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RPL23A

ribosomal protein L23a, the group of Small nucleolar RNA protein coding host genes|L ribosomal proteins

Basic information

Region (hg38): 17:28719984-28724359

Links

ENSG00000198242NCBI:6147OMIM:602326HGNC:10317Uniprot:P62750AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPL23A gene.

  • Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPL23A 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
4
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
2
clinvar
2
Total 0 0 6 0 0

Variants in RPL23A

This is a list of pathogenic ClinVar variants found in the RPL23A region.

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

Position Type Phenotype Significance ClinVar
17-28720710-C-T Inborn genetic diseases Uncertain significance (May 05, 2023)2517843
17-28720715-C-G Inborn genetic diseases Uncertain significance (Oct 29, 2021)2393447
17-28720742-G-C Inborn genetic diseases Uncertain significance (Aug 08, 2023)2617194
17-28720761-C-T Inborn genetic diseases Uncertain significance (Feb 07, 2023)2481811
17-28720772-G-T Inborn genetic diseases Uncertain significance (Jan 04, 2022)2269615
17-28720803-G-T Inborn genetic diseases Uncertain significance (Aug 08, 2022)2391090

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPL23Aprotein_codingprotein_codingENST00000422514 54967
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9060.0936125331011253320.00000399
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2428086.30.9270.000004151006
Missense in Polyphen88.0850.98948139
Synonymous0.2823234.10.9390.00000169306
Loss of Function2.5607.620.003.88e-7103

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)0.000008810.00000881
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. Binds a specific region on the 26S rRNA. May promote p53/TP53 degradation possibly through the stimulation of MDM2-mediated TP53 polyubiquitination (PubMed:26203195). {ECO:0000250, ECO:0000269|PubMed:26203195}.;
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 (Consensus)

Recessive Scores

pRec
0.162

Intolerance Scores

loftool
rvis_EVS
-0.1
rvis_percentile_EVS
46.2

Haploinsufficiency Scores

pHI
0.263
hipred
Y
hipred_score
0.756
ghis
0.641

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.981

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rpl23a
Phenotype

Zebrafish Information Network

Gene name
rpl23a
Affected structure
head
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
ribosomal large subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;cell population proliferation
Cellular component
nucleus;nucleolus;cytoplasm;cytosol;cytosolic large ribosomal subunit;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding;cadherin binding;large ribosomal subunit rRNA binding;TORC2 complex binding