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    CHKA choline kinase alpha [ Homo sapiens (human) ]

    Gene ID: 1119, updated on 2-May-2024

    Summary

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    Official Symbol
    CHKAprovided by HGNC
    Official Full Name
    choline kinase alphaprovided by HGNC
    Primary source
    HGNC:HGNC:1937
    See related
    Ensembl:ENSG00000110721 MIM:118491; AllianceGenome:HGNC:1937
    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; CHK; CKI; NEDMIMS
    Summary
    The major pathway for the biosynthesis of phosphatidylcholine occurs via the CDP-choline pathway. The protein encoded by this gene is the initial enzyme in the sequence and may play a regulatory role. The encoded protein also catalyzes the phosphorylation of ethanolamine. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 24.3), thyroid (RPKM 9.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    11q13.2
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (68052859..68121388, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68056500..68125033, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67820326..67888855, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67805851-67806472 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3657 Neighboring gene NADH:ubiquinone oxidoreductase core subunit S8 Neighboring gene microRNA 4691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67817396-67818388 Neighboring gene T cell immune regulator 1, ATPase H+ transporting V0 subunit a3 Neighboring gene microRNA 6753 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67834020-67834520 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67850572-67850749 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67861600-67861729 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67870988-67871188 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67886638-67887154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3658 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67888828-67889593 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67889594-67890360 Neighboring gene CHKA divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67907579-67907779 Neighboring gene lysine methyltransferase 5B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3661 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67981441-67982143

    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
    • 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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    Related articles in PubMed

    1. Bi-allelic variants in CHKA cause a neurodevelopmental disorder with epilepsy and microcephaly. Klöckner C, et al. Brain, 2022 Jun 30. PMID 35202461, Free PMC Article
    2. DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells. Mohamed Sa'dom SAF, et al. Genes (Basel), 2021 Jun 1. PMID 34205960, Free PMC Article
    3. [Knockdown of choline kinase α (CHKA) inhibits the proliferation, invasion and migration of human U87MG glioma cells]. Yue F, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2020 Aug. PMID 32958130
    4. Identification of a Unique Inhibitor-Binding Site on Choline Kinase α. Kall SL, et al. Biochemistry, 2018 Feb 27. PMID 29389115
    5. Choline Kinase α Mediates Interactions Between the Epidermal Growth Factor Receptor and Mechanistic Target of Rapamycin Complex 2 in Hepatocellular Carcinoma Cells to Promote Drug Resistance and Xenograft Tumor Progression. Lin XM, et al. Gastroenterology, 2017 Apr. PMID 28065789, Free PMC Article

    See all (71) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Correlation between choline kinase alpha expression and [11]C-choline accumulation in breast cancer using positron emission tomography/computed tomography: a retrospective study.
      Title: Correlation between choline kinase alpha expression and (11)C-choline accumulation in breast cancer using positron emission tomography/computed tomography: a retrospective study.
    2. Bi-allelic variants in CHKA cause a neurodevelopmental disorder with epilepsy and microcephaly.
      Title: Bi-allelic variants in CHKA cause a neurodevelopmental disorder with epilepsy and microcephaly.
    3. DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells.
      Title: DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells.
    4. Choline kinase alpha 2 acts as a protein kinase to promote lipolysis of lipid droplets.
      Title: Choline kinase alpha 2 acts as a protein kinase to promote lipolysis of lipid droplets.
    5. [Knockdown of choline kinase alpha (CHKA) inhibits the proliferation, invasion and migration of human U87MG glioma cells].
      Title: [Knockdown of choline kinase α (CHKA) inhibits the proliferation, invasion and migration of human U87MG glioma cells].
    6. During proliferation, KDM2B binds to the Box2 located in the Chka promoter repressing its transcription. KDM2B knockdown enhances the levels of CKalpha expression in neuroblast cells and induces neuronal differentiation. These results suggest that KDM2B is required for the appropriate regulation of CKalpha during neuronal differentiation and to the maintaining of the undifferentiated stage of neuroblast cells.
      Title: KDM2B regulates choline kinase expression and neuronal differentiation of neuroblastoma cells.
    7. miR-876-5p was able to significantly decrease the expression level of choline kinase alpha mRNA.
      Title: Downregulation of human choline kinase α gene expression by miR-876-5p.
    8. There is no correlation between single CHKA rs7928739 polymorphism and the incidence of intrauterine fetal death.
      Title: Polymorphic variants of genes involved in choline pathway and the risk of intrauterine fetal death.
    9. This study presents the detail the 2.35 A structure of choline kinase alpha in complex with inhibitor TCD-717.
      Title: Identification of a Unique Inhibitor-Binding Site on Choline Kinase α.
    10. Results indicate that choline kinase alpha (CHKA) contributes to tumor progression and metastasis and may serve as a prognostic biomarker and potential therapeutic target in colorectal carcinoma (CRC).
      Title: Overexpression of CHKA contributes to tumor progression and metastasis and predicts poor prognosis in colorectal carcinoma.
    Submit: New GeneRIF Correction See all GeneRIFs (50)

