RPS6KA6

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

Basic information

Region (hg38): X:84058345-84206356

Links

ENSG00000072133 ∙ NCBI:27330 ∙ OMIM:300303 ∙ HGNC:10435 ∙ Uniprot:Q9UK32 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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	1	2
missense			18	1	1	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 (Jan 04, 2022)
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-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)
X-84187888-G-A			Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

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: 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

• 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