Menu
GeneBe

RPS23

ribosomal protein S23, the group of S ribosomal proteins

Basic information

Region (hg38): 5:82273319-82278396

Links

ENSG00000186468NCBI:6228OMIM:603683HGNC:10410Uniprot:P62266AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Brachycephaly, trichomegaly, and developmental delayADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic26982655; 28257692

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS23 gene.

  • Brachycephaly, trichomegaly, and developmental delay (4 variants)
  • not provided (3 variants)
  • not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS23 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 2 2
missense 2 2 1 5
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 0
Total 2 0 2 2 1

Variants in RPS23

This is a list of pathogenic ClinVar variants found in the RPS23 region.

Position Type Phenotype Significance ClinVar
5-82276112-T-C Likely benign (Aug 24, 2018)link
5-82276183-A-T Brachycephaly, trichomegaly, and developmental delay Pathogenic (Aug 11, 2017)link
5-82276186-G-A Brachycephaly, trichomegaly, and developmental delay Uncertain significance (Aug 14, 2023)link
5-82276365-G-C Brachycephaly, trichomegaly, and developmental delay Benign (Nov 07, 2021)link
5-82276419-G-A Likely benign (Nov 15, 2018)link
5-82276483-C-T Brachycephaly, trichomegaly, and developmental delay Pathogenic (Aug 11, 2017)link
5-82277718-C-T Brachycephaly, trichomegaly, and developmental delay Uncertain significance (Jan 22, 2020)link
5-82277799-G-C not specified Uncertain significance (Feb 01, 2023)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS23protein_codingprotein_codingENST00000296674 45220
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8590.13900000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.362078.90.2540.00000380922
Missense in Polyphen112.0940.082687172
Synonymous-0.8823327.21.220.00000126289
Loss of Function2.3506.430.002.83e-779

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: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell (PubMed:28257692, PubMed:23636399, PubMed:25957688, PubMed:25901680). The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (PubMed:23636399, PubMed:25957688, PubMed:25901680). Plays an important role in translational accuracy (PubMed:28257692). {ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:25901680, ECO:0000269|PubMed:25957688, ECO:0000269|PubMed:28257692}.;
Disease
DISEASE: Brachycephaly, trichomegaly, and developmental delay (BTDD) [MIM:617412]: An autosomal dominant developmental disorder characterized by brachycephaly, ciliary trichomegaly, dysmorphic features of the face and hands, hearing loss, and developmental delay with short stature. Intellectual disability and autism spectrum disorder may be present in some patients. {ECO:0000269|PubMed:28257692}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
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
0.270

Intolerance Scores

loftool
rvis_EVS
-0.01
rvis_percentile_EVS
52.85

Haploinsufficiency Scores

pHI
0.983
hipred
Y
hipred_score
0.831
ghis
0.594

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.903

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rps23
Phenotype

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;stress granule assembly;maintenance of translational fidelity
Cellular component
nucleoplasm;endoplasmic reticulum;rough endoplasmic reticulum;cytosol;ribosome;membrane;cytosolic small ribosomal subunit;polysomal ribosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding