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GeneBe

RPL23

ribosomal protein L23, the group of L ribosomal proteins|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 17:38847859-38853764

Links

ENSG00000125691NCBI:9349OMIM:603662HGNC:10316Uniprot:P62829AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL23 gene.

  • not provided (13 variants)
  • not specified (2 variants)
  • Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL23 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 1
missense 5 1 6
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 1 1
non coding 5 1 6
Total 0 0 5 7 2

Variants in RPL23

This is a list of pathogenic ClinVar variants found in the RPL23 region.

Position Type Phenotype Significance ClinVar
17-38850161-T-C Uncertain significance (Aug 25, 2022)link
17-38850189-T-C Likely benign (Jul 14, 2022)link
17-38850224-AAAAAT-A not specified Likely benign (Oct 10, 2022)link
17-38850224-AAAAATAAAAT-A Likely benign (Sep 22, 2022)link
17-38850224-A-AAAAAT Likely benign (Sep 23, 2022)link
17-38850367-A-G Uncertain significance (Mar 28, 2022)link
17-38850422-C-T not specified • Inborn genetic diseases Conflicting interpretations of pathogenicity (Apr 18, 2022)link
17-38850436-C-T Inborn genetic diseases Uncertain significance (Nov 03, 2022)link
17-38850487-A-G Benign (Sep 15, 2022)link
17-38852715-T-C Uncertain significance (Oct 07, 2022)link
17-38852741-G-A Likely benign (Apr 30, 2022)link
17-38853014-G-C Benign (Jul 23, 2022)link
17-38853039-T-C Uncertain significance (May 10, 2022)link
17-38853115-T-C Likely benign (Jul 14, 2022)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL23protein_codingprotein_codingENST00000479035 55979
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3300.656125234011252350.00000399
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.953382.90.3980.00000429887
Missense in Polyphen118.9730.052706242
Synonymous0.5252730.70.8790.00000155291
Loss of Function2.0728.540.2345.24e-792

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0001090.0000545
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.0001090.0000545
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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;p53 pathway (Consensus)

Recessive Scores

pRec
0.363

Intolerance Scores

loftool
rvis_EVS
0.01
rvis_percentile_EVS
54.63

Haploinsufficiency Scores

pHI
0.891
hipred
Y
hipred_score
0.783
ghis
0.662

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.955

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rpl23
Phenotype

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;ribosomal protein import into nucleus;SRP-dependent cotranslational protein targeting to membrane;positive regulation of cell population proliferation;positive regulation of gene expression;protein-DNA complex disassembly;protein stabilization;negative regulation of cell cycle arrest;positive regulation of cell cycle arrest;cellular response to actinomycin D;positive regulation of signal transduction by p53 class mediator;negative regulation of ubiquitin protein ligase activity;negative regulation of ubiquitin-dependent protein catabolic process
Cellular component
nucleoplasm;nucleolus;cytoplasm;cytosol;ribosome;focal adhesion;postsynaptic density;membrane;cytosolic large ribosomal subunit;protein-containing complex;extracellular exosome
Molecular function
transcription coactivator binding;RNA binding;structural constituent of ribosome;protein binding;ubiquitin protein ligase binding;large ribosomal subunit rRNA binding;ubiquitin ligase inhibitor activity