    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
    Neurodevelopmental disorder with microcephaly, movement abnormalities, and seizures
    MedGen: C5774208 OMIM: 620023 GeneReviews: Not available
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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

    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 cholinesterase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein tyrosine kinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in CDP-choline pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lipid metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in lipid transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in phosphatidylcholine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in lipid droplet IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    choline kinase alpha
    Names
    CHETK-alpha
    ethanolamine kinase
    NP_001268.2
    NP_001363148.1
    NP_001363149.1
    NP_001363150.1
    NP_001363151.1
    NP_997634.1
    XP_047282271.1
    XP_047282272.1
    XP_047282273.1
    XP_047282274.1
    XP_047282275.1
    XP_047282277.1
    XP_047282278.1
    XP_047282279.1
    XP_054223517.1
    XP_054223518.1
    XP_054223519.1
    XP_054223520.1
    XP_054223521.1
    XP_054223522.1

    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.

    mRNA and Protein(s)

    1. NM_001277.3 → NP_001268.2  choline kinase alpha isoform a

      See identical proteins and their annotated locations for NP_001268.2

      Status: REVIEWED

      Source sequence(s)
      BC036471, BG703955, BG723115, BI195927, BU617910, D10704
      Consensus CDS
      CCDS8178.1
      UniProtKB/Swiss-Prot
      P35790, Q8NE29
      Related
      ENSP00000265689.4, ENST00000265689.9
      Conserved Domains (1) summary
      cd05156
      Location:111 → 452
      ChoK_euk; Euykaryotic Choline Kinase

    2. NM_001376219.1 → NP_001363148.1  choline kinase alpha isoform c

      Status: REVIEWED

      Source sequence(s)
      AP002807, AP002992
      Conserved Domains (1) summary
      cd05156
      Location:111 → 462
      ChoK_euk; Euykaryotic Choline Kinase

    3. NM_001376220.1 → NP_001363149.1  choline kinase alpha isoform d

      Status: REVIEWED

      Source sequence(s)
      AP002807, AP002992
      Conserved Domains (1) summary
      cd05156
      Location:111 → 414
      ChoK_euk; Euykaryotic Choline Kinase

    4. NM_001376221.1 → NP_001363150.1  choline kinase alpha isoform e

      Status: REVIEWED

      Source sequence(s)
      AP002807, AP002992
      Conserved Domains (1) summary
      cd05156
      Location:1 → 330
      ChoK_euk; Euykaryotic Choline Kinase

    5. NM_001376222.1 → NP_001363151.1  choline kinase alpha isoform f

      Status: REVIEWED

      Source sequence(s)
      AP002807, AP002992
      Conserved Domains (1) summary
      cd05156
      Location:1 → 312
      ChoK_euk; Euykaryotic Choline Kinase

    6. NM_212469.2 → NP_997634.1  choline kinase alpha isoform b

      See identical proteins and their annotated locations for NP_997634.1

      Status: REVIEWED

      Source sequence(s)
      AP002807, AP002992
      Consensus CDS
      CCDS8179.1
      UniProtKB/Swiss-Prot
      P35790
      Related
      ENSP00000348454.4, ENST00000356135.9
      Conserved Domains (2) summary
      PLN02236
      Location:99 → 437
      PLN02236; choline kinase
      cd05156
      Location:111 → 434
      ChoK_euk; Euykaryotic Choline Kinase

    RNA

    1. NR_164782.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP002807, AP002992

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      68052859..68121388 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426315.1 → XP_047282271.1  choline kinase alpha isoform X1

    2. XM_047426316.1 → XP_047282272.1  choline kinase alpha isoform X2

    3. XM_047426317.1 → XP_047282273.1  choline kinase alpha isoform X3

    4. XM_047426318.1 → XP_047282274.1  choline kinase alpha isoform X4

    5. XM_047426321.1 → XP_047282277.1  choline kinase alpha isoform X5

    6. XM_047426322.1 → XP_047282278.1  choline kinase alpha isoform X6

    7. XM_047426319.1 → XP_047282275.1  choline kinase alpha isoform X5

    8. XM_047426323.1 → XP_047282279.1  choline kinase alpha isoform X7

    RNA

    1. XR_007062448.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      68056500..68125033 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054367542.1 → XP_054223517.1  choline kinase alpha isoform X1

    2. XM_054367543.1 → XP_054223518.1  choline kinase alpha isoform X2

    3. XM_054367544.1 → XP_054223519.1  choline kinase alpha isoform X3

    4. XM_054367545.1 → XP_054223520.1  choline kinase alpha isoform X4

    5. XM_054367546.1 → XP_054223521.1  choline kinase alpha isoform X5

    6. XM_054367547.1 → XP_054223522.1  choline kinase alpha isoform X7

    RNA

    1. XR_008488334.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P35790.3 GenPept UniProtKB/Swiss-Prot:P35790

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