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RPS15

ribosomal protein S15, the group of S ribosomal proteins

Basic information

Region (hg38): 19:1438357-1440495

Links

ENSG00000115268NCBI:6209OMIM:180535HGNC:10388Uniprot:P62841AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS15 gene.

  • not provided (4 variants)
  • not specified (2 variants)
  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS15 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
1
clinvar
2
clinvar
3
missense
1
clinvar
1
clinvar
2
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 1 3

Variants in RPS15

This is a list of pathogenic ClinVar variants found in the RPS15 region.

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

Position Type Phenotype Significance ClinVar
19-1438866-C-T not specified Benign (May 04, 2021)440243
19-1440069-G-C not specified • RPS15-related condition Benign/Likely benign (May 04, 2021)440242
19-1440080-C-G not specified Uncertain significance (Jan 16, 2024)3156182
19-1440087-A-C not specified Uncertain significance (Jan 18, 2023)2472864
19-1440091-C-T RPS15-related condition Likely benign (Sep 27, 2023)3048640
19-1440172-G-A RPS15-related condition Likely benign (Sep 27, 2023)3038588
19-1440375-C-T Benign (Jul 04, 2018)718818
19-1440384-C-T Likely benign (Jul 01, 2022)2648921

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS15protein_codingprotein_codingENST00000586686 42226
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8330.16400000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.784694.80.4850.00000707916
Missense in Polyphen310.4110.28814149
Synonymous-3.106640.81.620.00000289283
Loss of Function2.2505.890.002.54e-774

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
0.185

Intolerance Scores

loftool
rvis_EVS
0.01
rvis_percentile_EVS
54.63

Haploinsufficiency Scores

pHI
0.161
hipred
N
hipred_score
0.483
ghis
0.623

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.824

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyLowLowLow
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rps15
Phenotype

Zebrafish Information Network

Gene name
rps15
Affected structure
post-vent region
Phenotype tag
abnormal
Phenotype quality
morphology

Gene ontology

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