RPL23

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

Basic information

Region (hg38): 17:38847860-38868644

Links

ENSG00000125691 ∙ NCBI:9349 ∙ OMIM:603662 ∙ HGNC:10316 ∙ Uniprot:P62829 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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				9		9
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	1	1	4
non coding				10	1	11
Total	0	0	9	19	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)
17-38850183-C-T			Likely benign (Mar 30, 2023)
17-38850189-T-C			Likely benign (Feb 25, 2023)
17-38850189-T-G			Likely benign (Jan 26, 2023)
17-38850224-AAAAAT-A		not specified	Likely benign (Sep 03, 2023)
17-38850224-AAAAATAAAAT-A			Likely benign (Sep 22, 2022)
17-38850224-A-AAAAAT			Likely benign (Jan 10, 2024)
17-38850345-C-T			Likely benign (Dec 18, 2023)
17-38850367-A-G			Uncertain significance (Mar 28, 2022)
17-38850388-A-G		not specified	Uncertain significance (Nov 15, 2023)
17-38850413-A-T			Uncertain significance (Mar 13, 2023)
17-38850422-C-T		not specified	Conflicting classifications of pathogenicity (Sep 04, 2023)
17-38850423-G-A			Likely benign (Nov 18, 2023)
17-38850423-G-T			Likely benign (Oct 13, 2023)
17-38850436-C-T		not specified	Uncertain significance (Jan 03, 2023)
17-38850437-G-C			Uncertain significance (Apr 14, 2023)
17-38850487-A-G			Benign (Jan 25, 2024)
17-38852608-T-C			Likely benign (Jan 22, 2024)
17-38852692-C-T			Likely benign (Dec 26, 2022)
17-38852715-T-C			Uncertain significance (Dec 11, 2023)
17-38852741-G-A			Likely benign (Apr 30, 2022)
17-38852744-T-C			Likely benign (Dec 25, 2023)
17-38852747-AAAT-A			Likely benign (Mar 28, 2023)
17-38853011-A-C			Likely benign (Dec 30, 2023)
17-38853014-G-C			Benign (Dec 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL23	protein_coding	protein_coding	ENST00000479035	5	5979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.330	0.656	125234	0	1	125235	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.95	33	82.9	0.398	0.00000429	887
Missense in Polyphen		1	18.973	0.052706		242
Synonymous	0.525	27	30.7	0.879	0.00000155	291
Loss of Function	2.07	2	8.54	0.234	5.24e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.0000545
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rpl23

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