RPS3A
Basic information
Region (hg38): 4:151099624-151104642
Previous symbols: [ "MFTL" ]
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 RPS3A 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 0 |
Variants in RPS3A
This is a list of pathogenic ClinVar variants found in the RPS3A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-151099681-C-G | not specified | Uncertain significance (Feb 28, 2024) | ||
| 4-151100479-A-T | Benign (Jun 13, 2018) | |||
| 4-151100526-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 4-151102889-G-A | not specified | Uncertain significance (Nov 22, 2021) | ||
| 4-151102899-A-G | not specified | Uncertain significance (Dec 28, 2022) | ||
| 4-151103016-A-T | not specified | Uncertain significance (Aug 27, 2024) | ||
| 4-151104535-C-A | not specified | Uncertain significance (Sep 16, 2021) | ||
| 4-151104583-A-G | not specified | Uncertain significance (Apr 22, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS3A | protein_coding | protein_coding | ENST00000274065 | 6 | 5080 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.970 | 0.0299 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.23 | 68 | 143 | 0.476 | 0.00000759 | 1757 |
| Missense in Polyphen | 2 | 13.213 | 0.15137 | 242 | ||
| Synonymous | -2.61 | 68 | 45.6 | 1.49 | 0.00000222 | 475 |
| Loss of Function | 3.05 | 0 | 10.9 | 0.00 | 5.40e-7 | 149 |
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: May play a role during erythropoiesis through regulation of transcription factor DDIT3. {ECO:0000255|HAMAP-Rule:MF_03122}.;
- Pathway
- Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;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);Ribosomal scanning and start codon recognition;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
- 0.302
Intolerance Scores
- loftool
- rvis_EVS
- 0.01
- rvis_percentile_EVS
- 54.63
Haploinsufficiency Scores
- pHI
- 0.997
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.654
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rps3a1
- Phenotype
Zebrafish Information Network
- Gene name
- rps3a
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- bent
Gene ontology
- Biological process
- nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;cell differentiation;negative regulation of apoptotic process
- Cellular component
- nucleus;nucleoplasm;nucleolus;cytoplasm;endoplasmic reticulum;cytosol;focal adhesion;cytosolic small ribosomal subunit;extracellular exosome;ribonucleoprotein complex
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding;mRNA 5'-UTR binding