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GeneBe

RPS25

ribosomal protein S25, the group of S ribosomal proteins

Basic information

Region (hg38): 11:119015711-119018691

Links

ENSG00000118181NCBI:6230OMIM:180465HGNC:10413Uniprot:P62851AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS25 gene.

  • not provided (11 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 RPS25 gene is commonly pathogenic or not.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 1
missense 1 1
nonsense 0
start loss 0
frameshift 0
inframe indel 0
splice variant 0
non coding 10 10
Total 0 0 1 0 11

Variants in RPS25

This is a list of pathogenic ClinVar variants found in the RPS25 region.

Position Type Phenotype Significance ClinVar
11-119015870-G-C Inborn genetic diseases Uncertain significance (Jul 13, 2021)link
11-119015893-G-A Benign (Jun 21, 2018)link
11-119018306-G-A Benign (May 26, 2021)link
11-119018318-G-A Benign (May 16, 2021)link
11-119018363-G-T Benign (May 15, 2021)link
11-119018404-A-G Benign (May 15, 2021)link
11-119018422-A-G Benign (May 15, 2021)link
11-119018475-T-C Benign (May 15, 2021)link
11-119018537-A-AG Benign (May 15, 2021)link
11-119018668-G-A Benign (May 15, 2021)link
11-119018686-G-GAGA Benign (May 30, 2021)link
11-119018686-G-GAGGAGA Benign (May 15, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS25protein_codingprotein_codingENST00000527673 42980
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8630.13500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.832364.20.3580.00000277807
Missense in Polyphen715.0450.46526224
Synonymous-1.163224.71.300.00000108244
Loss of Function2.3706.520.003.15e-791

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
0.171

Intolerance Scores

loftool
rvis_EVS
0.01
rvis_percentile_EVS
54.63

Haploinsufficiency Scores

pHI
0.943
hipred
Y
hipred_score
0.526
ghis
0.659

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 ImmunodeficiencyMediumLowMedium
CancerLowLowLow

Mouse Genome Informatics

Gene name
Rps25
Phenotype

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane
Cellular component
nucleus;nucleoplasm;nucleolus;cytosol;ribosome;postsynaptic density;small ribosomal subunit;cytosolic small ribosomal subunit;extracellular exosome
Molecular function
RNA binding;protein binding