Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	1460
Gene name	Casein kinase 2 beta
Gene symbol	CSNK2B
Synonyms (NCBI Gene)	CK2BCK2NCSK2BCkb1Ckb2G5APOBINDS
Chromosome	6
Chromosome location	6p21.33
Summary	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

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1562050885	G>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1583608433	G>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1583608557	C>-	Pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (13)

miRTarBase ID	miRNA	Experiments
MIRT912886	hsa-miR-1224-3p	CLIP-seq
MIRT912887	hsa-miR-1260	CLIP-seq
MIRT912888	hsa-miR-1260b	CLIP-seq
MIRT912889	hsa-miR-1279	CLIP-seq
MIRT912890	hsa-miR-1280	CLIP-seq
MIRT912891	hsa-miR-188-3p	CLIP-seq
MIRT912892	hsa-miR-3156-3p	CLIP-seq
MIRT912893	hsa-miR-3938	CLIP-seq
MIRT912894	hsa-miR-4659a-3p	CLIP-seq
MIRT912895	hsa-miR-4659b-3p	CLIP-seq
MIRT912896	hsa-miR-4775	CLIP-seq
MIRT2206523	hsa-miR-4766-5p	CLIP-seq
MIRT2206524	hsa-miR-488	CLIP-seq

Show/Hide all (1)

Transcription factor	Regulation	Reference
ETS1	Unknown	11389726

Show/Hide all (52)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	IDA	31341047
GO:0001650	Component	Fibrillar center	IDA
GO:0003682	Function	Chromatin binding	IDA	25519132
GO:0004674	Function	Protein serine/threonine kinase activity	IDA	15723517
GO:0004674	Function	Protein serine/threonine kinase activity	TAS	1856204, 28031292
GO:0005102	Function	Signaling receptor binding	IPI	19233263, 19592636
GO:0005515	Function	Protein binding	IPI	10094392, 11574463, 12769847, 14667819, 16977309, 19011756, 20664522, 21078624, 21282530, 21900206, 21968188, 21988832, 23455922, 23555304, 24535599, 25519132, 25852190, 26496610, 26562092, 26711270, 27705803, 29997244, 31980649, 32296183, 32707033, 32814053, 33961781, 35271311, 368
GO:0005576	Component	Extracellular region	TAS
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005634	Component	Nucleus	IDA	21282530
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	19233263
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IDA	19233263
GO:0005956	Component	Protein kinase CK2 complex	IBA
GO:0005956	Component	Protein kinase CK2 complex	IDA	15723517
GO:0005956	Component	Protein kinase CK2 complex	IEA
GO:0005956	Component	Protein kinase CK2 complex	IPI	22506723
GO:0005956	Component	Protein kinase CK2 complex	ISS
GO:0005956	Component	Protein kinase CK2 complex	NAS	2666134
GO:0007165	Process	Signal transduction	TAS	2513884
GO:0008285	Process	Negative regulation of cell population proliferation	TAS	19324893
GO:0016055	Process	Wnt signaling pathway	IEA
GO:0016605	Component	PML body	IDA	20719947
GO:0018107	Process	Peptidyl-threonine phosphorylation	IDA	15723517
GO:0019046	Process	Release from viral latency	IDA	31341047, 34893887
GO:0019887	Function	Protein kinase regulator activity	IBA
GO:0019887	Function	Protein kinase regulator activity	IEA
GO:0019887	Function	Protein kinase regulator activity	NAS	2666134
GO:0019904	Function	Protein domain specific binding	IPI	11984006
GO:0030674	Function	Protein-macromolecule adaptor activity	IDA	31341047
GO:0031519	Component	PcG protein complex	IDA	21282530
GO:0032435	Process	Negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IDA	28031292
GO:0032927	Process	Positive regulation of activin receptor signaling pathway	IMP	19592636
GO:0033211	Process	Adiponectin-activated signaling pathway	IDA	19233263
GO:0034774	Component	Secretory granule lumen	TAS
GO:0042802	Function	Identical protein binding	IPI	10094392, 14667819, 21282530, 21988832, 23555304
GO:0043537	Process	Negative regulation of blood vessel endothelial cell migration	IDA	19592636
GO:0046872	Function	Metal ion binding	IEA
GO:0060391	Process	Positive regulation of SMAD protein signal transduction	IDA	19592636
GO:0061154	Process	Endothelial tube morphogenesis	IMP	19592636
GO:0061629	Function	RNA polymerase II-specific DNA-binding transcription factor binding	IPI	19324893
GO:0065003	Process	Protein-containing complex assembly	NAS	19324893
GO:0070062	Component	Extracellular exosome	HDA	20458337
GO:0075342	Process	Symbiont-mediated disruption of host cell PML body	IDA	20719947
GO:0075342	Process	Symbiont-mediated disruption of host cell PML body	IDA	20719947
GO:1903901	Process	Negative regulation of viral life cycle	IDA	31341047
GO:1903901	Process	Negative regulation of viral life cycle	IDA	31341047
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

MIM	HGNC	e!Ensembl
115441	2460	ENSG00000204435

P67870

Protein name

Casein kinase II subunit beta (CK II beta) (Phosvitin) (Protein G5a)

Protein 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 contai

PDB

1DS5 , 1JWH , 1QF8 , 3EED , 4DGL , 4MD7 , 4MD8 , 4MD9 , 4NH1 , 6Q38

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01214	CK_II_beta	8 → 191	Casein kinase II regulatory subunit	Domain

