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GeneBe

RPS6KA6

ribosomal protein S6 kinase A6, the group of AGC family kinases|MAPK activated protein kinases

Basic information

Region (hg38): X:84058345-84206356

Links

ENSG00000072133NCBI:27330OMIM:300303HGNC:10435Uniprot:Q9UK32AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RPS6KA6 gene.

  • Inborn genetic diseases (10 variants)
  • not provided (5 variants)

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
1
clinvar
1
clinvar
2
missense
10
clinvar
1
clinvar
1
clinvar
12
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 10 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)2660996
X-84065009-C-T Benign (Jan 15, 2020)1288726
X-84065034-T-C Inborn genetic diseases Uncertain significance (Aug 12, 2021)2390933
X-84065098-T-C Inborn genetic diseases Uncertain significance (Jan 04, 2022)2352195
X-84097782-T-C Inborn genetic diseases Uncertain significance (Dec 15, 2022)2335534
X-84104544-T-C Inborn genetic diseases Uncertain significance (Mar 29, 2023)2521193
X-84104561-G-A Inborn genetic diseases Uncertain significance (May 23, 2023)2520850
X-84106947-G-A Inborn genetic diseases Uncertain significance (Jul 26, 2022)2303770
X-84106963-C-T Inborn genetic diseases Uncertain significance (Nov 08, 2021)2259107
X-84119931-C-T Inborn genetic diseases Uncertain significance (Feb 23, 2023)2488872
X-84135175-G-A Benign (Aug 16, 2018)723331
X-84135202-A-C Inborn genetic diseases Uncertain significance (Feb 06, 2023)2480785
X-84148121-A-C Likely benign (Oct 01, 2022)2660997
X-84187887-C-T Inborn genetic diseases Uncertain significance (May 23, 2023)2549754
X-84187888-G-A Likely benign (May 01, 2022)2660998

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RPS6KA6protein_codingprotein_codingENST00000262752 22123950
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9870.0135124005031240080.0000121
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.871552360.6580.00001664889
Missense in Polyphen3789.8480.411811900
Synonymous0.5847278.60.9160.000005461359
Loss of Function4.21326.30.1140.00000185569

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00008610.0000619
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001290.00000888
Middle Eastern0.000.00
South Asian0.000.00
Other0.0002400.000166

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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