RPS6
ribosomal protein S6, the group of S ribosomal proteins
Basic information
Region (hg38): 9:19375714-19380236
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (2 variants)
- Hemimegalencephaly (1 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 RPS6 gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 2 | 2 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 2 | 2 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 2 | 0 | 2 |
Variants in RPS6
This is a list of pathogenic ClinVar variants found in the RPS6 region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-19376299-C-G | Inborn genetic diseases | Uncertain significance (Jun 12, 2023) | ||
| 9-19376348-C-T | Hemimegalencephaly | Uncertain significance (May 14, 2019) | ||
| 9-19376395-A-G | Benign (Apr 26, 2018) | |||
| 9-19376576-C-T | Inborn genetic diseases | Uncertain significance (Oct 27, 2021) | ||
| 9-19378522-G-C | Benign (Dec 31, 2019) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RPS6 | protein_coding | protein_coding | ENST00000380394 | 6 | 4540 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.976 | 0.0241 | 123650 | 0 | 1 | 123651 | 0.00000404 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.33 | 107 | 154 | 0.697 | 0.00000942 | 1607 |
| Missense in Polyphen | 9 | 14.622 | 0.61552 | 215 | ||
| Synonymous | -4.36 | 87 | 48.4 | 1.80 | 0.00000227 | 502 |
| Loss of Function | 3.14 | 0 | 11.4 | 0.00 | 5.31e-7 | 155 |
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) | 0.00000889 | 0.00000889 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May play an important role in controlling cell growth and proliferation through the selective translation of particular classes of mRNA.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Ribosome - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);IL-5 Signaling Pathway;Leptin signaling pathway;Human Thyroid Stimulating Hormone (TSH) signaling pathway;Follicle Stimulating Hormone (FSH) signaling pathway;Prolactin Signaling Pathway;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;Interleukin-11 Signaling Pathway;Oncostatin M Signaling Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Kit receptor signaling pathway;MECP2 and Associated Rett Syndrome;VEGFA-VEGFR2 Signaling Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Hereditary Leiomyomatosis and Renal Cell Carcinoma Pathway;Cytoplasmic Ribosomal Proteins;IL-2 Signaling Pathway;Interferon type I signaling pathways;rRNA processing;Signal Transduction;mtor signaling pathway;SRP-dependent cotranslational protein targeting to membrane;skeletal muscle hypertrophy is regulated via akt-mtor pathway;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;mTORC1-mediated signalling;mTOR signalling;Metabolism of RNA;Formation of a pool of free 40S subunits;Metabolism;KitReceptor;insulin Mam;Nonsense-Mediated Decay (NMD);Selenoamino acid metabolism;BCR;Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC);ErbB1 downstream signaling;Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC);IL2;IL11;Gastrin;Ribosomal scanning and start codon recognition;L13a-mediated translational silencing of Ceruloplasmin expression;Leptin;Peptide chain elongation;Eukaryotic Translation Elongation;GTP hydrolysis and joining of the 60S ribosomal subunit;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol;Cap-dependent Translation Initiation;IL2 signaling events mediated by PI3K;insulin
(Consensus)
Recessive Scores
- pRec
- 0.586
Intolerance Scores
- loftool
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.667
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rps6
- Phenotype
- liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- G1/S transition of mitotic cell cycle;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;placenta development;T cell proliferation involved in immune response;rRNA processing;translation;translational initiation;SRP-dependent cotranslational protein targeting to membrane;activation-induced cell death of T cells;mitotic cell cycle checkpoint;gastrulation;mammalian oogenesis stage;TOR signaling;T cell differentiation in thymus;ribosomal small subunit biogenesis;glucose homeostasis;positive regulation of apoptotic process;negative regulation of apoptotic process;erythrocyte development
- Cellular component
- nucleus;nucleoplasm;nucleolus;endoplasmic reticulum;cytosol;polysome;small ribosomal subunit;membrane;cytosolic small ribosomal subunit;dendrite;cytoplasmic ribonucleoprotein granule;cell body;perinuclear region of cytoplasm;ribonucleoprotein complex
- Molecular function
- RNA binding;structural constituent of ribosome;protein binding;protein kinase binding