genetic diseases | Uncertain significance (Aug 12, 2021) | ||
| 22-39313642-G-A | Inborn genetic diseases | Uncertain significance (Jun 27, 2022) | ||
| 22-39315393-C-T | Inborn genetic diseases | Uncertain significance (Jun 30, 2022) | ||
| 22-39315424-A-C | Inborn genetic diseases | Uncertain significance (Nov 22, 2021) | ||
| 22-39316720-T-C | Inborn genetic diseases | Uncertain significance (Dec 16, 2022) | ||
| 22-39316756-T-C | Inborn genetic diseases | Uncertain significance (Sep 16, 2021) | ||
| 22-39317464-T-C | Inborn genetic diseases | Uncertain significance (Feb 28, 2023) | ||
| 22-39317473-A-T | not specified | Uncertain significance (May 04, 2022) | ||
| 22-39317633-C-CA | Benign (Mar 29, 2018) | |||
| 22-39318469-G-A | Inborn genetic diseases | Uncertain significance (Apr 06, 2023) | ||
| 22-39318485-C-T | Benign (Nov 05, 2019) | |||
| 22-39318527-G-C | Inborn genetic diseases | Uncertain significance (Apr 13, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPL3 | protein_coding | protein_coding | ENST00000216146 | 10 | 7508 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.994 | 0.00559 | 125741 | 0 | 1 | 125742 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.56 | 178 | 247 | 0.721 | 0.0000146 | 2650 |
| Missense in Polyphen | 25 | 46.948 | 0.53251 | 601 | ||
| Synonymous | -2.45 | 117 | 87.8 | 1.33 | 0.00000473 | 769 |
| Loss of Function | 3.92 | 1 | 19.8 | 0.0505 | 9.71e-7 | 238 |
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) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: The L3 protein is a component of the large subunit of cytoplasmic ribosomes. {ECO:0000305|PubMed:12962325}.;
- 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
- 0.273
Intolerance Scores
- loftool
- rvis_EVS
- -0.76
- rvis_percentile_EVS
- 13.33
Haploinsufficiency Scores
- pHI
- 0.304
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.946
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpl3
- Phenotype
Zebrafish Information Network
- Gene name
- rpl3
- Affected structure
- exocrine pancreas
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- ribosomal large subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;cellular response to interleukin-4
- Cellular component
- nucleus;nucleolus;cytoplasm;cytosol;focal adhesion;cytosolic large ribosomal subunit;protein-containing complex;extracellular exosome
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding