CHKB (choline kinase beta)

Gene

• Entrez ID: 1120
• Gene name: Choline kinase beta
• Gene symbol: CHKB
• Synonyms (NCBI Gene): CHETK, CHKL, CK, CKB, CKEKB, EK, EKB, MDCMC
• Chromosome: 22
• Chromosome location: 22q13.33
• Summary: Choline kinase (CK) and ethanolamine kinase (EK) catalyze the phosphorylation of choline/ethanolamine to phosphocholine/phosphoethanolamine. This is the first enzyme in the biosynthesis of phosphatidylcholine/phosphatidylethanolamine in all animal cells.

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT440947	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT440947	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT2200076	hsa-miR-3664-3p	CLIP-seq
MIRT2200077	hsa-miR-510	CLIP-seq
MIRT2200078	hsa-miR-873	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004103	Function	Choline kinase activity	IBA
GO:0004103	Function	Choline kinase activity	IDA	19915674
GO:0004103	Function	Choline kinase activity	IEA
GO:0004305	Function	Ethanolamine kinase activity	IBA
GO:0004305	Function	Ethanolamine kinase activity	IDA	19915674
GO:0004305	Function	Ethanolamine kinase activity	IEA
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IBA
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IDA	19915674
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IEA
GO:0006656	Process	Phosphatidylcholine biosynthetic process	IEA
GO:0006657	Process	CDP-choline pathway	IBA
GO:0007517	Process	Muscle organ development	IEA
GO:0008654	Process	Phospholipid biosynthetic process	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA

Other IDs

• MIM: 612395
• HGNC: 1938
• e!Ensembl: ENSG00000100288

Protein

• UniProt ID: Q9Y259
• Protein name: Choline/ethanolamine kinase (Choline kinase beta) (CK) (CKB) (EC 2.7.1.32) (Choline kinase-like protein) (Ethanolamine kinase) (EK) (EC 2.7.1.82) (Ethanolamine kinase beta) (EKB) (choline/ethanolamine kinase beta) (CKEKB)
• Protein function: Has a key role in phospholipid metabolism, and catalyzes the first step of phosphatidylethanolamine and phosphatidylcholine biosynthesis.
• PDB: 2IG7, 3FEG, 3LQ3
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01633	Choline_kinase	97 → 308		Family

• Sequence:

  MAAEATAVAGSGAVGGCLAKDGLQQSKCPDTTPKRRRASSLSRDAERRAYQWCREYLGGA
  WRRVQPEELRVYPVSGGLSNLLFRCSLPDHLPSVGEEPREVLLRLYGAILQGVDSLVLES
  VMFAILAERSLGPQLYGVFPEGRLEQYIPSRPLKTQELREPVLSAAIATKMAQFHGMEMP
  FTKEPHWLFGTMERYLKQIQDLPPTGLPEMNLLEMYSLKDEMGNLRKLLESTPSPVVFCH
  NDIQEGNILLLSEPENADSLMLVDFEYSSYNYRGFDIGNHFCEWVYDYTHEEWPFYKARP
  TDYPTQEQQLHFIRHYLAEAKKGETLSQEEQRKLEEDLLVEVSRYALASHFFWGLWSILQ
  ASMSTIEFGYLDYAQSRFQFYFQQKGQLTSVHSSS

• Sequence length: 395

Pathways

KEGG:

Glycerophospholipid metabolism
Metabolic pathways
Choline metabolism in cancer

Reactome:

Synthesis of PC
Synthesis of PE

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
CHKB-related disorder	Pathogenic	rs750764003	RCV004755750	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Megaconial type congenital muscular dystrophy	Pathogenic; Likely pathogenic	rs2146652075, rs80067609, rs2146653379, rs2146656234, rs1045370021, rs139059552, rs2146653193, rs771681297, rs786205118, rs1252318649, rs772568756, rs2522778329, rs2522775487, rs2522784063, rs2522783978, rs2522785657, rs1346110970, rs1406122283, rs2070708365, rs2522789883, rs371751084, rs750764003, rs387907068, rs786205117, rs387907069, rs373091820, rs1333100080, rs1555894289, rs1569054508, rs752436924, rs1569054086, rs757369551	RCV001388730 RCV001385174 RCV001542808 RCV001808876 RCV001928889 RCV002007590 RCV001946948 RCV001909114 RCV003090230 RCV002510642 RCV003031054 RCV003126383 RCV003126384 RCV003526487 RCV003526498 RCV003641813 RCV003640419 RCV003640599 RCV003641876 RCV003834060 RCV000329772 RCV000023942 RCV000023943 RCV000023944 RCV000023945 RCV000023946 RCV001255615 RCV000532491 RCV000644791 RCV000706926 RCV000779377 RCV000785116 RCV000791740	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Muscular dystrophy	Likely pathogenic	rs2146656742	RCV001795875	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Congenital Muscular Dystrophy, CHKB-related	Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL MYOPATHY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CUTANEOUS LEISHMANIASIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NARCOLEPSY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Seizure	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Severe global developmental delay	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
CAMPOMELIC DYSPLASIA	Campomelic Dysplasia	BEFREE	26067811		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	25022454, 25988710		★☆☆☆☆ Found in Text Mining only
Cardiomyopathy, Dilated	Cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	BEFREE	23945283, 25187204, 26067811, 26782016, 30791960, 30986505		★☆☆☆☆ Found in Text Mining only
Congenital muscular dystrophy (disorder)	Congenital muscular dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
CRANIOMETAPHYSEAL DYSPLASIA, AUTOSOMAL DOMINANT	Craniometaphyseal Dysplasia	BEFREE	26067811		★☆☆☆☆ Found in Text Mining only
Cytochrome c Oxidase Deficiency	Cytochrome c oxidase deficiency	Pubtator	22782513	Associate	★☆☆☆☆ Found in Text Mining only
Cytochrome-c Oxidase Deficiency	Cytochrome-C Oxidase Deficiency	BEFREE	22782513		★☆☆☆☆ Found in Text Mining only
Eczema	Eczema	Pubtator	27123443	Associate	★☆☆☆☆ Found in Text Mining only
Facial paralysis	Facial paralysis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypersomnia	Hypersomnia	BEFREE	19404393		★☆☆☆☆ Found in Text Mining only
Ichthyoses	Ichthyosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	26006750		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	26067811, 26782016		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lung Neoplasms	Lung neoplasms	Pubtator	25022454	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	25022454, 25988710		★☆☆☆☆ Found in Text Mining only
Megaconial congenital muscular dystrophy	Megaconial Congenital Muscular Dystrophy	Orphanet			★☆☆☆☆ Found in Text Mining only
Megaconial Myopathies	Megaconial Myopathies	BEFREE	26006750		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mitochondrial Myopathies	Mitochondrial myopathy	Pubtator	22782513	Associate	★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy	Muscular dystrophy	BEFREE	23692895, 25740612, 26548592		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Muscular Dystrophy	Muscular dystrophy	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Muscular Dystrophy, Congenital, Megaconial Type	Congenital Muscular Dystrophy	GENOMICS_ENGLAND_DG	16371353, 26782016, 27604308, 30986505		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Congenital, Megaconial Type	Congenital Muscular Dystrophy	CLINVAR_DG	21665002		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Congenital, Megaconial Type	Congenital Muscular Dystrophy	ORPHANET_DG	21665002, 22782513		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Congenital, Megaconial Type	Congenital Muscular Dystrophy	UNIPROT_DG	21665002, 22782513, 24997086, 25187204, 26006750, 26067811		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Congenital, Megaconial Type	Congenital Muscular Dystrophy	BEFREE	24997086, 26006750, 31216357		★☆☆☆☆ Found in Text Mining only
Muscular Dystrophy, Congenital, Megaconial Type	Congenital Muscular Dystrophy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Myopathy	Myopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	BEFREE	18820697, 21285061, 22177342, 24571861		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Narcolepsy	Narcolepsy	CTD_human_DG	18820697		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Narcolepsy	Narcolepsy	Pubtator	19404393, 24571861	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Narcolepsy-Cataplexy Syndrome	Narcolepsy-Cataplexy Syndrome	CTD_human_DG	18820697		★☆☆☆☆ Found in Text Mining only
Narcolepsy-Cataplexy Syndrome	Narcolepsy-Cataplexy Syndrome	BEFREE	19404393		★☆☆☆☆ Found in Text Mining only
Neonatal Hypotonia	Hypotonia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	16046538		★☆☆☆☆ Found in Text Mining only
Proximal Myopathy with Focal Depletion of Mitochondria	Proximal Myopathy With Focal Depletion Of Mitochondria	BEFREE	26782016, 30791960		★☆☆☆☆ Found in Text Mining only
Proximal Myopathy with Focal Depletion of Mitochondria	Proximal Myopathy With Focal Depletion Of Mitochondria	ORPHANET_DG	26782016, 27169979		★☆☆☆☆ Found in Text Mining only
Proximal myopathy with focal depletion of mitochondria	Proximal Myopathy With Focal Depletion Of Mitochondria	Orphanet			★☆☆☆☆ Found in Text Mining only
Pruritus	Pruritus	Pubtator	27123443	Associate	★☆☆☆☆ Found in Text Mining only
Restless Legs Syndrome	Restless Legs Syndrome	BEFREE	21285061		★☆☆☆☆ Found in Text Mining only
Sarcoma Experimental	Sarcoma	Pubtator	19404393	Associate	★☆☆☆☆ Found in Text Mining only
Skin Diseases	Skin disease	Pubtator	27123443	Associate	★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	22242139		★☆☆☆☆ Found in Text Mining only