RPS6KB2

ribosomal protein S6 kinase B2, the group of AGC family kinases

Basic information

Region (hg38): 11:67428459-67435401

Links

ENSG00000175634 ∙ NCBI:6199 ∙ OMIM:608939 ∙ HGNC:10437 ∙ Uniprot:Q9UBS0 ∙ 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 RPS6KB2 gene.

• Inborn genetic diseases (29 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPS6KB2 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
missense			29			29
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	29	1	0

Variants in RPS6KB2

This is a list of pathogenic ClinVar variants found in the RPS6KB2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-67428568-A-G		not specified	Uncertain significance (May 23, 2023)
11-67429572-T-C		not specified	Uncertain significance (Jan 19, 2022)
11-67431368-G-A		not specified	Uncertain significance (Nov 09, 2022)
11-67431402-A-G		not specified	Uncertain significance (Feb 23, 2023)
11-67431408-G-A		not specified	Uncertain significance (Jul 27, 2021)
11-67431455-G-A		not specified	Uncertain significance (Dec 21, 2022)
11-67431465-A-G		not specified	Uncertain significance (Apr 27, 2022)
11-67431513-G-A		not specified	Uncertain significance (Feb 15, 2023)
11-67432652-G-A			Likely benign (Nov 01, 2022)
11-67432740-C-G		not specified	Uncertain significance (Nov 10, 2022)
11-67432781-C-T		not specified	Uncertain significance (Dec 13, 2023)
11-67432796-A-G		not specified	Uncertain significance (Mar 21, 2023)
11-67432798-C-T		not specified	Uncertain significance (May 02, 2023)
11-67432813-G-A		not specified	Uncertain significance (Jun 03, 2022)
11-67433158-A-G		not specified	Uncertain significance (Jun 21, 2022)
11-67433161-G-A		not specified	Uncertain significance (Aug 10, 2021)
11-67433173-G-C			Uncertain significance (Jan 17, 2024)
11-67433199-G-A		not specified	Uncertain significance (Dec 20, 2021)
11-67433382-A-T		not specified	Uncertain significance (May 23, 2023)
11-67433409-C-T		not specified	Uncertain significance (Nov 07, 2023)
11-67433422-C-T		not specified	Uncertain significance (Dec 09, 2023)
11-67433430-C-G		not specified	Uncertain significance (Jan 04, 2024)
11-67433990-C-T			Likely benign (Nov 01, 2022)
11-67433995-T-C		not specified	Uncertain significance (Dec 20, 2022)
11-67434005-G-T		RPS6KB2-related disorder	Likely benign (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPS6KB2	protein_coding	protein_coding	ENST00000312629	15	6942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.96e-21	0.000431	124631	0	213	124844	0.000853

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.205	316	306	1.03	0.0000197	3090
Missense in Polyphen		128	112.41	1.1387		1196
Synonymous	-1.67	147	123	1.19	0.00000777	981
Loss of Function	-0.618	29	25.6	1.13	0.00000127	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00108
Ashkenazi Jewish	0.00	0.00
East Asian	0.00230	0.00228
Finnish	0.0000466	0.0000464
European (Non-Finnish)	0.000884	0.000874
Middle Eastern	0.00230	0.00228
South Asian	0.00128	0.00128
Other	0.000330	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Phosphorylates specifically ribosomal protein S6.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Gastric cancer - Homo sapiens (human);mTOR signaling pathway - Homo sapiens (human);Fc gamma R-mediated phagocytosis - Homo sapiens (human);TGF-beta signaling pathway - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Insulin resistance - Homo sapiens (human);HIF-1 signaling pathway - Homo sapiens (human);Longevity regulating pathway - multiple species - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Breast cancer - Homo sapiens (human);ErbB signaling pathway - Homo sapiens (human);Autophagy - animal - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Proteoglycans in cancer - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Colorectal cancer - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);IL-5 Signaling Pathway;AMP-activated Protein Kinase (AMPK) Signaling;Follicle Stimulating Hormone (FSH) signaling pathway;Angiopoietin Like Protein 8 Regulatory Pathway;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Cytoplasmic Ribosomal Proteins;Insulin Signaling;IL-2 Signaling Pathway;Disease;Signal Transduction;AKT phosphorylates targets in the nucleus;IL-7 signaling;PIP3 activates AKT signaling;JAK STAT pathway and regulation;EPO signaling;Constitutive Signaling by AKT1 E17K in Cancer;PI3K/AKT Signaling in Cancer;VEGF;Intracellular signaling by second messengers;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.286

Intolerance Scores

• rvis_EVS: -0.31
• rvis_percentile_EVS: 32.15

Haploinsufficiency Scores

• pHI: 0.240
• hipred: Y
• hipred_score: 0.512
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.905

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Rps6kb2
• Phenotype: neoplasm; 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); normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: translation;protein phosphorylation;signal transduction;intracellular signal transduction;protein kinase B signaling;positive regulation of translational initiation
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;ribosomal protein S6 kinase activity;ATP binding;peptide binding