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RPS15A

ribosomal protein S15a, the group of S ribosomal proteins

Basic information

Region (hg38): 16:18781294-18790383

Links

ENSG00000134419NCBI:6210OMIM:603674HGNC:10389Uniprot:P62244AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia 20 (Limited), mode of inheritance: AD
  • Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
  • Diamond-Blackfan anemia 20 (Limited), mode of inheritance: AD
  • Diamond-Blackfan anemia 20 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 20ADHematologic; OncologicSpecific treatment of anemia (eg, steroids, regular transfusions) can be effective; Surveillance for and early treatment of malignancy may be beneficialHematologic; Oncologic28280134

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS15A gene.

  • not provided (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS15A 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
5
clinvar
5
missense
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
2
clinvar
2
clinvar
4
Total 0 0 1 7 2

Variants in RPS15A

This is a list of pathogenic ClinVar variants found in the RPS15A region.

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

Position Type Phenotype Significance ClinVar
16-18784797-G-A Likely benign (Dec 12, 2023)2904148
16-18784831-A-G Likely benign (Nov 22, 2023)2414709
16-18784832-TAAC-T Likely benign (Oct 20, 2023)2746992
16-18784832-TAACAAC-T Likely benign (Dec 21, 2023)2867658
16-18784832-T-TAAC Likely benign (Jan 24, 2023)1903144
16-18788063-C-T Diamond-Blackfan anemia 20 Pathogenic (Apr 06, 2021)617665
16-18788093-A-T Likely benign (Nov 24, 2023)2177617
16-18788132-G-A Likely benign (Oct 11, 2022)1977655
16-18788293-C-A Benign (May 14, 2021)1259635
16-18788967-G-A Likely benign (Jun 21, 2023)2975320
16-18788994-C-G Likely benign (Dec 31, 2023)2963083
16-18789000-G-A Likely benign (Aug 01, 2023)2646266
16-18789006-C-G Likely benign (Mar 18, 2023)2646267
16-18789008-G-T Likely benign (Sep 08, 2023)2784941
16-18789009-G-C Likely benign (Aug 28, 2023)2997133
16-18789053-C-T Uncertain significance (Jan 14, 2023)2993763
16-18789063-G-T Likely benign (Oct 29, 2023)1899577
16-18789100-T-C Uncertain significance (May 13, 2022)2127841
16-18789316-G-C Benign (May 16, 2021)1290255

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS15Aprotein_codingprotein_codingENST00000322989 49089
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8020.19300000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.242074.20.2700.00000392859
Missense in Polyphen16.98540.14316113
Synonymous-0.7443328.01.180.00000156246
Loss of Function2.1405.360.002.26e-766

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
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

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
0.230

Intolerance Scores

loftool
rvis_EVS
0.06
rvis_percentile_EVS
58

Haploinsufficiency Scores

pHI
0.373
hipred
Y
hipred_score
0.748
ghis
0.580

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.973

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rps15a
Phenotype

Zebrafish Information Network

Gene name
rps15a
Affected structure
nucleate erythrocyte
Phenotype tag
abnormal
Phenotype quality
decreased amount

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;positive regulation of cell population proliferation;response to virus;positive regulation of cell cycle
Cellular component
nucleoplasm;cytoplasm;cytosol;membrane;cytosolic small ribosomal subunit;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding