CSNK2B

Summary

CSNK2B (casein kinase 2 beta, HGNC:2460) is a protein-coding gene on chromosome 6p21.33, encoding Casein kinase II subunit beta (P67870). Regulatory subunit of casein kinase II/CK2. It is a common-essential gene (DepMap: required in 94.8% of cancer cell lines).

This gene encodes the beta subunit of casein kinase II, a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme is composed of three subunits, alpha, alpha prime and beta, which form a tetrameric holoenzyme. The alpha and alpha prime subunits are catalytic, while the beta subunit serves regulatory functions. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus. Two transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 1460 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Poirier-Bienvenu neurodevelopmental syndrome (Definitive, ClinGen) — +1 more curated relationship
• GWAS associations: 27
• Clinical variants (ClinVar): 195 total — 53 pathogenic, 32 likely-pathogenic
• Phenotypes (HPO): 10
• Druggable target: yes — 14 molecules with ChEMBL bioactivity
• Cancer dependency (DepMap): dependent in 94.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_001320

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2460
Approved symbol	CSNK2B
Name	casein kinase 2 beta
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	Ckb1, Ckb2
Ensembl gene	ENSG00000204435
Ensembl biotype	protein_coding
OMIM	115441
Entrez	1460

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 4 retained_intron, 2 nonsense_mediated_decay

ENST00000375865, ENST00000375866, ENST00000375882, ENST00000375885, ENST00000465481, ENST00000468255, ENST00000475875, ENST00000481269, ENST00000677388, ENST00000677536, ENST00000677758

RefSeq mRNA: 2 — MANE Select: NM_001320 NM_001282385, NM_001320

CCDS: CCDS4712

Canonical transcript exons

ENST00000375882 — 7 exons

Exon	Start	End
ENSE00000000341	31669836	31670067
ENSE00001819731	31666080	31666208
ENSE00003466148	31669097	31669172
ENSE00003598293	31667868	31667970
ENSE00003620260	31666821	31666903
ENSE00003660472	31669319	31669508
ENSE00003678314	31668539	31668654

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 99.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 239.7440 / max 1637.8431, expressed in 1828 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67014	235.8351	1828
67017	1.4844	896
67016	0.9815	543
67013	0.6445	218
67010	0.6236	129
67011	0.1151	43
67012	0.0417	10
67009	0.0180	5

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	99.46	gold quality
right testis	UBERON:0004534	99.44	gold quality
skin of leg	UBERON:0001511	99.21	gold quality
zone of skin	UBERON:0000014	99.16	gold quality
skin of abdomen	UBERON:0001416	99.11	gold quality
ganglionic eminence	UBERON:0004023	98.88	gold quality
metanephros cortex	UBERON:0010533	98.76	gold quality
left ovary	UBERON:0002119	98.74	gold quality
stromal cell of endometrium	CL:0002255	98.73	gold quality
right ovary	UBERON:0002118	98.68	gold quality
mucosa of transverse colon	UBERON:0004991	98.68	gold quality
endocervix	UBERON:0000458	98.65	gold quality
ovary	UBERON:0000992	98.64	gold quality
lower esophagus mucosa	UBERON:0035834	98.63	gold quality
body of stomach	UBERON:0001161	98.62	gold quality
adenohypophysis	UBERON:0002196	98.61	gold quality
cortex of kidney	UBERON:0001225	98.60	gold quality
ectocervix	UBERON:0012249	98.60	gold quality
pituitary gland	UBERON:0000007	98.59	gold quality
fallopian tube	UBERON:0003889	98.59	gold quality
fundus of stomach	UBERON:0001160	98.58	gold quality
left lobe of thyroid gland	UBERON:0001120	98.57	gold quality
mucosa of stomach	UBERON:0001199	98.57	gold quality
testis	UBERON:0000473	98.56	gold quality
cortical plate	UBERON:0005343	98.56	gold quality
body of uterus	UBERON:0009853	98.56	gold quality
granulocyte	CL:0000094	98.55	gold quality
subcutaneous adipose tissue	UBERON:0002190	98.53	gold quality
right hemisphere of cerebellum	UBERON:0014890	98.53	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.53	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-GEOD-75140	yes	176.53
E-MTAB-7249	yes	11.25
E-ANND-3	yes	10.38
E-GEOD-100618	no	435.51

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ETS1

miRNA regulators (miRDB)

29 targeting CSNK2B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-10394-5P	99.65	66.83	1852
HSA-MIR-1205	99.65	66.76	1826
HSA-MIR-1260A	99.61	66.67	1098
HSA-MIR-1260B	99.61	66.67	1098
HSA-MIR-7844-5P	99.55	68.56	1428
HSA-MIR-32-3P	99.36	68.20	2517
HSA-MIR-3688-5P	99.12	69.67	1091
HSA-MIR-1286	99.09	66.23	1046
HSA-MIR-5681A	97.99	67.17	1658
HSA-MIR-6823-5P	96.26	65.69	919

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 94.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

