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    PCYT1A phosphate cytidylyltransferase 1A, choline [ Homo sapiens (human) ]

    Gene ID: 5130, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PCYT1Aprovided by HGNC
    Official Full Name
    phosphate cytidylyltransferase 1A, cholineprovided by HGNC
    Primary source
    HGNC:HGNC:8754
    See related
    Ensembl:ENSG00000161217 MIM:123695; AllianceGenome:HGNC:8754
    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
    CT; CTA; CCTA; CGL5; CTPCT; PCYT1; SMDCRD; CCTalpha
    Summary
    This gene belongs to the cytidylyltransferase family and is involved in the regulation of phosphatidylcholine biosynthesis. Mutations in this gene are associated with spondylometaphyseal dysplasia with cone-rod dystrophy. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2015]
    Expression
    Ubiquitous expression in duodenum (RPKM 22.3), small intestine (RPKM 20.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PCYT1A in Genome Data Viewer
    Location:
    3q29
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (196234368..196287726, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (198953844..199007214, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (195961239..196014597, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909479 Neighboring gene uncharacterized LOC105374304 Neighboring gene Sharpr-MPRA regulatory region 7098 Neighboring gene solute carrier family 51 member A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21082 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:195973646-195974845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195990064-195990615 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:195990616-195991166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:195999955-196000454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21083 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196005871-196006483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196013420-196014080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:196014081-196014740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21086 Neighboring gene dynein light chain Tctex-type 2B Neighboring gene TM4SF19-DYNLT2B readthrough (NMD candidate) Neighboring gene uncharacterized LOC107986031 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15060 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21087 Neighboring gene TM4SF19 antisense RNA 1 Neighboring gene transmembrane 4 L six family member 19

    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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    Related articles in PubMed

    1. Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy. Hoover-Fong J, et al. Am J Hum Genet, 2014 Jan 2. PMID 24387990, Free PMC Article
    2. Does rat liver Golgi have the capacity to synthesize phospholipids for lipoprotein secretion? Vance JE, et al. J Biol Chem, 1988 Apr 25. PMID 2833521
    3. Membrane-binding amphipathic alpha-helical peptide derived from CTP:phosphocholine cytidylyltransferase. Johnson JE, et al. Biochemistry, 1994 Apr 12. PMID 8155650
    4. PCYT1A suppresses proliferation and migration via inhibiting mTORC1 pathway in lung adenocarcinoma. Yu J, et al. Biochem Biophys Res Commun, 2020 Aug 20. PMID 32703435
    5. Mutations in the PCYT1A gene are responsible for isolated forms of retinal dystrophy. Testa F, et al. Eur J Hum Genet, 2017 May. PMID 28272537, Free PMC Article

    See all (66) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Methylome and transcriptome profiling revealed epigenetic silencing of LPCAT1 and PCYT1A associated with lipidome alterations in polycystic ovary syndrome.
      Title: Methylome and transcriptome profiling revealed epigenetic silencing of LPCAT1 and PCYT1A associated with lipidome alterations in polycystic ovary syndrome.
    2. De novo phosphatidylcholine synthesis is required for autophagosome membrane formation and maintenance during autophagy.
      Title: De novo phosphatidylcholine synthesis is required for autophagosome membrane formation and maintenance during autophagy.
    3. PCYT1A suppresses proliferation and migration via inhibiting mTORC1 pathway in lung adenocarcinoma.
      Title: PCYT1A suppresses proliferation and migration via inhibiting mTORC1 pathway in lung adenocarcinoma.
    4. Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets.
      Title: Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets.
    5. The membrane-adsorbed, folded allosteric linker of CCTA may partially cover the active site cleft and pull it close to the membrane surface.
      Title: Remodeling of the interdomain allosteric linker upon membrane binding of CCTα pulls its active site close to the membrane surface.
    6. CCTA activation by membrane binding is sensitive to mutations in the alphaE and J segments, especially within or proximal to the alphaE hinge.
      Title: Interdomain communication in the phosphatidylcholine regulatory enzyme, CCTα, relies on a modular αE helix.
    7. Our study shows that choline intake in Polish pregnant women is inadequate and that polymorphisms of PEMT rs12325817 and PCYT1A rs7639752 are associated with betaine but not choline concentrations.
      Title: PEMT rs12325817 and PCYT1A rs7639752 polymorphisms are associated with betaine but not choline concentrations in pregnant women.
    8. Mutations in PCYT1A gene is associated with impaired enzyme kinetics and folding resulting in lipodystrophy, spondylometaphyseal dysplasia with cone-rod dystrophy, and isolated retinal dystrophy
      Title: Disease-linked mutations in the phosphatidylcholine regulatory enzyme CCTα impair enzymatic activity and fold stability.
    9. There is no correlation between single PCYT1A rs712012 and PCYT1A rs7639752 polymorphisms and the incidence of intrauterine fetal death.
      Title: Polymorphic variants of genes involved in choline pathway and the risk of intrauterine fetal death.
    10. PCYT1A mutations were identified in patients with isolated retinal dystrophy without any skeletal involvement from two Italian families.
      Title: Mutations in the PCYT1A gene are responsible for isolated forms of retinal dystrophy.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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
    Lipodystrophy, congenital generalized, type 5
    MedGen: C5882745 OMIM: 620680 GeneReviews: Not available
    		not available
    Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
    MedGen: C1837073 OMIM: 608940 GeneReviews: Not available
    		Compare labs

    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 calmodulin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables choline-phosphate cytidylyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables choline-phosphate cytidylyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables choline-phosphate cytidylyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables molecular function inhibitor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylcholine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in B cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in CDP-choline pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in CDP-choline pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in isotype switching ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in phosphatidylcholine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in phosphatidylcholine biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in glycogen granule ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nuclear envelope IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    choline-phosphate cytidylyltransferase A
    Names
    CCT A
    CCT-alpha
    CT A
    CTP:phosphocholine cytidylyltransferase A
    CTP:phosphocholine cytidylyltransferase-alpha
    choline-phosphate cytidylyltransferase alpha
    phosphate cytidylyltransferase 1, choline, alpha
    phosphorylcholine transferase A
    phosphorylcholine transferase alpha
    NP_001299602.1
    NP_005008.2

    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_042817.2 RefSeqGene

      Range
      5000..58358
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001312673.2 → NP_001299602.1  choline-phosphate cytidylyltransferase A

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a 5' non-coding exon, thus has a shorter 5' UTR compared to variant 1. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC069257, AK304534, AK309073, DB223595, L28957
      Consensus CDS
      CCDS3315.1
      UniProtKB/Swiss-Prot
      A9LYK9, D3DXB1, P49585, Q86Y88
      UniProtKB/TrEMBL
      B2R8P1
      Related
      ENSP00000394617.1, ENST00000431016.6
      Conserved Domains (1) summary
      cd02174
      Location:75 → 224
      CCT; CTP:phosphocholine cytidylyltransferase

    2. NM_005017.4 → NP_005008.2  choline-phosphate cytidylyltransferase A

      See identical proteins and their annotated locations for NP_005008.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC069257, AK309073, BC046355, DB223595
      Consensus CDS
      CCDS3315.1
      UniProtKB/Swiss-Prot
      A9LYK9, D3DXB1, P49585, Q86Y88
      UniProtKB/TrEMBL
      B2R8P1
      Related
      ENSP00000292823.2, ENST00000292823.6
      Conserved Domains (1) summary
      cd02174
      Location:75 → 224
      CCT; CTP:phosphocholine cytidylyltransferase

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      196234368..196287726 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      198953844..199007214 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P49585.2 GenPept UniProtKB/Swiss-Prot:P49585

    Gene LinkOut

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

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