CSNK2B

casein kinase 2 beta

Basic information

Region (hg38): 6:31665226-31670343

Links

ENSG00000204435 ∙ NCBI:1460 ∙ OMIM:115441 ∙ HGNC:2460 ∙ Uniprot:P67870 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
• Poirier-Bienvenu neurodevelopmental syndrome (Strong), mode of inheritance: AD
• Poirier-Bienvenu neurodevelopmental syndrome (Definitive), mode of inheritance: AD
• Poirier-Bienvenu neurodevelopmental syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Poirier-Bienvenu neurodevelopmental syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Dental; Neurologic	28585349; 28762608; 30655572; 31784560

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSNK2B gene.

• not provided (52 variants)
• Poirier-Bienvenu neurodevelopmental syndrome (39 variants)
• Inborn genetic diseases (14 variants)
• CSNK2B-related condition (3 variants)
• CSNK2B-related intellectual disability with or without epilepsy (2 variants)
• Neurodevelopmental disorder (2 variants)
• not specified (1 variants)
• Seizure;Intellectual disability;Developmental delay (1 variants)
• See cases (1 variants)
• Autism spectrum disorder (1 variants)
• 12 conditions (1 variants)
• Autosomal dominant non-syndromic intellectual disability;Poirier-Bienvenu neurodevelopmental syndrome (1 variants)
• CSNK2B-Related Disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK2B 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	2	1	4
missense	6	7	24			37
nonsense	12	6				18
start loss	1	2				3
frameshift	7	4	2			13
inframe indel			1			1
splice donor/acceptor (+/-2bp)	3	10				13
splice region		1	1			2
non coding			1		7	8
Total	29	29	29	2	8

Highest pathogenic variant AF is 0.0000131

Variants in CSNK2B

This is a list of pathogenic ClinVar variants found in the CSNK2B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31666793-A-C			Benign (May 11, 2021)
6-31666831-G-C		CSNK2B-related disorder	Likely benign (Nov 21, 2022)
6-31666832-A-G			Pathogenic/Likely pathogenic (Jun 01, 2020)
6-31666833-T-A			Likely pathogenic (Jun 26, 2018)
6-31666833-T-G			Pathogenic (Jul 12, 2021)
6-31666837-C-T		CSNK2B-related disorder	Likely benign (Jan 23, 2024)
6-31666844-G-T			Pathogenic (Feb 01, 2023)
6-31666856-TG-T			Pathogenic (Nov 03, 2017)
6-31666858-G-A			Pathogenic (Mar 21, 2023)
6-31666863-C-T			Uncertain significance (Jun 07, 2022)
6-31666867-G-A		Poirier-Bienvenu neurodevelopmental syndrome	Pathogenic/Likely pathogenic (Nov 29, 2023)
6-31666889-G-GAATT			Pathogenic (Feb 01, 2024)
6-31666891-ATTC-A			Uncertain significance (Jul 24, 2019)
6-31666898-T-C		Inborn genetic diseases	Uncertain significance (May 14, 2021)
6-31666899-G-T			Uncertain significance (Nov 01, 2019)
6-31666901-G-T		CSNK2B-related disorder	not provided (-)
6-31666904-G-A		Inborn genetic diseases • Poirier-Bienvenu neurodevelopmental syndrome	Pathogenic/Likely pathogenic (Jun 25, 2020)
6-31666904-G-T		Autism spectrum disorder	Likely pathogenic (Sep 30, 2020)
6-31666905-T-G		Autosomal dominant non-syndromic intellectual disability;Poirier-Bienvenu neurodevelopmental syndrome	Likely pathogenic (Mar 29, 2022)
6-31666981-G-A			Benign (May 10, 2021)
6-31667866-A-G		Inborn genetic diseases	Likely pathogenic (Aug 01, 2016)
6-31667867-G-A		Poirier-Bienvenu neurodevelopmental syndrome	Likely pathogenic (Jul 01, 2021)
6-31667886-C-T		Poirier-Bienvenu neurodevelopmental syndrome	Pathogenic (Dec 03, 2020)
6-31667889-G-A		Inborn genetic diseases • CSNK2B-related intellectual disability with or without epilepsy • 12 conditions • CSNK2B-related disorder • Poirier-Bienvenu neurodevelopmental syndrome	Conflicting classifications of pathogenicity (Feb 08, 2023)
6-31667889-G-T		Poirier-Bienvenu neurodevelopmental syndrome	Pathogenic (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK2B	protein_coding	protein_coding	ENST00000375882	6	5108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.917	0.0826	125701	0	2	125703	0.00000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	27	126	0.215	0.00000695	1430
Missense in Polyphen		6	48.722	0.12315		529
Synonymous	0.914	39	47.0	0.830	0.00000291	371
Loss of Function	3.00	1	12.4	0.0807	5.83e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in Wnt signaling (By similarity). Plays a complex role in regulating the basal catalytic activity of the alpha subunit. {ECO:0000250, ECO:0000269|PubMed:11239457, ECO:0000269|PubMed:16818610}.
• Pathway: Adherens junction - Homo sapiens (human);Ribosome biogenesis in eukaryotes - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Measles - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Wnt Signaling Pathway;Developmental Biology;Neutrophil degranulation;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Signaling by WNT;Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;Generic Transcription Pathway;Regulation of PTEN stability and activity;Metabolism of lipids;Metabolism of proteins;RNA Polymerase II Transcription;Chaperonin-mediated protein folding;Innate Immune System;Immune System;Metabolism;Fibroblast growth factor-1;Synthesis of PC;Receptor Mediated Mitophagy;Mitophagy;PTEN Regulation;PIP3 activates AKT signaling;Protein folding;Regulation of TP53 Activity through Phosphorylation;Condensation of Prometaphase Chromosomes;Signal transduction by L1;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Mitotic Prometaphase;L1CAM interactions;Glycerophospholipid biosynthesis;Phospholipid metabolism;Axon guidance;M Phase;Cell Cycle;Cell Cycle, Mitotic;Intracellular signaling by second messengers;WNT mediated activation of DVL;Transcriptional regulation by RUNX1;ALK1 signaling events;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.201

Intolerance Scores

• loftool: 0.116
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.616
• ghis: 0.634

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csnk2b
• Phenotype: growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Biological process: signal transduction;negative regulation of cell population proliferation;positive regulation of pathway-restricted SMAD protein phosphorylation;Wnt signaling pathway;peptidyl-threonine phosphorylation;positive regulation of activin receptor signaling pathway;adiponectin-activated signaling pathway;response to testosterone;cellular protein-containing complex assembly;neutrophil degranulation;negative regulation of blood vessel endothelial cell migration;regulation of protein kinase activity;regulation of DNA binding;endothelial tube morphogenesis;liver regeneration;regulation of signal transduction by p53 class mediator
• Cellular component: chromatin;extracellular region;nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;cilium;protein kinase CK2 complex;nuclear matrix;PcG protein complex;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: chromatin binding;protein serine/threonine kinase activity;signaling receptor binding;protein binding;transcription factor binding;protein kinase regulator activity;protein domain specific binding;identical protein binding;ribonucleoprotein complex binding;metal ion binding