• Mapping of the interaction domain of the protein kinase CKII beta subunit with target proteins. (PMID:11710515)
• HIV-1 Rev transactivator: a beta-subunit directed substrate and effector of protein kinase CK2 (PMID:11827166)
• Response of cancer cells to molecular interruption of the CK2 signal. (PMID:11827168)
• Characterization of CK2 holoenzyme variants with regard to crystallization (PMID:11827171)
• Transcriptional coordination of the genes encoding catalytic (CK2alpha) and regulatory (CK2beta) subunits of human protein kinase CK2. (PMID:11827174)
• Consequences of CK2 signaling to the nuclear matrix. (PMID:11827176)
• Localization of individual subunits of protein kinase CK2 to the endoplasmic reticulum and to the Golgi apparatus (PMID:11827177)
• Association and regulation of casein kinase 2 activity by adenomatous polyposis coli protein (PMID:11972058)
• Protein kinase CK2 dependent phosphorylation of the E2 ubiquitin conjugating enzyme UBC3B induces its interaction with beta-TRCp and enhances beta-catenin degradation. (PMID:12037680)
• sequencing of full-length DNA encoding subunits in platelets and megakaryocytic cells (PMID:12102635)
• FGF-1 binds to both the catalytic alpha-subunit & to the regulatory beta-subunit of CK2.The presence of FGF-1 or FGF-2 was found to enhance the autophosphorylation of CK2 beta. (PMID:12145206)
• results show that the Ring-H2 finger motif of CKBBP1 is necessary for efficient binding to CKIIbeta, as well as for optimal cell proliferation (PMID:12470599)
• microtubule-associated protein that confers microtubule stability in a phosphorylation-independent manner (PMID:14634006)
• Casein kinase II (CKII) phosphorylates synphilin-1; beta subunit of this enzyme complex binds to synphilin-1. CKII-mediated phosphorylation of synphilin-1, rather than alpha-synuclein, modulates the aggregation into inclusion bodies. (PMID:14645218)
• CK2 phosphorylation of La can affect production of the translational machinery (PMID:15485924)
• These findings support the notion that CK2beta can act as a general modulator of remote docking sites in protein kinase–substrate interactions. (PMID:15940255)
• In vitro phosphorylation of eIF2beta also pointed to Ser2 as a preferred site for CK2 phosphorylation (PMID:16225457)
• CK2 activity in Chinese Hamster Ovary (CHO) cells is entirely accounted for by the holoenzyme. (PMID:16806200)
• there is a functional link between S6K1 II and CK2 signaling, which involves the regulation of S6K1 II nuclear export by CK2-mediated phosphorylation of Ser-17 (PMID:16895915)
• hNopp140 serves as a negative regulator of CK2 and InsP(6) stimulates the activity of CK2 by blocking the interaction between hNopp140 and CK2 (PMID:17038328)
• a stabilized form of CK2beta can be used to inhibit cell proliferation (PMID:17681943)
• protein kinase CK2 is involved in cell cycle regulation and indicate the mechanism by which CDC25A turnover might be regulated by Chk1 in the absence of DNA damage. (PMID:17912454)
• There was a positive correlation between the expressions of CK2alpha and CK2beta in laryngeal squamous cell carcinoma. (PMID:18062282)
• Further studies in transgenic mice and cultured cells suggest that cellular toxicity, including proteasomal dysfunction, increases casein kinase 2 activity, which results in elevated Ser129 alpha-syn phosphorylation. (PMID:18451726)
• The regulatory beta-subunit of protein kinase CK2 regulates cell-cycle progression. (PMID:18469858)
• Transcript amounts of the subunits CK2alpha and CK2beta and holoenzyme CK2 activity in 34 muscle biopsies of human patients with different muscle pathologies, were determined. (PMID:18553059)
• These findings support the view that CK2beta regulates various intracellular processes by modulating the activity of protein kinases that are distinct from CK2. (PMID:18560763)
• Data show that these CK2-targeted motifs in MDC1 are required to mediate NBS1 association with chromatin-flanking sites of unrepaired DNA double-strand breaks. (PMID:18583988)
• In epithelial cells, a fraction of CK2 is associated to the plasma membrane and that this localization is controlled by cell-matrix interactions. (PMID:18587631)
• presents unbound three-dimensional structure of a CK2beta construct that is fully capable of CK2alpha recruitment and quantify its affinity to CK2alpha thermodynamically (PMID:18824508)
• CK2beta is widely expressed in endometrial carcinoma , and suggest a role in cell proliferation and anchorage-independent cell growth (PMID:19056846)
• Casein kinase 2 phosphorylates human cytomegalovirus pUL84, and this interaction is required for oriLyt-dependent DNA replication. (PMID:19091862)
• CK2-dependent phosphorylation controls the nuclear localization, aggregation and stability of ataxin-3. (PMID:19542537)
• These studies support CK2beta as an important regulator of ALK-1 signaling and ALK-1-mediated functions in endothelial cells. (PMID:19592636)
• These experiments indicate that casein kinase II phosphorylation of varicella-zoster virus open reading frame 63 S186 occurs in the nucleus and possibly identify an initial molecular event operative in virus reactivation. (PMID:19759161)
• CK2 could phosphorylate TNFAIP1 in vitro and in vivo, which facilitated the distribution of TNFAIP1 in nucleus and enhanced its interaction with PCNA. (PMID:19851886)
• The Casein Kinase 2 (CK2) was identified as a binding and regulatory partner for Mitogen- and stress-activated protein kinase(MSK1). (PMID:20044958)
• analysis of interaction sites between Wee1 kinase and the regulatory beta-subunit of protein kinase CK2 (PMID:20372791)
• Freshly isolated peripheral blood mononuclear cells from patients with chronic lymphocytic leukemia (n = 44) showed significantly higher levels of phosphorylated Akt1,PTEN, and casein kinase 2 than healthy persons (n = 8). (PMID:20576813)
• Threonine at amino acid (aa) 770 and serine at aa 854 to 855 of RIG-I are phosphorylated by casein kinase II (CK2) in the resting state of the cell and dephosphorylated when cells are infected by RNA virus. (PMID:21068236)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	csnk2b	ENSDARG00000077776
mus_musculus	Csnk2b	ENSMUSG00000024387
rattus_norvegicus	Csnk2b	ENSRNOG00000000847
drosophila_melanogaster	CkIIbeta	FBGN0000259
caenorhabditis_elegans	kin-10	WBGENE00002196

Protein

Protein identifiers

Casein kinase II subunit beta — P67870 (reviewed: P67870)

Alternative names: Phosvitin, Protein G5a

All UniProt accessions (6): P67870, A0A7I2V500, A0A7I2YQ78, A0A7I2YQQ2, N0E4C7, Q5SRQ6

UniProt curated annotations — full annotation on UniProt →

Function. Regulatory subunit of casein kinase II/CK2. As part of the kinase complex regulates the basal catalytic activity of the alpha subunit a constitutively active serine/threonine-protein kinase that phosphorylates a large number of substrates containing acidic residues C-terminal to the phosphorylated serine or threonine. Participates in Wnt signaling. (Microbial infection) Upon infection with Epstein-Barr virus (EBV), the interaction with viral EBNA1 increases the association of CK2 with PML proteins, which increases PML phosphorylation by CK2, triggering the polyubiquitylation and degradation of PML. Seems to also suppress EBV reactivation by mediating ARK2N and JUN at the Z promoter which inhibits BZLF1 transcrition.

Subunit / interactions. Casein kinase II/CK2 is a tetramer composed of an alpha subunit, an alpha’ subunit and two beta subunits. The beta subunit dimerization is mediated by zinc ions. Interacts with DYNLT2. Interacts with CD163. Also a component of a CK2-SPT16-SSRP1 complex composed of SSRP1, SUPT16H, CSNK2A1, CSNK2A2 and CSNK2B, the complex associating following UV irradiation. Interacts with MUSK; mediates phosphorylation of MUSK by CK2. Interacts with FGF1; this interaction is increased in the presence of FIBP, suggesting a possible cooperative interaction between CSNKB and FIBP in binding to FGF1. Interacts (via KSSR motif) with ARK2N. Interacts with JUN and ARK2N; mediates the interaction between ARK2N and JUN. (Microbial infection) Interacts (via KSSR motif) with Epstein-Barr virus EBNA1; the interaction requires phosphorylation of EBNA1, is independent and simultaneous to EBNA1 interaction with USP7 as well as necessary for PML nuclear bodies disruption by EBNA1. EBNA1, USP7 and CSNK2B form a ternary complex.

Subcellular location. Nucleus.

Post-translational modifications. Phosphorylated by alpha subunit.

Disease relevance. Poirier-Bienvenu neurodevelopmental syndrome (POBINDS) [MIM:618732] An autosomal dominant neurodevelopmental disorder characterized by onset of seizures in infancy, developmental delay, impaired intellectual development, and poor or absent speech. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The KSSR motif is part of a protein interaction pocket that mediates interaction with cellular and viral proteins.

Similarity. Belongs to the casein kinase 2 subunit beta family.

RefSeq proteins (2): NP_001269314, NP_001311* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000704	Casein_kinase_II_reg-sub	Family
IPR016149	Casein_kin_II_reg-sub_N	Homologous_superfamily
IPR035991	Casein_kinase_II_beta-like	Homologous_superfamily

Pfam: PF01214

UniProt features (52 total): helix 14, modified residue 8, strand 8, sequence variant 6, turn 5, binding site 4, initiator methionine 1, chain 1, cross-link 1, region of interest 1, mutagenesis site 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
1QF8	X-RAY DIFFRACTION	1.74
6Q38	X-RAY DIFFRACTION	1.74
3EED	X-RAY DIFFRACTION	2.8
4DGL	X-RAY DIFFRACTION	3
1JWH	X-RAY DIFFRACTION	3.1
4MD7	X-RAY DIFFRACTION	3.1
1DS5	X-RAY DIFFRACTION	3.16
4MD8	X-RAY DIFFRACTION	3.3
4NH1	X-RAY DIFFRACTION	3.3
4MD9	X-RAY DIFFRACTION	3.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P67870-F1	93.70	0.87

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (4): 109; 114; 137; 140

Post-translational modifications (9): 3, 8, 37, 69, 209, 212, 212, 2, 2

Mutagenesis-validated functional residues (1):

Position	Phenotype
147–150	no effect on interaction alpha subunit csnk2a1. loss on interaction with ark2n and epstein-barr virus ebna1.

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

ID	Pathway
R-HSA-1483191	Synthesis of PC
R-HSA-201688	WNT mediated activation of DVL
R-HSA-2514853	Condensation of Prometaphase Chromosomes
R-HSA-445144	Signal transduction by L1
R-HSA-6798695	Neutrophil degranulation
R-HSA-6804756	Regulation of TP53 Activity through Phosphorylation
R-HSA-6814122	Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding
R-HSA-8934903	Receptor Mediated Mitophagy
R-HSA-8939243	RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-8948751	Regulation of PTEN stability and activity
R-HSA-9755511	KEAP1-NFE2L2 pathway
R-HSA-9768727	Regulation of CDH1 posttranslational processing and trafficking to plasma membrane
R-HSA-9828806	Maturation of hRSV A proteins
R-HSA-9929491	SPOP-mediated proteasomal degradation of PD-L1(CD274)
R-HSA-9931529	Phosphorylation and nuclear translocation of BMAL1 (ARNTL) and CLOCK
R-HSA-9931530	Phosphorylation and nuclear translocation of the CRY:PER:kinase complex

MSigDB gene sets: 387 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_SMAD_PROTEIN_SIGNAL_TRANSDUCTION, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, REACTOME_INNATE_IMMUNE_SYSTEM, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, MORF_ESPL1, REACTOME_ADAPTIVE_IMMUNE_SYSTEM, GOBP_RESPONSE_TO_PEPTIDE, GOCC_SECRETORY_GRANULE, MODULE_151, GOBP_NEGATIVE_REGULATION_OF_BLOOD_VESSEL_ENDOTHELIAL_CELL_MIGRATION, ENK_UV_RESPONSE_KERATINOCYTE_UP, GCM_NPM1

GO Biological Process (14): signal transduction (GO:0007165), negative regulation of cell population proliferation (GO:0008285), Wnt signaling pathway (GO:0016055), negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435), positive regulation of activin receptor signaling pathway (GO:0032927), adiponectin-activated signaling pathway (GO:0033211), negative regulation of blood vessel endothelial cell migration (GO:0043537), positive regulation of SMAD protein signal transduction (GO:0060391), endothelial tube morphogenesis (GO:0061154), protein-containing complex assembly (GO:0065003), symbiont-mediated disruption of host cell PML body (GO:0075342), negative regulation of viral life cycle (GO:1903901), peptidyl-threonine phosphorylation (GO:0018107), release from viral latency (GO:0019046)

GO Molecular Function (11): chromatin binding (GO:0003682), protein serine/threonine kinase activity (GO:0004674), signaling receptor binding (GO:0005102), protein kinase regulator activity (GO:0019887), protein domain specific binding (GO:0019904), protein-macromolecule adaptor activity (GO:0030674), identical protein binding (GO:0042802), metal ion binding (GO:0046872), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), protein binding (GO:0005515), kinase activity (GO:0016301)

GO Cellular Component (17): chromatin (GO:0000785), fibrillar center (GO:0001650), extracellular region (GO:0005576), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), protein kinase CK2 complex (GO:0005956), PML body (GO:0016605), perinuclear theca (GO:0033011), secretory granule lumen (GO:0034774), extracellular exosome (GO:0070062), sperm midpiece (GO:0097225), sperm glycocalyx (GO:0120238), ficolin-1-rich granule lumen (GO:1904813), plasma membrane (GO:0005886), PcG protein complex (GO:0031519)

Reactome top-level categories

Rollup of top-15 pathways:

Category	Pathways
Circadian clock	2
Glycerophospholipid biosynthesis	1
TCF dependent signaling in response to WNT	1
Mitotic Prometaphase	1
L1CAM interactions	1
Innate Immune System	1
Regulation of TP53 Activity	1
Chaperonin-mediated protein folding	1
Mitophagy	1
Transcriptional regulation by RUNX1	1
PTEN Regulation	1
Cellular response to chemical stress	1
Regulation of CDH1 Expression and Function	1
Respiratory syncytial virus (RSV) genome replication, transcription and translation	1
Regulation of PD-L1(CD274) Post-translational modification	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	7
protein binding	4
positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway	2
binding	2
protein kinase activity	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
cell population proliferation	1
regulation of cell population proliferation	1
negative regulation of cellular process	1
cell surface receptor signaling pathway	1
regulation of proteasomal ubiquitin-dependent protein catabolic process	1
proteasome-mediated ubiquitin-dependent protein catabolic process	1
negative regulation of proteasomal protein catabolic process	1
negative regulation of ubiquitin-dependent protein catabolic process	1
activin receptor signaling pathway	1
regulation of activin receptor signaling pathway	1
hormone-mediated signaling pathway	1
cytokine-mediated signaling pathway	1
negative regulation of endothelial cell migration	1
blood vessel endothelial cell migration	1
regulation of blood vessel endothelial cell migration	1
regulation of SMAD protein signal transduction	1
SMAD protein signal transduction	1
positive regulation of intracellular signal transduction	1
morphogenesis of an endothelium	1
epithelial tube morphogenesis	1
cellular component assembly	1
protein-containing complex organization	1
symbiont-mediated disruption of host cellular anatomical structure	1
viral life cycle	1
negative regulation of viral process	1
regulation of viral life cycle	1
protein phosphorylation	1
peptidyl-threonine modification	1
viral process	1
latent virus replication	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

536 interactions, top by confidence:

A	B	Type	Score
CSNK2A1	CSNK2B	psi-mi:“MI:0407”(direct interaction)	0.980
CSNK2A1	CSNK2B	psi-mi:“MI:0915”(physical association)	0.980
CSNK2B	CSNK2A1	psi-mi:“MI:2364”(proximity)	0.980
CSNK2B	CSNK2A1	psi-mi:“MI:0915”(physical association)	0.980
CSNK2B	CSNK2A2	psi-mi:“MI:0915”(physical association)	0.960
CSNK2A2	CSNK2B	psi-mi:“MI:0915”(physical association)	0.960
CSNK2A1	CSNK2A2	psi-mi:“MI:0914”(association)	0.920
RYBP	CSNK2A2	psi-mi:“MI:0914”(association)	0.900
PCGF5	CSNK2A2	psi-mi:“MI:0914”(association)	0.880
CSNK2B	CSNK2B	psi-mi:“MI:0915”(physical association)	0.870
POLR2E	POLR3A	psi-mi:“MI:0914”(association)	0.870
RYBP	BMI1	psi-mi:“MI:0914”(association)	0.850
RPS6KA3	CSNK2B	psi-mi:“MI:0915”(physical association)	0.840
AUTS2	CSNK2B	psi-mi:“MI:0914”(association)	0.760
HEXIM2	AHCYL1	psi-mi:“MI:0914”(association)	0.740
VSX1	USP12	psi-mi:“MI:0914”(association)	0.730
CSNK2B	RBM39	psi-mi:“MI:0915”(physical association)	0.670
Bmal1	CSNK2B	psi-mi:“MI:0915”(physical association)	0.650
Bmal1	CSNK2B	psi-mi:“MI:0407”(direct interaction)	0.650
PCGF6	CBX4	psi-mi:“MI:0914”(association)	0.640
YAF2	E2F6	psi-mi:“MI:0914”(association)	0.640

BioGRID (950): CSNK2B (Affinity Capture-RNA), CSNK2B (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), CSNK2B (Two-hybrid), CSNK2B (Two-hybrid), CSNK2B (Two-hybrid), CSNK2B (Two-hybrid), CSNK2B (Two-hybrid), DEC1 (Two-hybrid), BHLHE41 (Two-hybrid)

ESM2 similar proteins: A1ZB91, B3MJV4, B4GH42, B4Q9T2, B5E0H4, H2KYU6, O59906, O76485, O80507, O81275, O94281, O96863, P08182, P28021, P28548, P32914, P38930, P40228, P40229, P40232, P43639, P67868, P67869, P67870, P67871, P67872, P67873, P67874, P81205, P91133, Q24536, Q4I5W5, Q54PF1, Q5AK73, Q6FMX1, Q752J8, Q7KV12, Q7KV13, Q7KV14, Q7KV15

Diamond homologs: O59906, O76485, O80507, O81275, O94281, O96863, P08182, P28021, P28548, P38930, P40228, P40229, P40232, P43639, P67868, P67869, P67870, P67871, P67872, P67873, P67874, Q24536, Q54PF1, Q7KV12, Q7KV13, Q7KV14, Q7KV15, Q7KV19, Q7KV22, Q7KV23, Q8TG11, Q8TG12, Q91398, Q9NIV2

SIGNOR signaling

48 interactions.

A	Effect	B	Mechanism
CSNK2B	down-regulates	IKZF1	phosphorylation
CSNK2B	down-regulates	SET	phosphorylation
CSNK2B	“up-regulates activity”	BID	phosphorylation
CSNK2B	unknown	CDC34	phosphorylation
CSNK2B	unknown	CSNK2B	phosphorylation
CSNK2B	“down-regulates activity”	CTDP1	phosphorylation
CSNK2B	“up-regulates activity”	CTNNB1	phosphorylation
CSNK2B	“up-regulates activity”	EIF5	phosphorylation
CSNK2B	unknown	MME	phosphorylation
CSNK2B	unknown	OCLN	phosphorylation
CSNK2B	“up-regulates activity”	RNF7	phosphorylation
CSNK2B	“up-regulates activity”	SEC63	phosphorylation
CSNK2B	“up-regulates activity”	FGF14	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 159 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
MAPK targets/ Nuclear events mediated by MAP kinases	5	28.0×	2e-04
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known	8	24.8×	6e-07
MAP kinase activation	5	15.9×	1e-03
Transcriptional Regulation by E2F6	5	15.1×	1e-03
Interleukin-17 signaling	5	13.1×	2e-03
PTEN Regulation	5	11.8×	3e-03
Toll Like Receptor 10 (TLR10) Cascade	5	11.1×	3e-03
Toll Like Receptor 5 (TLR5) Cascade	5	11.1×	3e-03

GO biological processes:

GO term	Partners	Fold	FDR
negative regulation of proteasomal ubiquitin-dependent protein catabolic process	5	15.1×	4e-03
protein phosphorylation	11	5.6×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

195 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	53
Likely pathogenic	32
Uncertain significance	55
Likely benign	11
Benign	8

