RPL28
Basic information
Region (hg38): 19:55385932-55403250
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 RPL28 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 | 0 | |||||
missense | 4 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 4 | |||||
Total | 0 | 0 | 6 | 1 | 1 |
Variants in RPL28
This is a list of pathogenic ClinVar variants found in the RPL28 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
19-55386389-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
19-55386595-A-G | not specified | Uncertain significance (Dec 19, 2022) | ||
19-55386622-A-G | not specified | Uncertain significance (Mar 31, 2023) | ||
19-55387966-C-A | not specified | Uncertain significance (Jun 10, 2024) | ||
19-55388016-C-T | not specified | Uncertain significance (Aug 28, 2023) | ||
19-55391581-C-T | not specified | Uncertain significance (Aug 17, 2021) | ||
19-55391605-C-A | not specified | Uncertain significance (Apr 08, 2024) | ||
19-55391634-T-C | Benign (Apr 10, 2018) | |||
19-55391665-G-A | not specified | Likely benign (Nov 15, 2021) | ||
19-55391735-C-A | not specified | Uncertain significance (Sep 26, 2023) | ||
19-55401446-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
19-55401453-C-A | not specified | Uncertain significance (Jun 03, 2022) | ||
19-55401467-G-A | not specified | Uncertain significance (May 10, 2024) | ||
19-55401481-C-T | not specified | Likely benign (Jan 04, 2024) | ||
19-55401541-C-T | Benign (Jul 20, 2018) | |||
19-55401545-C-A | not specified | Uncertain significance (Jun 03, 2022) | ||
19-55401545-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
19-55401564-C-T | not specified | Uncertain significance (May 03, 2023) | ||
19-55401578-T-G | Benign (Dec 31, 2019) | |||
19-55401601-A-C | Likely benign (Jul 02, 2018) | |||
19-55401603-C-T | not specified | Uncertain significance (Apr 25, 2022) | ||
19-55401610-G-A | Benign (Jun 14, 2018) | |||
19-55401618-C-T | not specified | Uncertain significance (Apr 07, 2023) | ||
19-55401633-C-T | not specified | Uncertain significance (Dec 14, 2023) | ||
19-55401660-G-T | not specified | Uncertain significance (Jul 05, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPL28 | protein_coding | protein_coding | ENST00000558815 | 4 | 17900 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.769 | 0.224 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.0677 | 101 | 103 | 0.981 | 0.00000609 | 1086 |
Missense in Polyphen | 23 | 22.222 | 1.035 | 321 | ||
Synonymous | -1.19 | 49 | 39.5 | 1.24 | 0.00000204 | 343 |
Loss of Function | 2.04 | 0 | 4.85 | 0.00 | 2.04e-7 | 61 |
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: Component of the large ribosomal subunit. {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
- 0.221
Intolerance Scores
- loftool
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 60.31
Haploinsufficiency Scores
- pHI
- 0.618
- hipred
- N
- hipred_score
- 0.281
- ghis
- 0.609
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.747
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rpl28
- Phenotype
Zebrafish Information Network
- Gene name
- rpl28
- Affected structure
- anatomical system
- Phenotype tag
- abnormal
- Phenotype quality
- quality
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
- Cellular component
- cytosol;membrane;cytosolic large ribosomal subunit;dendrite;cytoplasmic ribonucleoprotein granule;cell body;extracellular exosome
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding