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GeneBe

RPS4X

ribosomal protein S4 X-linked, the group of S ribosomal proteins

Basic information

Region (hg38): X:72255678-72277248

Links

ENSG00000198034NCBI:6191OMIM:312760HGNC:10424Uniprot:P62701AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS4X gene.

  • not provided (2 variants)
  • Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS4X gene is commonly pathogenic or not.

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

Variants in RPS4X

This is a list of pathogenic ClinVar variants found in the RPS4X region.

Position Type Phenotype Significance ClinVar
X-72275603-C-T Uncertain significance (Dec 16, 2022)link
X-72275649-T-G Inborn genetic diseases Uncertain significance (Feb 16, 2023)link
X-72275682-G-A Inborn genetic diseases Uncertain significance (Dec 06, 2022)link
X-72275731-C-A Benign (Aug 16, 2018)link
X-72276231-G-A Inborn genetic diseases Uncertain significance (Dec 17, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS4Xprotein_codingprotein_codingENST00000316084 721622
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9320.067500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.29411080.3800.000008831725
Missense in Polyphen312.8410.23363305
Synonymous0.6883237.30.8570.00000294524
Loss of Function2.7108.570.007.37e-7144

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)

Intolerance Scores

loftool
rvis_EVS
0.06
rvis_percentile_EVS
58

Haploinsufficiency Scores

pHI
0.890
hipred
Y
hipred_score
0.750
ghis
0.624

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.925

Mouse Genome Informatics

Gene name
Rps4x
Phenotype

Zebrafish Information Network

Gene name
rps4x
Affected structure
post-vent region
Phenotype tag
abnormal
Phenotype quality
bent

Gene ontology

Biological process
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;multicellular organism development;positive regulation of cell population proliferation;positive regulation of translation
Cellular component
nucleoplasm;cytosol;ribosome;polysome;focal adhesion;small ribosomal subunit;membrane;cytosolic small ribosomal subunit;cytoplasmic ribonucleoprotein granule;synapse;extracellular exosome;ribonucleoprotein complex
Molecular function
RNA binding;structural constituent of ribosome;protein binding;rRNA binding