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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
    mouse all
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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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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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
    		not available

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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