Sequence

MSSSEEVSWISWFCGLRGNEFFCEVDEDYIQDKFNLTGLNEQVPHYRQALDMILDLEPDE
ELEDNPNQSDLIEQAAEMLYGLIHARYILTNRGIAQMLEKYQQGDFGYCPRVYCENQPML
PIGLSDIPGEAMVKLYCPKCMDVYTPKSSRHHHTDGAYFGTGFPHMLFMVHPEYRPKRPA
NQFVPRLYGFKIHPMAYQLQLQAASNFKSPVKTIR

Sequence length

215

Interactions

View interactions

	KEGG		Reactome
	Ribosome biogenesis in eukaryotes Polycomb repressive complex NF-kappa B signaling pathway Mitophagy - animal Wnt signaling pathway Adherens junction Alzheimer disease Prion disease Pathways of neurodegeneration - multiple diseases Measles PD-L1 expression and PD-1 checkpoint pathway in cancer		Synthesis of PC WNT mediated activation of DVL Condensation of Prometaphase Chromosomes Signal transduction by L1 Neutrophil degranulation Regulation of TP53 Activity through Phosphorylation Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding Receptor Mediated Mitophagy RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known Regulation of PTEN stability and activity

112

Show/Hide Causal Diseases (15)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism spectrum disorder	Likely pathogenic	rs1801761541	RCV003127240
Autosomal dominant non-syndromic intellectual disability	Likely pathogenic	rs2151182244	RCV002052288
CSNK2B-related disorder	Likely pathogenic; Pathogenic	rs2536958403, rs1085307703, rs1554169984	RCV003397265 RCV003942606 RCV003411469
CSNK2B-related intellectual disability with or without epilepsy	Pathogenic	rs2151187292	RCV001563630
Developmental delay	Likely pathogenic	rs1583610622	RCV000845042
Intellectual disability	Likely pathogenic	rs1583610622	RCV000845042
Intellectual disability and seizures	Pathogenic	rs1131692161	RCV000495848
Intellectual disability-craniodigital syndrome	Pathogenic	rs1554169984	RCV002221707
Medulloblastoma WNT activated	Likely pathogenic; Pathogenic	rs1801961640	RCV006254257
Melanoma	Likely pathogenic	rs2151187350	RCV005925734
Neurodevelopmental disorder	Pathogenic; Likely pathogenic	rs2151188957, rs2151188789	RCV002277651 RCV002277666
Nonpapillary renal cell carcinoma	Likely pathogenic; Pathogenic	rs2536958403	RCV005932755
Poirier-Bienvenu neurodevelopmental syndrome	Likely pathogenic; Pathogenic	rs1802000298, rs2151185359, rs2151188896, rs2151188416, rs2151188333, rs2151185341, rs1802055133, rs2151189840, rs2151188903, rs2151182244, rs2151187350, rs2151188756, rs2151188371, rs1802001080, rs2151187172 View all (32 more)	RCV001331966 RCV001376051 RCV001730004 RCV001733825 RCV001775375 RCV001775388 RCV002255105 RCV001808922 RCV001825158 RCV006249774 RCV002052288 RCV002071022 RCV002221700 RCV002227636 RCV002468656 RCV002246197 RCV002249016 RCV002249017 RCV002249847 RCV004770436 RCV004596533 RCV002289423 RCV002290076 RCV002468693 RCV003143862 RCV003149116 RCV003225013 RCV004796791 RCV003330297 RCV004798041 RCV003885419 RCV004594924 RCV002468581 RCV000993566 RCV003448326 RCV004797842 RCV003139949 RCV002221588 RCV000993565 RCV000993567 RCV000993568 RCV000993570 RCV001003349 RCV004726946 RCV001249833 RCV001253734 RCV001261948 RCV001732100 RCV004796398 RCV002246284
See cases	Likely pathogenic; Pathogenic	rs1802026476	RCV001291643
Seizure	Likely pathogenic	rs1583610622	RCV000845042

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Familial prostate cancer	Uncertain significance	rs2151189797	RCV005920726

Show/Hide Text Mining Associations (27)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Body Dysmorphic Disorders	Associate	35205321
Breast Neoplasms	Associate	25486430, 27527857
Carcinoma Hepatocellular	Associate	36157211, 36617978
Cholangiocarcinoma	Associate	23828693
Colorectal Neoplasms	Associate	16207476
Congenital Abnormalities	Associate	34983633
Developmental Disabilities	Associate	31784560, 34041744, 34983633, 40317201
Distal myopathy Nonaka type	Associate	34983633
Drug Resistant Epilepsy	Associate	27094248, 34983633
Endometrial Neoplasms	Associate	19056846
Epilepsy	Associate	31784560, 34041744, 35205321, 40211296
Facial Dysmorphism with Multiple Malformations	Associate	34983633
Hypoxia	Associate	37020036
Intellectual Disability	Associate	31784560, 34041744, 34983633, 35205321, 36833176, 40211296, 40317201
Learning Disabilities	Associate	34041744
Mohr Tranebjaerg syndrome	Associate	27094248
Muscle Hypotonia	Associate	34983633
Neoplasm Invasiveness	Stimulate	25541719
Neoplasms	Associate	23828693
Polydactyly Postaxial	Associate	34983633
Polythelia Familial	Associate	34983633
Scott Bryant Graham syndrome	Associate	34983633, 36833176
Seizures	Associate	31784560, 34041744, 36833176, 40211296, 40317201
Status Epilepticus	Associate	34041744
Syndrome	Associate	35205321, 36833176
Triple Negative Breast Neoplasms	Associate	27276707
Vascular Diseases	Associate	35205321

CSNK2B (casein kinase 2 beta)