RPS3A
ribosomal protein S3A, the group of Small nucleolar RNA protein coding host genes|S ribosomal proteins
Basic information
Region (hg38): 4:151099623-151104642
Previous symbols: [ "MFTL" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (3 variants)
- not provided (1 variants)
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 3 | 3 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 1 | 1 | ||||
non coding | 0 | |||||
Total | 0 | 0 | 3 | 0 | 1 |
Variants in RPS3A
This is a list of pathogenic ClinVar variants found in the RPS3A region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
4-151100479-A-T | Benign (Jun 13, 2018) | |||
4-151102889-G-A | Inborn genetic diseases | Uncertain significance (Nov 22, 2021) | ||
4-151102899-A-G | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
4-151104535-C-A | Inborn genetic diseases | Uncertain significance (Sep 16, 2021) |
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