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RPS16

ribosomal protein S16, the group of S ribosomal proteins

Basic information

Region (hg38): 19:39433136-39435949

Links

ENSG00000105193NCBI:6217OMIM:603675HGNC:10396Uniprot:P62249AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS16 gene.

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS16 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
4
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 4 0 1

Variants in RPS16

This is a list of pathogenic ClinVar variants found in the RPS16 region.

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

Position Type Phenotype Significance ClinVar
19-39433301-C-T Inborn genetic diseases Uncertain significance (Aug 14, 2023)2617931
19-39433345-G-A Benign (May 08, 2018)781484
19-39433567-T-G Inborn genetic diseases Uncertain significance (Mar 29, 2022)2280285
19-39435624-G-A Inborn genetic diseases Uncertain significance (Nov 05, 2021)2354104
19-39435706-C-A Inborn genetic diseases Uncertain significance (Jan 23, 2023)2478178

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS16protein_codingprotein_codingENST00000251453 52742
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6870.3091241100561241660.000226
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.625398.20.5390.00000612922
Missense in Polyphen221.4750.093131297
Synonymous-1.905136.41.400.00000193312
Loss of Function2.3118.100.1244.27e-790

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001190.000119
Ashkenazi Jewish0.00009930.0000993
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0004400.000440
Middle Eastern0.000.00
South Asian0.000.00
Other0.0003280.000328

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)

Intolerance Scores

loftool
rvis_EVS
-0.19
rvis_percentile_EVS
39.68

Haploinsufficiency Scores

pHI
0.870
hipred
Y
hipred_score
0.610
ghis
0.641

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.890

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rps16
Phenotype

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;ribosomal small subunit biogenesis;liver regeneration;cellular response to leukemia inhibitory factor
Cellular component
nucleoplasm;cytosol;focal adhesion;small ribosomal subunit;membrane;cytosolic small ribosomal subunit;extracellular exosome
Molecular function
RNA binding;structural constituent of ribosome;protein binding