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1065509	NM_001320.7(CSNK2B):c.91C>T (p.Gln31Ter)	Pathogenic
1199211	NM_001320.7(CSNK2B):c.268dup (p.Thr90fs)	Pathogenic
1254603	NM_001320.7(CSNK2B):c.2T>G (p.Met1Arg)	Pathogenic
1299532	NM_001320.7(CSNK2B):c.472del (p.Tyr158fs)	Pathogenic
1301884	NM_001320.7(CSNK2B):c.367+1G>A	Pathogenic
1320202	NM_001320.7(CSNK2B):c.332G>C (p.Arg111Pro)	Pathogenic
1329627	NM_001320.7(CSNK2B):c.557+1G>A	Pathogenic
1343861	NM_001320.7(CSNK2B):c.474C>G (p.Tyr158Ter)	Pathogenic
1676313	NM_001320.7(CSNK2B):c.374C>G (p.Ser125Ter)	Pathogenic
1676324	NM_001320.7(CSNK2B):c.94G>C (p.Asp32His)	Pathogenic
1679612	NM_001320.7(CSNK2B):c.349C>T (p.Gln117Ter)	Pathogenic
1684046	NM_001320.7(CSNK2B):c.304C>T (p.Gln102Ter)	Pathogenic
1685680	NM_001320.7(CSNK2B):c.94G>T (p.Asp32Tyr)	Pathogenic
1690342	NM_001320.7(CSNK2B):c.107T>C (p.Leu36Pro)	Pathogenic
1701847	NM_001320.7(CSNK2B):c.495_496del (p.Met166fs)	Pathogenic
1712706	NM_001320.7(CSNK2B):c.286C>T (p.Gln96Ter)	Pathogenic
2285081	NM_001320.7(CSNK2B):c.464_467del (p.Asp155fs)	Pathogenic
2446135	NM_001320.7(CSNK2B):c.27G>A (p.Trp9Ter)	Pathogenic
2500355	NM_001320.7(CSNK2B):c.310G>T (p.Gly104Ter)	Pathogenic
2504917	NM_001320.7(CSNK2B):c.307C>T (p.Gln103Ter)	Pathogenic
2579310	NM_001320.7(CSNK2B):c.368G>A (p.Gly123Asp)	Pathogenic
2581063	NM_001320.7(CSNK2B):c.124C>T (p.Gln42Ter)	Pathogenic
2583035	NM_001320.7(CSNK2B):c.192del (p.Asp64fs)	Pathogenic
2656412	NM_001320.7(CSNK2B):c.13G>T (p.Glu5Ter)	Pathogenic
3024534	NM_001320.7(CSNK2B):c.95A>C (p.Asp32Ala)	Pathogenic
3027351	NM_001320.7(CSNK2B):c.59_62dup (p.Phe21fs)	Pathogenic
3254741	NM_001320.7(CSNK2B):c.408C>G (p.Tyr136Ter)	Pathogenic
3336864	NM_001320.7(CSNK2B):c.367+1G>C	Pathogenic
3342385	NM_001320.7(CSNK2B):c.409T>C (p.Cys137Arg)	Pathogenic
3342386	NM_001320.7(CSNK2B):c.558-2A>G	Pathogenic

SpliceAI

1379 predictions. Top by Δscore:

Variant	Effect	Δscore
6:31666160:G:GT	donor_gain	1.0000
6:31666205:GCCG:G	donor_gain	1.0000
6:31666206:CCGGT:C	donor_loss	1.0000
6:31666207:CGG:C	donor_loss	1.0000
6:31666207:CGGT:C	donor_loss	1.0000
6:31666208:GGT:G	donor_loss	1.0000
6:31666209:G:GG	donor_gain	1.0000
6:31666210:T:G	donor_loss	1.0000
6:31666816:TCTA:T	acceptor_loss	1.0000
6:31666818:TA:T	acceptor_loss	1.0000
6:31666818:TAGCT:T	acceptor_loss	1.0000
6:31666819:A:AG	acceptor_gain	1.0000
6:31666819:A:G	acceptor_loss	1.0000
6:31666819:AGCT:A	acceptor_gain	1.0000
6:31666819:AGCTG:A	acceptor_loss	1.0000
6:31666820:G:A	acceptor_loss	1.0000
6:31666820:G:GA	acceptor_gain	1.0000
6:31666820:GC:G	acceptor_gain	1.0000
6:31666820:GCT:G	acceptor_gain	1.0000
6:31666820:GCTG:G	acceptor_gain	1.0000
6:31666820:GCTGA:G	acceptor_gain	1.0000
6:31666822:T:A	acceptor_gain	1.0000
6:31666899:GTGAA:G	donor_gain	1.0000
6:31666900:TG:T	donor_gain	1.0000
6:31666900:TGAA:T	donor_gain	1.0000
6:31666900:TGAAG:T	donor_loss	1.0000
6:31666901:GAA:G	donor_gain	1.0000
6:31666901:GAAG:G	donor_gain	1.0000
6:31666902:AAGT:A	donor_loss	1.0000
6:31666903:AGTG:A	donor_loss	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000010643 (6:31669921 C>T), RS1000552968 (6:31665533 C>T), RS1000896848 (6:31665677 C>A), RS1002874034 (6:31670103 G>A), RS1003888690 (6:31666216 T>C), RS1004534017 (6:31665009 C>T), RS1004541573 (6:31668958 A>C), RS1006213953 (6:31667323 G>T), RS1006217739 (6:31669538 A>G), RS1006330748 (6:31669740 A>G), RS1007344306 (6:31665940 T>C), RS1007360459 (6:31665770 T>G), RS1007503753 (6:31668431 C>T), RS1008014949 (6:31668889 G>A), RS1008074035 (6:31666602 T>C)

Disease associations

OMIM: gene MIM:115441 | disease phenotypes: MIM:618732, MIM:176700

GenCC curated gene-disease

Disease	Classification	Inheritance
Poirier-Bienvenu neurodevelopmental syndrome	Definitive	Autosomal dominant
autosomal dominant non-syndromic intellectual disability	Supportive	Autosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
Poirier-Bienvenu neurodevelopmental syndrome	Definitive	AD

Mondo (8): Poirier-Bienvenu neurodevelopmental syndrome (MONDO:0032889), autosomal dominant non-syndromic intellectual disability (MONDO:0015802), neurodevelopmental disorder (MONDO:0700092), autism spectrum disorder (MONDO:0005258), intellectual disability (MONDO:0001071), enophthalmos (MONDO:0001210), autosomal dominant prognathism (MONDO:0008312), syndactyly (MONDO:0021002)

Orphanet (5): Poirier-Bienvenu neurodevelopmental syndrome (Orphanet:689397), Autosomal dominant non-syndromic intellectual disability (Orphanet:178469), Autosomal dominant prognathism (Orphanet:2964), NON RARE IN EUROPE: Autism (Orphanet:106), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

