CSNK2B (casein kinase 2 beta)

Gene

• Entrez ID: 1460
• Gene name: Casein kinase 2 beta
• Gene symbol: CSNK2B
• Synonyms (NCBI Gene): CK2B, CK2N, CSK2B, Ckb1, Ckb2, G5A, POBINDS
• 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

SNPs

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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
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

Transcription factors

Transcription factor	Regulation	Reference
ETS1	Unknown	11389726

Gene ontology (GO)

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

Other IDs

• MIM: 115441
• HGNC: 2460
• e!Ensembl: ENSG00000204435

Protein

• UniProt ID: 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

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Autism spectrum disorder	Likely pathogenic	rs1801761541	RCV003127240	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Autosomal dominant non-syndromic intellectual disability	Likely pathogenic	rs2151182244	RCV002052288	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CSNK2B-related disorder	Likely pathogenic; Pathogenic	rs2536958403, rs1085307703, rs1554169984	RCV003397265 RCV003942606 RCV003411469	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CSNK2B-related intellectual disability with or without epilepsy	Pathogenic	rs2151187292	RCV001563630	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental delay	Likely pathogenic	rs1583610622	RCV000845042	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Likely pathogenic	rs1583610622	RCV000845042	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability and seizures	Pathogenic	rs1131692161	RCV000495848	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability-craniodigital syndrome	Pathogenic	rs1554169984	RCV002221707	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Medulloblastoma WNT activated	Likely pathogenic; Pathogenic	rs1801961640	RCV006254257	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Melanoma	Likely pathogenic	rs2151187350	RCV005925734	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neurodevelopmental disorder	Pathogenic; Likely pathogenic	rs2151188957, rs2151188789	RCV002277651 RCV002277666	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nonpapillary renal cell carcinoma	Likely pathogenic; Pathogenic	rs2536958403	RCV005932755	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Poirier-Bienvenu neurodevelopmental syndrome	Likely pathogenic; Pathogenic	rs1802000298, rs2151185359, rs2151188896, rs2151188416, rs2151188333, rs2151185341, rs1802055133, rs2151189840, rs2151188903, rs2151182244, rs2151187350, rs2151188756, rs2151188371, rs1802001080, rs2151187172, rs2151185431, rs2151187334, rs1554169984, rs2151188957, rs2151188789, rs2536957939, rs2536967921, rs2536971072, rs2151189070, rs2536963193, rs2536966071, rs2536966052, rs1339457069, rs2536958403, rs2536957931, rs2536967665, rs1085307703, rs1131692161, rs1554169462, rs1554169967, rs1583610622, rs1583605716, rs1583611843, rs1583613268, rs1583611290, rs1583610610, rs1801755635, rs1802000840, rs1802030746, rs1801761541, rs1801961640, rs1802026476	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	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Seizure	Likely pathogenic	rs1583610622	RCV000845042	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTISM SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, SQUAMOUS CELL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLASS III MALOCCLUSION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CLINODACTYLY OF TOE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTANEOUS LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKEMIA-LYMPHOMA, ADULT T-CELL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SKIN NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYNDACTYLY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYSTEMIC LUPUS ERYTHEMATOSUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenomatous Polyposis Coli	Multiple polyposis syndrome	LHGDN	11972058		★☆☆☆☆ Found in Text Mining only
Adult T-Cell Lymphoma/Leukemia	T-Cell Lymphoma/Leukemia	CTD_human_DG	26437031		★☆☆☆☆ Found in Text Mining only
Autosomal dominant non-syndromic intellectual disability	Non-Syndromic Intellectual Disability	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Breast Carcinoma	Breast Carcinoma	BEFREE	25837326		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	25486430, 27527857	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36157211, 36617978	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	29071797		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	BEFREE	23828693		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	23828693	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	16207476	Associate	★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Congenital abnormalities	Pubtator	34983633	Associate	★☆☆☆☆ Found in Text Mining only
Congenital contractural arachnodactyly	Congenital Contractural Arachnodactyly	BEFREE	23828693		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	31784560, 34041744, 34983633, 40317201	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	GWASDB_DG	17632545		★☆☆☆☆ Found in Text Mining only
Diffuse Large B-Cell Lymphoma	Diffuse Lymphoma	BEFREE	27276707		★☆☆☆☆ Found in Text Mining only
Distal myopathy Nonaka type	Distal myopathy	Pubtator	34983633	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial Neoplasms	LHGDN	19056846		★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	19056846	Associate	★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	BEFREE	31784560		★☆☆☆☆ Found in Text Mining only
Epilepsy	Epilepsy	Pubtator	31784560, 34041744, 35205321, 40211296	Associate	★☆☆☆☆ Found in Text Mining only
Facial Dysmorphism with Multiple Malformations	Facial dysmorphism syndrome	Pubtator	34983633	Associate	★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	30655572, 31784560		★☆☆☆☆ Found in Text Mining only
HEMIHYPERPLASIA, ISOLATED	Hemihyperplasia	BEFREE	28490073		★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	37020036	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	28585349, 30655572, 31784560		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual Disability	Intellectual developmental disorder	Pubtator	31784560, 34041744, 34983633, 35205321, 36833176, 40211296, 40317201	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Learning Disabilities	Learning disorders	Pubtator	34041744	Associate	★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	17143510		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Cutaneous	Lupus Erythematosus	GWASCAT_DG	25827949		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	GWASCAT_DG	26316170		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	25837326		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	29071797		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of skin	Skin cancer	CTD_human_DG	18572023		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	26388159		★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsy	Myoclonic Epilepsy	BEFREE	28585349		★☆☆☆☆ Found in Text Mining only
Neurodevelopmental Disorders	Neurodevelopmental Disorders	BEFREE	28585349, 30655572		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Polydactyly Postaxial	Polydactyly	Pubtator	34983633	Associate	★☆☆☆☆ Found in Text Mining only
Rheumatoid Arthritis	Rheumatoid arthritis	GWASDB_DG	21156761		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	BEFREE	29483533, 30446647		★☆☆☆☆ Found in Text Mining only
Seizures	Seizures	Pubtator	31784560, 34041744, 36833176, 40211296, 40317201	Associate	★☆☆☆☆ Found in Text Mining only
Skin Neoplasms	Skin Neoplasms	CTD_human_DG	18572023		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Squamous cell carcinoma	Carcinoma	CTD_human_DG	18572023		★☆☆☆☆ Found in Text Mining only
Status Epilepticus	Status epilepticus	Pubtator	34041744	Associate	★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple negative breast cancer	Pubtator	27276707	Associate	★☆☆☆☆ Found in Text Mining only
Vascular Diseases	Vascular disease	Pubtator	35205321	Associate	★☆☆☆☆ Found in Text Mining only