RPS23

ribosomal protein S23, the group of S ribosomal proteins

Basic information

Region (hg38): 5:82273319-82278396

Links

ENSG00000186468 ∙ NCBI:6228 ∙ OMIM:603683 ∙ HGNC:10410 ∙ Uniprot:P62266 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• brachycephaly, trichomegaly, and developmental delay (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Brachycephaly, trichomegaly, and developmental delay	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Audiologic/Otolaryngologic; Craniofacial; Musculoskeletal; Neurologic	26982655; 28257692

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS23 gene.

• Brachycephaly, trichomegaly, and developmental delay (3 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS23 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				2		2
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	3	2	1

Variants in RPS23

This is a list of pathogenic ClinVar variants found in the RPS23 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-82276112-T-C			Likely benign (Aug 24, 2018)
5-82276183-A-T		Brachycephaly, trichomegaly, and developmental delay	Pathogenic (Aug 11, 2017)
5-82276186-G-A		Brachycephaly, trichomegaly, and developmental delay	Uncertain significance (Aug 14, 2023)
5-82276365-G-C		Brachycephaly, trichomegaly, and developmental delay	Benign (Nov 07, 2021)
5-82276419-G-A			Likely benign (Nov 15, 2018)
5-82276483-C-T		Brachycephaly, trichomegaly, and developmental delay	Pathogenic (Aug 11, 2017)
5-82277718-C-T		Brachycephaly, trichomegaly, and developmental delay	Uncertain significance (Jan 22, 2020)
5-82277799-G-C		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS23	protein_coding	protein_coding	ENST00000296674	4	5220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.859	0.139	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	20	78.9	0.254	0.00000380	922
Missense in Polyphen		1	12.094	0.082687		172
Synonymous	-0.882	33	27.2	1.22	0.00000126	289
Loss of Function	2.35	0	6.43	0.00	2.83e-7	79

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)	0.00	0.00
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 (PubMed:28257692, PubMed:23636399, PubMed:25957688, PubMed:25901680). The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (PubMed:23636399, PubMed:25957688, PubMed:25901680). Plays an important role in translational accuracy (PubMed:28257692). {ECO:0000269|PubMed:23636399, ECO:0000269|PubMed:25901680, ECO:0000269|PubMed:25957688, ECO:0000269|PubMed:28257692}.
• Disease: DISEASE: Brachycephaly, trichomegaly, and developmental delay (BTDD) [MIM:617412]: An autosomal dominant developmental disorder characterized by brachycephaly, ciliary trichomegaly, dysmorphic features of the face and hands, hearing loss, and developmental delay with short stature. Intellectual disability and autism spectrum disorder may be present in some patients. {ECO:0000269|PubMed:28257692}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Ribosome - Homo sapiens (human);Cytoplasmic Ribosomal Proteins;SRP-dependent cotranslational protein targeting to membrane;Formation of the ternary complex, and subsequently, the 43S complex;Translation initiation complex formation;Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S;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);Ribosomal scanning and start codon recognition;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: 0.270

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.983
• hipred: Y
• hipred_score: 0.831
• ghis: 0.594

Essentials

• essential_gene_CRISPR: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps23

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;cytoplasmic translation;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;stress granule assembly;maintenance of translational fidelity
• Cellular component: nucleoplasm;endoplasmic reticulum;rough endoplasmic reticulum;cytosol;ribosome;membrane;cytosolic small ribosomal subunit;polysomal ribosome
• Molecular function: RNA binding;structural constituent of ribosome;protein binding