10 total (12 of 10 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000194	Open mouth
HP:0000303	Mandibular prognathia
HP:0000319	Smooth philtrum
HP:0001249	Intellectual disability
HP:0001290	Generalized hypotonia
HP:0002714	Downturned corners of mouth
HP:0010808	Protruding tongue
HP:0031936	Delayed ability to walk
HP:0032794	Myoclonic seizure
HP:0000490	Deeply set eye
HP:0001159	Syndactyly

GWAS associations

27 associations (top):

Study	Trait	p-value
GCST002884_5	Cutaneous lupus erythematosus	3.000000e-14
GCST003103_7	Systemic lupus erythematosus	8.000000e-08
GCST004131_25	Inflammatory bowel disease	2.000000e-31
GCST004133_79	Ulcerative colitis	5.000000e-65
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_126	Autism spectrum disorder or schizophrenia	2.000000e-10
GCST004521_154	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST004521_17	Autism spectrum disorder or schizophrenia	2.000000e-12
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_213	Autism spectrum disorder or schizophrenia	5.000000e-13
GCST004521_224	Autism spectrum disorder or schizophrenia	5.000000e-10
GCST004521_227	Autism spectrum disorder or schizophrenia	4.000000e-12
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_281	Autism spectrum disorder or schizophrenia	5.000000e-09
GCST004521_45	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_81	Autism spectrum disorder or schizophrenia	1.000000e-14
GCST008916_111	Asthma	2.000000e-14
GCST008916_114	Asthma	1.000000e-09
GCST008916_30	Asthma	1.000000e-09
GCST008917_2	Asthma (childhood onset)	4.000000e-07
GCST008921_1	Asthma and major depressive disorder	2.000000e-16
GCST010725_43	Malaria	5.000000e-07
GCST010725_62	Malaria	3.000000e-06
GCST90020028_1148	Hip circumference adjusted for BMI	4.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008039	BMI-adjusted hip circumference

MeSH disease descriptors (5)

Descriptor	Name	Tree numbers
D015841	Enophthalmos	C11.675.319
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D008313	Malocclusion, Angle Class III	C07.793.494.650
D065886	Neurodevelopmental Disorders	F03.625
D013576	Syndactyly	C05.116.099.370.894.819; C05.660.585.800; C05.660.906.819; C16.131.621.585.800; C16.131.621.906.819

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (6): CHEMBL2095191 (PROTEIN COMPLEX GROUP), CHEMBL2358 (SINGLE PROTEIN), CHEMBL3038477 (PROTEIN COMPLEX), CHEMBL3832943 (PROTEIN FAMILY), CHEMBL3883328 (PROTEIN COMPLEX), CHEMBL3885539 (PROTEIN COMPLEX)

Molecules with ChEMBL bioactivity

14 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 353,495 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

Molecule	Name	Phase	Patents
CHEMBL189963	PALBOCICLIB	4	13,102
CHEMBL58	MITOXANTRONE	4	166,878
CHEMBL50	QUERCETIN	3	74,559
CHEMBL3265032	ENTOSPLETINIB	3	1,628
CHEMBL1230165	SILMITASERTIB	2	593
CHEMBL31574	FISETIN	2	7,745
CHEMBL6246	ELLAGIC ACID	2	23,148
CHEMBL1232461	MOLIBRESIB	2	1,538
CHEMBL105442	CI-1040	2	3,936
CHEMBL151	LUTEOLIN	2	23,523
CHEMBL1738758	ONVANSERTIB	2	780
CHEMBL8260	BAICALEIN	2	8,592
CHEMBL83628	CHROMOCARB	2	1,533
CHEMBL150	KAEMPFEROL	1	25,940

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Casein kinase 2 (CK2) family

Binding affinities (BindingDB)

5 measured of 916 human assays (916 total across all organisms); most potent 5 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value	Patent
US9303033, Q47, Table 58A, Compound 14	IC50	3740 nM	US-9303033: Pyrazolopyrimidines and related heterocycles as CK2 inhibitors
US9303033, N47, Table 58A, Compound 11	IC50	3820 nM	US-9303033: Pyrazolopyrimidines and related heterocycles as CK2 inhibitors
BDBM220085	IC50	4730 nM	US-9303033: Pyrazolopyrimidines and related heterocycles as CK2 inhibitors
US9303033, D49, Table 59A, Compound 14	IC50	19700 nM	US-9303033: Pyrazolopyrimidines and related heterocycles as CK2 inhibitors
US9303033, P48, Table 58A, Compound 39	IC50	31600 nM	US-9303033: Pyrazolopyrimidines and related heterocycles as CK2 inhibitors

ChEMBL bioactivities

855 potent at pChembl≥5 of 981 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
10.08	Ki	0.084	nM	CHEMBL5419810
9.66	Ki	0.22	nM	SILMITASERTIB
9.64	IC50	0.23	nM	CHEMBL4848224
9.52	IC50	0.3	nM	SILMITASERTIB
9.42	Ki	0.38	nM	SILMITASERTIB
9.40	IC50	0.4	nM	CHEMBL1934184
9.38	Ki	0.42	nM	CHEMBL4846181
9.38	Ki	0.42	nM	CHEMBL1682283
9.34	IC50	0.46	nM	CHEMBL4862003
9.30	IC50	0.5	nM	CHEMBL1934172
9.30	IC50	0.5	nM	CHEMBL1934181
9.30	IC50	0.5	nM	CHEMBL1934182
9.22	IC50	0.6	nM	CHEMBL4872225
9.22	IC50	0.6	nM	CHEMBL1934180
9.21	IC50	0.61	nM	CHEMBL4875513
9.18	IC50	0.66	nM	CHEMBL4860630
9.12	IC50	0.76	nM	CHEMBL4848072
9.10	IC50	0.79	nM	CHEMBL4875815
9.05	IC50	0.89	nM	CHEMBL4878998
9.00	IC50	1	nM	CHEMBL3103191
9.00	IC50	1	nM	CHEMBL1652710
9.00	IC50	1	nM	SILMITASERTIB
9.00	IC50	1	nM	CHEMBL1934166
9.00	IC50	1	nM	CHEMBL1934318
8.96	IC50	1.1	nM	CHEMBL1934160
8.92	IC50	1.2	nM	CHEMBL1934173
8.89	IC50	1.3	nM	CHEMBL1934164
8.81	IC50	1.54	nM	SILMITASERTIB
8.77	IC50	1.7	nM	CHEMBL4649511
8.75	IC50	1.78	nM	CHEMBL4857079
8.74	IC50	1.8	nM	SILMITASERTIB
8.70	IC50	2	nM	CHEMBL2017356
8.70	IC50	2	nM	CHEMBL2409175
8.68	IC50	2.1	nM	CHEMBL1934319
8.64	IC50	2.3	nM	CHEMBL1682283
8.60	Ki	2.5	nM	CHEMBL5421618
8.57	IC50	2.7	nM	CHEMBL1934165
8.54	IC50	2.9	nM	CHEMBL1934163
8.52	IC50	3	nM	SILMITASERTIB
8.52	IC50	3	nM	CHEMBL1652704
8.52	IC50	3	nM	CHEMBL1652738
8.52	IC50	3	nM	CHEMBL1682283
8.48	IC50	3.3	nM	CHEMBL5276409
8.46	IC50	3.5	nM	CHEMBL4637423
8.46	IC50	3.43	nM	CHEMBL4857107
8.46	IC50	3.5	nM	CHEMBL1934171
8.46	IC50	3.5	nM	CHEMBL1934178
8.43	IC50	3.7	nM	SILMITASERTIB
8.43	IC50	3.7	nM	CHEMBL1934193
8.40	IC50	4	nM	CHEMBL2017324

