CSNK2B
casein kinase 2 beta
Basic information
Region (hg38): 6:31665227-31670343
Links
Phenotypes
GenCC
Source:
- 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
- Poirier-Bienvenu neurodevelopmental syndrome (Strong), mode of inheritance: AD
- Poirier-Bienvenu neurodevelopmental syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
| 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
- not_provided (83 variants)
- Poirier-Bienvenu_neurodevelopmental_syndrome (78 variants)
- Inborn_genetic_diseases (21 variants)
- CSNK2B-related_disorder (11 variants)
- Intellectual_disability (3 variants)
- Seizure (2 variants)
- Neurodevelopmental_disorder (2 variants)
- not_specified (2 variants)
- Autism_spectrum_disorder (1 variants)
- Deeply_set_eye (1 variants)
- Tapered_finger (1 variants)
- Toe_clinodactyly (1 variants)
- Intellectual_disability-craniodigital_syndrome (1 variants)
- Pointed_chin (1 variants)
- Developmental_delay (1 variants)
- CSNK2B-related_intellectual_disability_with_or_without_epilepsy (1 variants)
- See_cases (1 variants)
- Asymmetry_of_the_ears (1 variants)
- Mandibular_prognathia (1 variants)
- Autosomal_dominant_non-syndromic_intellectual_disability (1 variants)
- Abnormal_facial_shape (1 variants)
- Syndactyly (1 variants)
- Intellectual_disability_and_seizures (1 variants)
- Underdeveloped_nasal_alae (1 variants)
- Thin_upper_lip_vermilion (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. These statistics are base on transcript: NM_000001320.7. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 11 | |||||
| missense | 19 | 38 | 66 | |||
| nonsense | 15 | 23 | ||||
| start loss | 1 | 3 | 1 | 5 | ||
| frameshift | 15 | 23 | ||||
| splice donor/acceptor (+/-2bp) | 11 | 13 | 25 | |||
| Total | 51 | 48 | 44 | 9 | 1 |
Highest pathogenic variant AF is 0.000021917327
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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
- pHI
- 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