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RPS24

ribosomal protein S24, the group of S ribosomal proteins

Basic information

Region (hg38): 10:78033759-78056813

Links

ENSG00000138326NCBI:6229OMIM:602412HGNC:10411Uniprot:P62847AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 3ADCardiovascular; Hematologic; OncologicSpecific 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 managementCardiovascular; Craniofacial; Hematologic; Oncologic16317735; 17186470; 20301769

ClinVar

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

  • Diamond-Blackfan anemia (77 variants)
  • not provided (31 variants)
  • Diamond-Blackfan anemia 3 (30 variants)
  • not specified (9 variants)
  • Pol III-related leukodystrophy (1 variants)
  • Abnormality of blood and blood-forming tissues (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
clinvar
22
clinvar
1
clinvar
25
missense
1
clinvar
23
clinvar
1
clinvar
25
nonsense
2
clinvar
2
start loss
2
clinvar
1
clinvar
3
frameshift
2
clinvar
2
clinvar
4
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
?
1
5
5
1
12
non coding
?
1
clinvar
30
clinvar
14
clinvar
45
Total 7 3 29 53 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
10-78033760-A-G Diamond-Blackfan anemia 3 Uncertain significance (Jan 12, 2018)301087
10-78033793-A-G Pol III-related leukodystrophy • Diamond-Blackfan anemia • Diamond-Blackfan anemia 3 Benign (Jan 12, 2018)301088
10-78033852-G-A Diamond-Blackfan anemia 3 • not specified Likely benign (Feb 05, 2018)301089
10-78033855-T-G Diamond-Blackfan anemia 3 Uncertain significance (Jan 15, 2018)877451
10-78033865-C-T Diamond-Blackfan anemia 3 Likely benign (Jan 12, 2018)877452
10-78033866-T-G Diamond-Blackfan anemia 3 Benign (Jan 13, 2018)301090
10-78033870-C-T Diamond-Blackfan anemia 3 Benign (Jan 15, 2018)877453
10-78033879-C-T Diamond-Blackfan anemia 3 Likely benign (Jan 13, 2018)877454
10-78033894-T-G Diamond-Blackfan anemia • not specified • Pol III-related leukodystrophy • Diamond-Blackfan anemia 3 Benign/Likely benign (Mar 29, 2022)301091
10-78033895-C-A Diamond-Blackfan anemia 3 Benign (Jan 13, 2018)877455
10-78033897-C-T Likely benign (Dec 01, 2022)2640628
10-78033898-C-T not specified Uncertain significance (Jun 13, 2019)1337223
10-78033902-A-G Diamond-Blackfan anemia Pathogenic (Jul 13, 2021)265439
10-78033903-T-C Diamond-Blackfan anemia Pathogenic (Feb 12, 2016)1798673
10-78033904-G-A Diamond-Blackfan anemia 3 Uncertain significance (May 20, 2021)1698829
10-78033911-C-G Diamond-Blackfan anemia Likely benign (Jan 13, 2022)2196372
10-78033911-C-T Diamond-Blackfan anemia 3 • Diamond-Blackfan anemia Conflicting classifications of pathogenicity (Sep 16, 2022)696301
10-78033913-C-T Likely benign (Jul 07, 2018)704120
10-78033919-G-A Diamond-Blackfan anemia 3 Likely benign (Jan 13, 2018)878476
10-78033920-C-T Diamond-Blackfan anemia Likely benign (Jun 08, 2022)1972027
10-78033921-C-T Diamond-Blackfan anemia Likely benign (Oct 05, 2022)1595855
10-78033930-C-T Diamond-Blackfan anemia 3 Benign (Nov 07, 2021)1327973
10-78034119-C-T Benign (Sep 26, 2018)1260481
10-78034124-C-T Benign (Sep 26, 2018)1275226
10-78035063-G-A Likely benign (Nov 10, 2018)1220083

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS24protein_codingprotein_codingENST00000440692 523053
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6810.315108960021089620.00000918
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.161131530.7370.000008611862
Missense in Polyphen518.860.26511267
Synonymous0.1355657.30.9770.00000347567
Loss of Function2.3018.030.1255.26e-792

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006510.0000651
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps24
Phenotype

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