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

Gene ID: 5130, updated on 10-Dec-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
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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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 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
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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

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

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