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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:P62829AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (17 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.

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
3
clinvar
3
missense
6
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
2
non coding
5
clinvar
1
clinvar
6
Total 0 0 6 8 1

Variants in RPL23

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

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
17-38850161-T-C Uncertain significance (Aug 25, 2022)1978113
17-38850183-C-T Likely benign (Mar 30, 2023)2869009
17-38850189-T-C Likely benign (Feb 25, 2023)2063593
17-38850189-T-G Likely benign (Jan 26, 2023)2999503
17-38850224-AAAAAT-A not specified Likely benign (Sep 03, 2023)1338054
17-38850224-AAAAATAAAAT-A Likely benign (Sep 22, 2022)2031940
17-38850224-A-AAAAAT Likely benign (Jan 10, 2024)1971298
17-38850345-C-T Likely benign (Dec 18, 2023)2783036
17-38850367-A-G Uncertain significance (Mar 28, 2022)2164105
17-38850413-A-T Uncertain significance (Mar 13, 2023)2845454
17-38850422-C-T not specified • Inborn genetic diseases Conflicting classifications of pathogenicity (Sep 04, 2023)1338129
17-38850423-G-A Likely benign (Nov 18, 2023)2899492
17-38850423-G-T Likely benign (Oct 13, 2023)2814569
17-38850436-C-T Inborn genetic diseases Uncertain significance (Jan 03, 2023)2322450
17-38850437-G-C Uncertain significance (Apr 14, 2023)2877955
17-38850487-A-G Benign (Jan 25, 2024)1972183
17-38852608-T-C Likely benign (Jan 22, 2024)2710718
17-38852692-C-T Likely benign (Dec 26, 2022)2716314
17-38852715-T-C Uncertain significance (Dec 11, 2023)1946095
17-38852741-G-A Likely benign (Apr 30, 2022)2014851
17-38852744-T-C Likely benign (Dec 25, 2023)2875628
17-38852747-AAAT-A Likely benign (Mar 28, 2023)2868840
17-38853011-A-C Likely benign (Dec 30, 2023)2782417
17-38853014-G-C Benign (Dec 17, 2023)2076204
17-38853016-C-T Uncertain significance (Oct 22, 2023)2904041

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