RPS6KA6
Basic information
Region (hg38): X:84058345-84206356
Links
Phenotypes
GenCC
Source:
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 RPS6KA6 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 | 2 | |||||
missense | 18 | 20 | ||||
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 | 18 | 2 | 2 |
Variants in RPS6KA6
This is a list of pathogenic ClinVar variants found in the RPS6KA6 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-84064396-T-C | Likely benign (Oct 01, 2022) | |||
X-84065009-C-T | Benign (Jan 15, 2020) | |||
X-84065034-T-C | not specified | Uncertain significance (Aug 12, 2021) | ||
X-84065098-T-C | not specified | Uncertain significance (Apr 30, 2024) | ||
X-84096239-G-T | not specified | Uncertain significance (Dec 09, 2023) | ||
X-84097782-T-C | not specified | Uncertain significance (Dec 15, 2022) | ||
X-84104544-T-C | not specified | Uncertain significance (Mar 29, 2023) | ||
X-84104561-G-A | not specified | Uncertain significance (May 23, 2023) | ||
X-84104610-T-G | not specified | Uncertain significance (Jan 08, 2024) | ||
X-84105840-T-C | not specified | Uncertain significance (Jan 03, 2024) | ||
X-84105866-T-C | not specified | Uncertain significance (Sep 29, 2023) | ||
X-84106918-T-C | not specified | Uncertain significance (Jan 29, 2024) | ||
X-84106947-G-A | not specified | Uncertain significance (Jul 26, 2022) | ||
X-84106963-C-T | not specified | Uncertain significance (Nov 08, 2021) | ||
X-84119931-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
X-84119953-C-T | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
X-84135174-C-A | not specified | Uncertain significance (Dec 21, 2023) | ||
X-84135175-G-A | Benign (Aug 16, 2018) | |||
X-84135202-A-C | not specified | Uncertain significance (Feb 06, 2023) | ||
X-84148121-A-C | Likely benign (Oct 01, 2022) | |||
X-84156122-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
X-84164344-T-A | not specified | Uncertain significance (Jun 13, 2024) | ||
X-84164347-C-T | not specified | Uncertain significance (Dec 11, 2023) | ||
X-84164381-C-G | not specified | Uncertain significance (Aug 05, 2021) | ||
X-84187887-C-T | not specified | Uncertain significance (May 23, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPS6KA6 | protein_coding | protein_coding | ENST00000262752 | 22 | 123950 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.987 | 0.0135 | 124005 | 0 | 3 | 124008 | 0.0000121 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.87 | 155 | 236 | 0.658 | 0.0000166 | 4889 |
Missense in Polyphen | 37 | 89.848 | 0.41181 | 1900 | ||
Synonymous | 0.584 | 72 | 78.6 | 0.916 | 0.00000546 | 1359 |
Loss of Function | 4.21 | 3 | 26.3 | 0.114 | 0.00000185 | 569 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000861 | 0.0000619 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000129 | 0.00000888 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.000240 | 0.000166 |
dbNSFP
Source:
- Function
- FUNCTION: Constitutively active serine/threonine-protein kinase that exhibits growth-factor-independent kinase activity and that may participate in p53/TP53-dependent cell growth arrest signaling and play an inhibitory role during embryogenesis. {ECO:0000269|PubMed:15042092, ECO:0000269|PubMed:15632195}.;
- Pathway
- mTOR signaling pathway - Homo sapiens (human);Long-term potentiation - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Insulin resistance - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Thermogenesis - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Progesterone-mediated oocyte maturation - Homo sapiens (human);Angiopoietin Like Protein 8 Regulatory Pathway;Cytoplasmic Ribosomal Proteins;Insulin Signaling;Developmental Biology;Recycling pathway of L1;Neuronal System;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;L1CAM interactions;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;Axon guidance;RSK activation;CREB phosphorylation through the activation of Ras;Post NMDA receptor activation events;Activation of NMDA receptor and postsynaptic events;VEGF
(Consensus)
Recessive Scores
- pRec
- 0.165
Intolerance Scores
- loftool
- rvis_EVS
- -0.09
- rvis_percentile_EVS
- 46.74
Haploinsufficiency Scores
- pHI
- 0.202
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.569
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.960
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rps6ka6
- Phenotype
- growth/size/body region phenotype; embryo phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);
Gene ontology
- Biological process
- protein phosphorylation;DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;signal transduction;central nervous system development;negative regulation of embryonic development;negative regulation of ERK1 and ERK2 cascade;negative regulation of mesoderm development
- Cellular component
- fibrillar center;nucleus;nucleoplasm;nucleolus;mitochondrion;cytosol
- Molecular function
- magnesium ion binding;protein kinase activity;ribosomal protein S6 kinase activity;ATP binding;kinase activity