PubChem BioAssay actives

691 with measured affinity, of 2169 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
(2S)-6-amino-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2S)-3-carboxy-2-[[(2R)-3-carboxy-2-[8-(4,5,6,7-tetraiodobenzimidazol-1-yl)octanoylamino]propanoyl]amino]propanoyl]amino]propanoyl]amino]propanoyl]amino]propanoyl]amino]propanoyl]amino]hexanoic acid	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0001	uM
2-fluoroethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0002	uM
5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ki	0.0002	uM
5-(3-cyanoanilino)pyrimido[4,5-c]quinoline-8-carboxylic acid	1750468: Inhibition of CK2 (unknown origin)	ki	0.0004	uM
5-(5-chlorothiophen-2-yl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0004	uM
5-(3-ethynylanilino)pyrimido[4,5-c]quinoline-8-carboxylic acid	2028056: Binding affinity to CK2 (unknown origin) assessed as inhibition constant	ki	0.0004	uM
5-thiophen-3-ylbenzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0005	uM
5-(4-chlorophenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0005	uM
5-(4-chlorophenyl)-3-(ethylamino)pyrimido[4,5-c]quinoline-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0005	uM
5-(3-chloroanilino)-N-(2-morpholin-4-ylethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0005	uM
2,2-difluoroethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0006	uM
2-hydroxyethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0006	uM
3-(cyclopropylamino)-5-phenylpyrimido[4,5-c]quinoline-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0006	uM
5-(3-chloroanilino)-N-(2-hydroxyethyl)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0007	uM
2-iodoethyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0008	uM
methyl 3-[[5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carbonyl]amino]propanoate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0008	uM
N-(2-aminoethyl)-5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0009	uM
5-(4-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	566117: Inhibition of human recombinant CK2 assessed as inhibition of [gamma33P]ATP incorporation into substrate by luminescence assay	ic50	0.0010	uM
5-(3-hydroxyphenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0010	uM
5-(3-chlorophenyl)sulfanylbenzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0010	uM
N-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-[2-(dimethylamino)ethyl-methylamino]phenyl]acetamide	1301598: Inhibition of CK2 in human DLD1 HA-myr-AKT1 cells assessed as suppression of AKTser129 phosphorylation after 3 to 24 hrs by Western blot analysis	ic50	0.0010	uM
5-phenylbenzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0011	uM
5-(4-fluorophenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0012	uM
5-(3-fluorophenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0013	uM
5-[[8-(hydroxyamino)-8-oxooctyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid;2,2,2-trifluoroacetic acid	1652189: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate preincubated for 30 mins followed by substrate addition and measured after 60 mins by ADP-Glo kinase assay	ic50	0.0017	uM
N-(2-bromoethyl)-5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxamide	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0018	uM
N-(3-ethynylphenyl)-6-(1H-1,2,4-triazol-5-yl)thieno[3,2-c]quinolin-4-amine	657060: Inhibition of human recombinant CK2 (alphaalpha-betabeta) holoenzyme using RRRDDDSDDD as substrate and 15 uM ATP by radiometric assay	ic50	0.0020	uM
N-[5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]-2-methylphenyl]acetamide	1301598: Inhibition of CK2 in human DLD1 HA-myr-AKT1 cells assessed as suppression of AKTser129 phosphorylation after 3 to 24 hrs by Western blot analysis	ic50	0.0020	uM
5-[(3-chlorophenyl)methyl]benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0021	uM
4-(6,8-dibromo-3-hydroxy-4-oxochromen-2-yl)benzoic acid	2028061: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate incubated for 20 mins in presence of [gamma-32p]-ATP and ATP by beta-counter analysis	ki	0.0025	uM
5-(3-aminophenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0027	uM
5-(3-chlorophenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0029	uM
5-(2-phenylethylamino)benzo[c][2,6]naphthyridine-8-carboxylic acid	566117: Inhibition of human recombinant CK2 assessed as inhibition of [gamma33P]ATP incorporation into substrate by luminescence assay	ic50	0.0030	uM
5-(3-cyanoanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	566117: Inhibition of human recombinant CK2 assessed as inhibition of [gamma33P]ATP incorporation into substrate by luminescence assay	ic50	0.0030	uM
(2Z)-7-bromo-2-[(3-bromo-4-hydroxyphenyl)methylidene]-1-benzofuran-3-one	1934407: Inhibition of recombinant human CK2 using RRRDDDSDDD as substrate in presence of [gamma-33P-ATP] incubated for 20 mins by beta-counter analysis	ic50	0.0033	uM
3,3-dichloropropyl 5-(3-chloroanilino)benzo[c][2,6]naphthyridine-8-carboxylate	1750390: Inhibition of human CK2 incubated for 2 hrs	ic50	0.0034	uM
5-[[6-(hydroxyamino)-6-oxohexyl]amino]benzo[c][2,6]naphthyridine-8-carboxylic acid;2,2,2-trifluoroacetic acid	1652189: Inhibition of human recombinant CK2 using RRRDDDSDDD peptide as substrate preincubated for 30 mins followed by substrate addition and measured after 60 mins by ADP-Glo kinase assay	ic50	0.0035	uM
5-(3-carbamoylphenyl)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0035	uM
5-(3-hydroxyphenyl)pyrimido[4,5-c]quinoline-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0035	uM
5-(3-chlorophenoxy)benzo[c][2,6]naphthyridine-8-carboxylic acid	637248: Inhibition of human recombinant CK2alpha/CK2beta using RRRDDDSDDD peptide as substrate by radiometric assay	ic50	0.0037	uM
N-[2-[[(2R)-2-aminopropyl]-methylamino]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]acetamide	1301598: Inhibition of CK2 in human DLD1 HA-myr-AKT1 cells assessed as suppression of AKTser129 phosphorylation after 3 to 24 hrs by Western blot analysis	ic50	0.0040	uM
N-[2-[[(2S)-2-aminopropyl]-methylamino]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]acetamide	1301598: Inhibition of CK2 in human DLD1 HA-myr-AKT1 cells assessed as suppression of AKTser129 phosphorylation after 3 to 24 hrs by Western blot analysis	ic50	0.0040	uM
6,8-dibromo-2-(4-hydroxy-3-methoxyphenyl)chromen-4-one	779046: Inhibition of recombinant human CK2 using RRRDDDSDDD as substrate after 20 mins by beta counting analysis in presence of [gamma-labeled 32P]ATP	ic50	0.0040	uM
3-[(6-methyl-5-phenylthieno[2,3-d]pyrimidin-4-yl)amino]benzoic acid	1294149: Competitive inhibition of recombinant human CK2 holoenzyme by Lineweaver-Burk plot analysis	ki	0.0040	uM
5-(3-methoxyanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	566117: Inhibition of human recombinant CK2 assessed as inhibition of [gamma33P]ATP incorporation into substrate by luminescence assay	ic50	0.0040	uM
5-(3-chloro-4-fluoroanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	566117: Inhibition of human recombinant CK2 assessed as inhibition of [gamma33P]ATP incorporation into substrate by luminescence assay	ic50	0.0040	uM
5-(4-phenoxyanilino)benzo[c][2,6]naphthyridine-8-carboxylic acid	566117: Inhibition of human recombinant CK2 assessed as inhibition of [gamma33P]ATP incorporation into substrate by luminescence assay	ic50	0.0040	uM
N-(2-fluorophenyl)-6-(1H-1,2,4-triazol-5-yl)thieno[3,2-c]quinolin-4-amine	657060: Inhibition of human recombinant CK2 (alphaalpha-betabeta) holoenzyme using RRRDDDSDDD as substrate and 15 uM ATP by radiometric assay	ic50	0.0040	uM
3-amino-5-(3-chloroanilino)pyrimido[4,5-c]quinoline-8-carboxylic acid	579515: Inhibition of human recombinant CK2 by radiometric assay	ic50	0.0040	uM
N-[2-[2-aminoethyl(methyl)amino]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]acetamide	1301598: Inhibition of CK2 in human DLD1 HA-myr-AKT1 cells assessed as suppression of AKTser129 phosphorylation after 3 to 24 hrs by Western blot analysis	ic50	0.0040	uM

