RPS24

ribosomal protein S24, the group of S ribosomal proteins

Basic information

Region (hg38): 10:78033760-78056813

Links

ENSG00000138326 ∙ NCBI:6229 ∙ OMIM:602412 ∙ HGNC:10411 ∙ Uniprot:P62847 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Diamond-Blackfan anemia 3 (Strong), mode of inheritance: AD
• Diamond-Blackfan anemia 3 (Definitive), mode of inheritance: AD
• Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
• Diamond-Blackfan anemia (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diamond-Blackfan anemia 3	AD	Cardiovascular; Hematologic; Oncologic	Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may allow early detection and management; Individuals with DBA may manifest a variety of congenital malformations (eg, cardiac anomalies), and awareness may allow prompt detection and management	Cardiovascular; Craniofacial; Hematologic; Oncologic	16317735; 17186470; 20301769

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS24 gene.

• Diamond-Blackfan anemia (6 variants)
• Diamond-Blackfan anemia 3 (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS24 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	27	1	30
missense	1		26	1		28
nonsense	2					2
start loss	2		1			3
frameshift	2	2				4
inframe indel			2			2
splice donor/acceptor (+/-2bp)		1				1
splice region		1	5	7		13
non coding				38	14	52
Total	7	3	31	66	15

Variants in RPS24

This is a list of pathogenic ClinVar variants found in the RPS24 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-78033793-A-G		POLR3-related leukodystrophy • Diamond-Blackfan anemia • Diamond-Blackfan anemia 3	Benign (Jan 12, 2018)
10-78033852-G-A		Diamond-Blackfan anemia 3 • not specified	Likely benign (Feb 05, 2018)
10-78033855-T-G		Diamond-Blackfan anemia 3	Uncertain significance (Jan 15, 2018)
10-78033865-C-T		Diamond-Blackfan anemia 3	Likely benign (Jan 12, 2018)
10-78033866-T-G		Diamond-Blackfan anemia 3	Benign (Jan 13, 2018)
10-78033870-C-T		Diamond-Blackfan anemia 3	Benign (Jan 15, 2018)
10-78033879-C-T		Diamond-Blackfan anemia 3	Likely benign (Jan 13, 2018)
10-78033894-T-G		Diamond-Blackfan anemia • POLR3-related leukodystrophy • not specified • Diamond-Blackfan anemia 3	Benign/Likely benign (Mar 29, 2022)
10-78033895-C-A		Diamond-Blackfan anemia 3	Benign (Jan 13, 2018)
10-78033897-C-T			Likely benign (Dec 01, 2022)
10-78033898-C-T		not specified • RPS24-related disorder	Uncertain significance (Jun 13, 2019)
10-78033902-A-G		Diamond-Blackfan anemia	Pathogenic (Jan 12, 2018)
10-78033903-T-C		Diamond-Blackfan anemia	Pathogenic (Feb 12, 2016)
10-78033904-G-A		Diamond-Blackfan anemia 3	Uncertain significance (May 20, 2021)
10-78033911-C-G		Diamond-Blackfan anemia	Likely benign (Jan 13, 2022)
10-78033911-C-T		Diamond-Blackfan anemia 3 • Diamond-Blackfan anemia	Conflicting classifications of pathogenicity (Sep 16, 2022)
10-78033913-C-T		Diamond-Blackfan anemia	Likely benign (Sep 10, 2023)
10-78033918-G-C		Diamond-Blackfan anemia	Likely benign (Aug 04, 2023)
10-78033919-G-A		Diamond-Blackfan anemia 3	Likely benign (Jan 13, 2018)
10-78033920-C-T		Diamond-Blackfan anemia	Likely benign (Nov 20, 2023)
10-78033921-C-T		Diamond-Blackfan anemia	Likely benign (Jun 18, 2023)
10-78033924-T-A		Diamond-Blackfan anemia	Likely benign (Dec 15, 2022)
10-78033930-C-T		Diamond-Blackfan anemia 3	Benign (Nov 07, 2021)
10-78034119-C-T			Benign (Sep 26, 2018)
10-78034124-C-T			Benign (Sep 26, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS24	protein_coding	protein_coding	ENST00000440692	5	23053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.681	0.315	108960	0	2	108962	0.00000918

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.16	113	153	0.737	0.00000861	1862
Missense in Polyphen		5	18.86	0.26511		267
Synonymous	0.135	56	57.3	0.977	0.00000347	567
Loss of Function	2.30	1	8.03	0.125	5.26e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000651	0.0000651
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: Required for processing of pre-rRNA and maturation of 40S ribosomal subunits. {ECO:0000269|PubMed:18230666}.
• 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: 0.203

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.953
• hipred: Y
• hipred_score: 0.651
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.724

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rps24

Zebrafish Information Network

• Gene name: rps24
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;erythrocyte homeostasis;ribosomal small subunit biogenesis
• Cellular component: nucleus;nucleoplasm;cytosol;small ribosomal subunit;membrane;cytosolic small ribosomal subunit
• Molecular function: RNA binding;structural constituent of ribosome;translation initiation factor binding