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
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.
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 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 2 | 2 | ||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in RPS6
This is a list of pathogenic ClinVar variants found in the RPS6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 9-19376299-C-G | not specified | Uncertain significance (Jun 12, 2023) | ||
| 9-19376303-C-T | not specified | Uncertain significance (Jan 29, 2024) | ||
| 9-19376348-C-T | Hemimegalencephaly | Uncertain significance (May 14, 2019) | ||
| 9-19376395-A-G | Benign (Apr 26, 2018) | |||
| 9-19376576-C-T | not specified | Uncertain significance (Oct 27, 2021) | ||
| 9-19378522-G-C | Benign (Dec 31, 2019) | |||
| 9-19378724-C-A | not specified | Uncertain significance (Dec 28, 2023) |
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