RPS4X
ribosomal protein S4 X-linked, the group of S ribosomal proteins
Basic information
Region (hg38): X:72255678-72277248
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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) | |||
| X-72275649-T-G | Inborn genetic diseases | Uncertain significance (Feb 16, 2023) | ||
| X-72275682-G-A | Inborn genetic diseases | Uncertain significance (Dec 06, 2022) | ||
| X-72275731-C-A | Benign (Aug 16, 2018) | |||
| X-72276231-G-A | Inborn genetic diseases | Uncertain significance (Dec 17, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS4X | protein_coding | protein_coding | ENST00000316084 | 7 | 21622 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.932 | 0.0675 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.29 | 41 | 108 | 0.380 | 0.00000883 | 1725 |
| Missense in Polyphen | 3 | 12.841 | 0.23363 | 305 | ||
| Synonymous | 0.688 | 32 | 37.3 | 0.857 | 0.00000294 | 524 |
| Loss of Function | 2.71 | 0 | 8.57 | 0.00 | 7.37e-7 | 144 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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