RPS6KA2
Basic information
Region (hg38): 6:166409363-166906451
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 RPS6KA2 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 | 3 | |||||
missense | 19 | 21 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region ? | 0 | |||||
non coding ? | 1 | |||||
Total | 0 | 1 | 19 | 5 | 1 |
Variants in RPS6KA2
This is a list of pathogenic ClinVar variants found in the RPS6KA2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-166412777-C-G | Benign (Jul 13, 2018) | |||
6-166412782-G-T | not specified | Uncertain significance (Jul 12, 2022) | ||
6-166412864-A-C | not specified | Uncertain significance (Jun 04, 2024) | ||
6-166413793-C-G | Likely pathogenic (Feb 06, 2024) | |||
6-166413816-C-T | not specified | Uncertain significance (May 23, 2023) | ||
6-166413885-G-A | not specified | Uncertain significance (Feb 16, 2023) | ||
6-166413894-T-C | not specified | Uncertain significance (Feb 10, 2022) | ||
6-166418248-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
6-166418284-C-T | not specified | Uncertain significance (Jun 24, 2022) | ||
6-166419933-G-A | not specified | Uncertain significance (Dec 19, 2022) | ||
6-166423303-C-T | Autism spectrum disorder | association (-) | ||
6-166423304-G-A | Benign/Likely benign (Mar 01, 2023) | |||
6-166430535-C-T | not specified | Likely benign (Aug 17, 2021) | ||
6-166430536-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
6-166430565-C-T | not specified | Uncertain significance (Sep 17, 2021) | ||
6-166430593-A-C | not specified | Uncertain significance (Jan 10, 2023) | ||
6-166432418-T-C | not specified | Uncertain significance (Jun 07, 2024) | ||
6-166448729-C-T | not specified | Uncertain significance (Apr 12, 2024) | ||
6-166448738-C-T | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
6-166448785-C-A | not specified | Uncertain significance (Oct 17, 2023) | ||
6-166451148-G-A | Likely benign (Mar 01, 2023) | |||
6-166451216-G-A | not specified | Uncertain significance (Dec 06, 2021) | ||
6-166459460-C-T | not specified | Uncertain significance (Nov 07, 2022) | ||
6-166459463-G-A | not specified | Uncertain significance (May 29, 2024) | ||
6-166459541-C-T | not specified | Uncertain significance (May 24, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RPS6KA2 | protein_coding | protein_coding | ENST00000503859 | 22 | 497088 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00941 | 0.991 | 125717 | 0 | 31 | 125748 | 0.000123 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.58 | 310 | 467 | 0.664 | 0.0000298 | 4836 |
Missense in Polyphen | 85 | 163.06 | 0.52128 | 1670 | ||
Synonymous | 0.171 | 195 | 198 | 0.985 | 0.0000140 | 1430 |
Loss of Function | 4.55 | 13 | 46.4 | 0.280 | 0.00000265 | 496 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000335 | 0.000333 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000113 | 0.000109 |
Finnish | 0.0000953 | 0.0000924 |
European (Non-Finnish) | 0.000150 | 0.000149 |
Middle Eastern | 0.000113 | 0.000109 |
South Asian | 0.0000673 | 0.0000653 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Serine/threonine-protein kinase that acts downstream of ERK (MAPK1/ERK2 and MAPK3/ERK1) signaling and mediates mitogenic and stress-induced activation of transcription factors, regulates translation, and mediates cellular proliferation, survival, and differentiation. May function as tumor suppressor in epithelial ovarian cancer cells. {ECO:0000269|PubMed:16878154, ECO:0000269|PubMed:7623830}.;
- 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);Prolactin Signaling Pathway;Angiopoietin Like Protein 8 Regulatory Pathway;EGF-EGFR Signaling Pathway;Cytoplasmic Ribosomal Proteins;Insulin Signaling;Developmental Biology;Signaling by GPCR;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signal Transduction;Recycling pathway of L1;Signaling by Interleukins;Prolactin;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;Innate Immune System;Immune System;Nuclear Events (kinase and transcription factor activation);Neuronal System;Cellular responses to external stimuli;IL-7 signaling;Signaling by NTRK1 (TRKA);CREB phosphorylation;Signaling by NTRKs;ERK/MAPK targets;EGFR1;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome;JAK STAT pathway and regulation;EPO signaling;L1CAM interactions;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;Axon guidance;Leptin;RSK activation;CREB phosphorylation through the activation of Ras;Post NMDA receptor activation events;Activation of NMDA receptor and postsynaptic events;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;VEGF;Gastrin-CREB signalling pathway via PKC and MAPK;G alpha (q) signalling events;GPCR downstream signalling;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 8.14
Haploinsufficiency Scores
- pHI
- 0.623
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.519
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
- Rps6ka2
- Phenotype
- muscle phenotype; homeostasis/metabolism 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;signal transduction;negative regulation of cell population proliferation;intracellular signal transduction;positive regulation of apoptotic process;negative regulation of cell cycle
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- magnesium ion binding;protein serine/threonine kinase activity;ribosomal protein S6 kinase activity;protein serine/threonine/tyrosine kinase activity;protein binding;ATP binding;kinase activity