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GeneBe

RPS15

ribosomal protein S15, the group of S ribosomal proteins

Basic information

Region (hg38): 19:1438357-1440495

Links

ENSG00000115268NCBI:6209OMIM:180535HGNC:10388Uniprot:P62841AlphaFoldGenCCjaxSfariGnomADPubmed

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 (3 variants)
  • not specified (2 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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 2 2
missense 1 1
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 0
Total 0 0 0 0 3

Variants in RPS15

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

Position Type Phenotype Significance ClinVar
19-1438866-C-T not specified Benign (May 04, 2021)link
19-1440069-G-C not specified Benign (May 04, 2021)link
19-1440087-A-C Inborn genetic diseases Uncertain significance (Jan 18, 2023)link
19-1440375-C-T Benign (Jul 04, 2018)link

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