CTD chemical–gene interactions

30 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression, affects expression	2
sodium arsenite	decreases expression, increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
FR900359	decreases phosphorylation	1
multi-kinase inhibitor 108600	decreases reaction, affects binding	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, increases reaction	1
di-n-butylphosphoric acid	affects expression	1
chromium hexavalent ion	increases expression	1
nickel acetate	affects expression	1
silmitasertib	affects binding, decreases reaction, decreases activity	1
Temozolomide	increases expression	1
Adenosine Triphosphate	affects binding, decreases reaction	1
Air Pollutants, Occupational	affects expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases expression	1
Capsaicin	increases phosphorylation	1
Cisplatin	increases expression	1
Doxorubicin	increases expression	1
Ivermectin	decreases expression	1
Lead	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	affects binding	1
Selenium	increases expression	1
Smoke	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Vitamin E	increases expression	1

ChEMBL screening assays

421 unique, capped per target: 419 binding, 2 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL1020723	Binding	Inhibition of human CK2 at 10 umol/L	Design, synthesis, and evaluation of indolinones as triple angiokinase inhibitors and the discovery of a highly specific 6-methoxycarbonyl-substituted indolinone (BIBF 1120). — J Med Chem
CHEMBL620984	Functional	Inhibition of CK-II-mediated 60S acidic ribosomal P protein activity at 10 uM	Casein kinase II inhibitors isolated from two Brazilian plants Hymenaea parvifolia and Wulffia baccata. — Bioorg Med Chem Lett

Clinical trials (associated diseases)

202 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT04586348	PHASE4	UNKNOWN	Prenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115	PHASE4	UNKNOWN	Double-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102	PHASE3	COMPLETED	Dexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079	PHASE3	COMPLETED	Study of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480	PHASE3	RECRUITING	Reducing Missed Appointments
NCT07377032	PHASE3	RECRUITING	TAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959	PHASE2	COMPLETED	Sulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348	PHASE2	RECRUITING	Sertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372	PHASE2	COMPLETED	Safety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191	PHASE1	COMPLETED	NeuroModulation Technique Treatment of Autism
NCT04475848	PHASE1	COMPLETED	A Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398	PHASE1	COMPLETED	IAMA-6 Oral Dose Study in Healthy Adults
NCT01783041	PHASE2/PHASE3	COMPLETED	Effect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385	PHASE2/PHASE3	RECRUITING	Fetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098	EARLY_PHASE1	NOT_YET_RECRUITING	Central Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783	Not specified	COMPLETED	CYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504	Not specified	RECRUITING	Studying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784	Not specified	UNKNOWN	High Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791	Not specified	COMPLETED	Nutrition and Pregnancy Intervention Study
NCT01942525	Not specified	UNKNOWN	Influence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170	Not specified	COMPLETED	Etiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649	Not specified	ACTIVE_NOT_RECRUITING	Enhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191	Not specified	TERMINATED	Biomarkers, Neurodevelopment and Preterm Infants
NCT02690675	Not specified	COMPLETED	Iron Supplement Effect on Child Development
NCT02694003	Not specified	COMPLETED	Better Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894	Not specified	COMPLETED	Family Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674	Not specified	UNKNOWN	Good Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157	Not specified	COMPLETED	Analyzing Retinal Microanatomy in ROP
NCT02898298	Not specified	COMPLETED	Positive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780	Not specified	UNKNOWN	Introduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293	Not specified	COMPLETED	n-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644	Not specified	COMPLETED	Improving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991	Not specified	UNKNOWN	Early Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189	Not specified	TERMINATED	Effect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028	Not specified	COMPLETED	Developmental Origins of Mental Health Disorders
NCT03148782	Not specified	COMPLETED	Brain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104	Not specified	COMPLETED	Neurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375	Not specified	RECRUITING	SQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928	Not specified	COMPLETED	Clinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489	Not specified	UNKNOWN	Study for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice