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RPS25

ribosomal protein S25, the group of S ribosomal proteins

Basic information

Region (hg38): 11:119015711-119018691

Links

ENSG00000118181NCBI:6230OMIM:180465HGNC:10413Uniprot:P62851AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (3 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.

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
1
missense
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
2
clinvar
2
Total 0 0 1 0 3

Variants in RPS25

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

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

Position Type Phenotype Significance ClinVar
11-119015870-G-C not specified Uncertain significance (Jul 13, 2021)2236597
11-119015893-G-A Benign (Jun 21, 2018)785892
11-119018306-G-A Benign (May 26, 2021)1237792
11-119018318-G-A Benign (May 16, 2021)1247282
11-119018363-G-T Benign (May 15, 2021)1264702
11-119018404-A-G Benign (May 15, 2021)1267945
11-119018422-A-G Benign (May 15, 2021)1270573
11-119018475-T-C Benign (May 15, 2021)1226681
11-119018537-A-AG Benign (May 15, 2021)1236244
11-119018668-G-A Benign (May 15, 2021)1240845
11-119018686-G-GAGA Benign (May 30, 2021)1250697
11-119018686-G-GAGGAGA Benign (May 15, 2021)1226476

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