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GeneBe

RPS6KA2

ribosomal protein S6 kinase A2, the group of AGC family kinases|MAPK activated protein kinases|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:166409363-166906451

Links

ENSG00000071242NCBI:6196OMIM:601685HGNC:10431Uniprot:Q15349AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS6KA2 gene.

  • Inborn genetic diseases (17 variants)
  • not provided (5 variants)

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
2
clinvar
1
clinvar
3
missense
16
clinvar
1
clinvar
17
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
?
0
non coding
?
1
clinvar
1
Total 0 1 16 4 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)781018
6-166412782-G-T Inborn genetic diseases Uncertain significance (Jul 12, 2022)2405330
6-166413793-C-G Likely pathogenic (Feb 06, 2024)2692109
6-166413816-C-T Inborn genetic diseases Uncertain significance (May 23, 2023)2523454
6-166413885-G-A Inborn genetic diseases Uncertain significance (Feb 16, 2023)2459127
6-166413894-T-C Inborn genetic diseases Uncertain significance (Feb 10, 2022)2276384
6-166418248-C-T Inborn genetic diseases Uncertain significance (Oct 03, 2022)2403350
6-166418284-C-T Inborn genetic diseases Uncertain significance (Jun 24, 2022)2296435
6-166419933-G-A Inborn genetic diseases Uncertain significance (Dec 19, 2022)2403309
6-166423303-C-T Autism spectrum disorder association (-)996726
6-166423304-G-A Benign/Likely benign (Mar 01, 2023)770932
6-166430535-C-T Inborn genetic diseases Likely benign (Aug 17, 2021)2405000
6-166430536-G-A Inborn genetic diseases Uncertain significance (Jun 02, 2023)2546788
6-166430565-C-T Inborn genetic diseases Uncertain significance (Sep 17, 2021)2218278
6-166430593-A-C Inborn genetic diseases Uncertain significance (Jan 10, 2023)2465156
6-166451148-G-A Likely benign (Mar 01, 2023)2657124
6-166451216-G-A Inborn genetic diseases Uncertain significance (Dec 06, 2021)2215463
6-166459541-C-T Inborn genetic diseases Uncertain significance (May 24, 2023)2510447
6-166459545-A-G Inborn genetic diseases Uncertain significance (Oct 26, 2021)2209033
6-166504534-T-C Inborn genetic diseases Uncertain significance (Jul 15, 2021)2230132
6-166531281-G-A Likely benign (Oct 01, 2022)2657125
6-166531288-C-T Inborn genetic diseases Uncertain significance (Jul 11, 2023)2599187
6-166538733-A-G Inborn genetic diseases Uncertain significance (Jun 14, 2023)2560301
6-166770890-G-A Likely benign (Jan 01, 2023)2657126
6-166858204-T-C Inborn genetic diseases Uncertain significance (Jun 18, 2021)2233369

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS6KA2protein_codingprotein_codingENST00000503859 22497088
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.009410.9911257170311257480.000123
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.583104670.6640.00002984836
Missense in Polyphen85163.060.521281670
Synonymous0.1711951980.9850.00001401430
Loss of Function4.551346.40.2800.00000265496

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003350.000333
Ashkenazi Jewish0.000.00
East Asian0.0001130.000109
Finnish0.00009530.0000924
European (Non-Finnish)0.0001500.000149
Middle Eastern0.0001130.000109
South Asian0.00006730.0000653
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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