RPL23A

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

Basic information

Region (hg38): 17:28719985-28724359

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.

not_specified (21 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. These statistics are base on transcript: NM_000000984.6. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			21 clinvar			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0

Loading clinvar variants...

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

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

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

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