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GeneBe

RPS10

ribosomal protein S10, the group of S ribosomal proteins

Basic information

Region (hg38): 6:34417453-34426069

Links

ENSG00000124614NCBI:6204OMIM:603632HGNC:10383Uniprot:P46783AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia 9 (Strong), mode of inheritance: AD
  • Diamond-Blackfan anemia 9 (Strong), mode of inheritance: AD
  • Diamond-Blackfan anemia 9 (Strong), 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 9ADHematologic; OncologicSpecific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may be beneficial; Individuals with DBA may manifest a variety of congenital malformations, and awareness may allow prompt detection and managementCraniofacial; Hematologic; Oncologic16317735; 20116044; 20301769; 23812780

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS10 gene.

  • Diamond-Blackfan anemia (87 variants)
  • Diamond-Blackfan anemia 9 (28 variants)
  • not provided (23 variants)
  • not specified (8 variants)
  • Inborn genetic diseases (4 variants)
  • RPS10-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS10 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
3
clinvar
24
clinvar
27
missense
26
clinvar
1
clinvar
1
clinvar
28
nonsense
1
clinvar
1
start loss
1
clinvar
1
frameshift
2
clinvar
1
clinvar
3
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
4
3
1
8
non coding
7
clinvar
28
clinvar
16
clinvar
51
Total 4 3 38 53 17

Variants in RPS10

This is a list of pathogenic ClinVar variants found in the RPS10 region.

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

Position Type Phenotype Significance ClinVar
6-34417463-T-C Diamond-Blackfan anemia 9 Benign (Jan 12, 2018)356417
6-34417481-C-A Diamond-Blackfan anemia 9 Uncertain significance (Jan 12, 2018)356418
6-34417511-G-C Diamond-Blackfan anemia Uncertain significance (Dec 11, 2021)2043241
6-34417523-C-A Diamond-Blackfan anemia Uncertain significance (Oct 25, 2023)2699015
6-34417525-C-T Diamond-Blackfan anemia Uncertain significance (Nov 17, 2022)1383769
6-34417531-C-T Diamond-Blackfan anemia Uncertain significance (Mar 18, 2022)2188557
6-34417533-A-T Diamond-Blackfan anemia Likely benign (Jul 21, 2023)3019220
6-34417541-C-T Diamond-Blackfan anemia Uncertain significance (Mar 04, 2022)2178780
6-34417542-G-A Diamond-Blackfan anemia Likely benign (Sep 05, 2023)2816014
6-34417547-T-C Diamond-Blackfan anemia Uncertain significance (Sep 25, 2023)2820912
6-34417553-A-G Diamond-Blackfan anemia Likely benign (Dec 06, 2023)1097562
6-34417721-A-G Likely benign (Mar 20, 2019)1213487
6-34417740-A-T Benign (Jul 17, 2018)1178824
6-34418142-G-GT Benign (Dec 21, 2018)1228151
6-34418362-TACTC-T Diamond-Blackfan anemia Uncertain significance (Jul 31, 2020)1021090
6-34418381-G-A not specified • Diamond-Blackfan anemia • Diamond-Blackfan anemia 9 Benign/Likely benign (Jan 22, 2024)1336843
6-34418388-G-A Diamond-Blackfan anemia 9 Benign (Jan 13, 2018)904984
6-34418393-A-C Diamond-Blackfan anemia 9 • Diamond-Blackfan anemia Benign/Likely benign (Nov 27, 2023)906570
6-34418400-G-A Diamond-Blackfan anemia Uncertain significance (Mar 29, 2021)1488698
6-34418405-G-A Diamond-Blackfan anemia Likely benign (Dec 08, 2023)2912885
6-34418416-C-T Diamond-Blackfan anemia Uncertain significance (Dec 20, 2022)2716893
6-34418417-G-A Diamond-Blackfan anemia 9 • RPS10-related condition • Diamond-Blackfan anemia • not specified • RPS10-NUDT3-related condition Benign/Likely benign (Jan 31, 2024)356419
6-34418417-G-T Diamond-Blackfan anemia Likely benign (Dec 11, 2023)1064351
6-34418422-C-A Inborn genetic diseases • Diamond-Blackfan anemia Uncertain significance (Dec 13, 2023)2302403
6-34418426-T-C Diamond-Blackfan anemia Likely pathogenic (May 20, 2019)834960

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS10protein_codingprotein_codingENST00000326199 58672
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9710.0289125746021257480.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.24671020.6550.000006971061
Missense in Polyphen514.130.35386225
Synonymous0.7643035.80.8380.00000216326
Loss of Function3.07010.90.007.38e-7106

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006400.0000615
Ashkenazi Jewish0.00009920.0000992
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: Component of the 40S ribosomal subunit.;
Disease
DISEASE: Diamond-Blackfan anemia 9 (DBA9) [MIM:613308]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:20116044}. 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;EGFR1;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
0.105

Intolerance Scores

loftool
rvis_EVS
-0.14
rvis_percentile_EVS
42.88

Haploinsufficiency Scores

pHI
0.247
hipred
Y
hipred_score
0.681
ghis
0.572

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.961

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps10
Phenotype

Gene ontology

Biological process
ribosomal small subunit assembly;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
Cellular component
nucleoplasm;nucleolus;cytosol;ribosome;focal adhesion;membrane;cytosolic small ribosomal subunit
Molecular function
RNA binding;structural constituent of ribosome;protein binding