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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

ENSG00000145425NCBI:6189OMIM:180478HGNC:10421Uniprot:P61247AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS3A gene.

  • 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.

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
3
clinvar
3
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 3 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)3156190
4-151100479-A-T Benign (Jun 13, 2018)778160
4-151102889-G-A not specified Uncertain significance (Nov 22, 2021)2354036
4-151102899-A-G not specified Uncertain significance (Dec 28, 2022)2340423
4-151104535-C-A not specified Uncertain significance (Sep 16, 2021)2204768

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS3Aprotein_codingprotein_codingENST00000274065 65080
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9700.029900000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.23681430.4760.000007591757
Missense in Polyphen213.2130.15137242
Synonymous-2.616845.61.490.00000222475
Loss of Function3.05010.90.005.40e-7149

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumLowMedium
Primary ImmunodeficiencyMediumLowMedium
CancerMediumMediumMedium

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