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CHKB choline kinase beta [ Homo sapiens (human) ]

Gene ID: 1120, updated on 14-Nov-2024

Summary

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Official Symbol
CHKBprovided by HGNC
Official Full Name
choline kinase betaprovided by HGNC
Primary source
HGNC:HGNC:1938
See related
Ensembl:ENSG00000100288 MIM:612395; AllianceGenome:HGNC:1938
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CK; EK; CKB; EKB; CHKL; CHETK; CKEKB; MDCMC
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. The highly purified CKs from mammalian sources and their recombinant gene products have been shown to have EK activity also, indicating that both activities reside on the same protein. The choline kinase-like protein encoded by CHKL belongs to the choline/ethanolamine kinase family; however, its exact function is not known. Read-through transcripts are expressed from this locus that include exons from the downstream CPT1B locus. [provided by RefSeq, Jun 2009]
Expression
Ubiquitous expression in spleen (RPKM 35.8), lymph node (RPKM 28.9) and 25 other tissues See more
Orthologs
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Genomic context

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See CHKB in Genome Data Viewer
Location:
22q13.33
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (50578963..50582849, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (51089491..51093377, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (51017392..51021278, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene synaptonemal complex central element protein 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:50999771-50999969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13997 Neighboring gene uncharacterized LOC107985568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19331 Neighboring gene CHKB-CPT1B readthrough (NMD candidate) Neighboring gene carnitine palmitoyltransferase 1B Neighboring gene Sharpr-MPRA regulatory region 1531 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13998 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13999 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14000 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14001 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14002 Neighboring gene CHKB divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:51039601-51040101 Neighboring gene mitogen-activated protein kinase 8 interacting protein 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:51047655-51048439

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Frameshift mutations of immunomodulatory BTN2A1, BTN2A2, and BTNL3 genes in colon cancers.
    Title: Frameshift mutations of immunomodulatory BTN2A1, BTN2A2, and BTNL3 genes in colon cancers.
  2. Megaconial congenital muscular dystrophy due to CHKB gene variants, the first report of thirteen Iranian patients.
    Title: Megaconial congenital muscular dystrophy due to CHKB gene variants, the first report of thirteen Iranian patients.
  3. Large heterozygous deletion and uniparental disomy masquerading as homozygosity in CHKB gene.
    Title: Large heterozygous deletion and uniparental disomy masquerading as homozygosity in CHKB gene.
  4. Megaconial congenital muscular dystrophy secondary to novel CHKB mutations resemble atypical Rett syndrome.
    Title: Megaconial congenital muscular dystrophy secondary to novel CHKB mutations resemble atypical Rett syndrome.
  5. Megaconial congenital muscular dystrophy: Same novel homozygous mutation in CHKB gene in two unrelated Chinese patients.
    Title: Megaconial congenital muscular dystrophy: Same novel homozygous mutation in CHKB gene in two unrelated Chinese patients.
  6. Alteration of mitochondrial membrane inner potential in three Italian patients with megaconial congenital muscular dystrophy carrying new mutations in CHKB gene.
    Title: Alteration of mitochondrial membrane inner potential in three Italian patients with megaconial congenital muscular dystrophy carrying new mutations in CHKB gene.
  7. findings suggest that CKbeta, in concert with CKalpha, and depending on its phosphorylation status, might play a critical role as a druggable target in carcinogenesis
    Title: Phosphorylation of Human Choline Kinase Beta by Protein Kinase A: Its Impact on Activity and Inhibition.
  8. The whole exome sequencing revealed a novel homozygous missense mutation in the Choline Kinase-Beta (CHKB) gene in exon 9.
    Title: Importance of Skin Changes in the Differential Diagnosis of Congenital Muscular Dystrophies.
  9. A new form of congenital muscular dystrophy with multisystem involvement and characteristic mitochondrial structural changes, due to choline kinase beta gene defects has been characterized.
    Title: Clinical characteristics of megaconial congenital muscular dystrophy due to choline kinase beta gene defects in a series of 15 patients.
  10. A novel silent variant in the choline kinase beta causing muscular dystrophy.
    Title: New splicing mutation in the choline kinase beta (CHKB) gene causing a muscular dystrophy detected by whole-exome sequencing.
Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Megaconial type congenital muscular dystrophy
MedGen: C1865233 OMIM: 602541 GeneReviews: CHKB-Related Muscular Dystrophy
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EBI GWAS Catalog

Description
Variant between CPT1B and CHKB associated with susceptibility to narcolepsy.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Readthrough CHKB-CPT1B

Readthrough gene: CHKB-CPT1B, Included gene: CPT1B

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables choline kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables choline kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ethanolamine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ethanolamine kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in CDP-choline pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in muscle organ development IEA
Inferred from Electronic Annotation
more info
  
involved_in phosphatidylethanolamine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in phosphatidylethanolamine biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphatidylethanolamine biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
choline/ethanolamine kinase
Names
choline kinase-like protein
ethanolamine kinase beta
NP_005189.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029213.1 RefSeqGene

    Range
    5001..9042
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_855

mRNA and Protein(s)

  1. NM_005198.5 → NP_005189.2  choline/ethanolamine kinase

    See identical proteins and their annotated locations for NP_005189.2

    Status: REVIEWED

    Source sequence(s)
    AB029886, BE676287
    Consensus CDS
    CCDS14099.1
    UniProtKB/Swiss-Prot
    A0PJM6, Q13388, Q9Y259
    Related
    ENSP00000384400.3, ENST00000406938.3
    Conserved Domains (2) summary
    PLN02236
    Location:57 → 388
    PLN02236; choline kinase
    cd05156
    Location:69 → 385
    ChoK_euk; Euykaryotic Choline Kinase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    50578963..50582849 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    51089491..51093377 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_152253.1: Suppressed sequence

    Description
    NM_152253.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y259.3 GenPept UniProtKB/Swiss-Prot:Q9Y259

Gene LinkOut

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