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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:P62701AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

  • Inborn genetic diseases (3 variants)
  • not provided (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.

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
0
missense
4
clinvar
4
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 4 0 0

Variants in RPS4X

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

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

Position Type Phenotype Significance ClinVar
X-72273943-A-C not specified Uncertain significance (Dec 14, 2023)3156191
X-72275603-C-T Uncertain significance (Dec 16, 2022)2429036
X-72275649-T-G not specified Uncertain significance (Feb 16, 2023)2467192
X-72275682-G-A not specified Uncertain significance (Dec 06, 2022)2400621
X-72275731-C-A Benign (Aug 16, 2018)756091
X-72276231-G-A not specified Uncertain significance (Jan 16, 2024)2211985

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