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

ENSG00000198242 ∙ NCBI:6147 ∙ OMIM:602326 ∙ HGNC:10317 ∙ Uniprot:P62750 ∙ 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 RPL23A gene.

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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	8	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
17-28720009-G-A		not specified	Uncertain significance (Oct 25, 2022)
17-28720710-C-T		not specified	Uncertain significance (May 05, 2023)
17-28720715-C-G		not specified	Uncertain significance (Oct 29, 2021)
17-28720742-G-C		not specified	Uncertain significance (Aug 08, 2023)
17-28720761-C-T		not specified	Uncertain significance (Feb 07, 2023)
17-28720772-G-T		not specified	Uncertain significance (Jan 04, 2022)
17-28720803-G-T		not specified	Uncertain significance (Aug 08, 2022)
17-28720853-C-G		not specified	Uncertain significance (Oct 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPL23A	protein_coding	protein_coding	ENST00000422514	5	4967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.906	0.0936	125331	0	1	125332	0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	80	86.3	0.927	0.00000415	1006
Missense in Polyphen		8	8.085	0.98948		139
Synonymous	0.282	32	34.1	0.939	0.00000169	306
Loss of Function	2.56	0	7.62	0.00	3.88e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000881
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

• 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

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

Mouse Genome Informatics

• Gene name: Rpl23a

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