RPL3
Basic information
Region (hg38): 22:39312882-39320389
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | |||||
missense | 17 | 18 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | 2 | |||
non coding | 2 | |||||
Total | 0 | 0 | 18 | 2 | 2 |
Variants in RPL3
This is a list of pathogenic ClinVar variants found in the RPL3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-39312960-C-T | not specified | Likely benign (Feb 10, 2023) | ||
22-39313212-C-T | not specified | Uncertain significance (Jul 06, 2021) | ||
22-39313286-G-A | not specified | Uncertain significance (Oct 12, 2022) | ||
22-39313289-G-A | not specified | Uncertain significance (Oct 20, 2023) | ||
22-39313303-A-G | not specified | Uncertain significance (Aug 12, 2021) | ||
22-39313642-G-A | not specified | Uncertain significance (Jun 27, 2022) | ||
22-39314213-ATGAACAAGAAGGG-A | Uncertain significance (Nov 01, 2023) | |||
22-39314788-G-A | Likely benign (Oct 01, 2022) | |||
22-39314810-C-T | not specified | Uncertain significance (Mar 28, 2024) | ||
22-39315393-C-T | not specified | Uncertain significance (Jun 30, 2022) | ||
22-39315424-A-C | not specified | Uncertain significance (Nov 22, 2021) | ||
22-39315440-G-A | not specified | Uncertain significance (Jun 22, 2024) | ||
22-39315444-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
22-39316720-T-C | not specified | Uncertain significance (Dec 16, 2022) | ||
22-39316756-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
22-39316765-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
22-39316911-G-A | Benign (Dec 01, 2022) | |||
22-39317464-T-C | not specified | Uncertain significance (Feb 28, 2023) | ||
22-39317468-T-C | not specified | Uncertain significance (Jan 24, 2024) | ||
22-39317473-A-T | not specified | Uncertain significance (May 04, 2022) | ||
22-39317613-C-G | not specified | Uncertain significance (Jun 07, 2024) | ||
22-39317633-C-CA | Benign (Mar 29, 2018) | |||
22-39318435-G-C | not specified | Uncertain significance (Sep 29, 2023) | ||
22-39318466-T-C | not specified | Uncertain significance (May 24, 2024) | ||
22-39318469-G-A | not specified | Uncertain significance (Apr 06, 2023) |
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