PCYT1A Gene

Name	phosphate cytidylyltransferase 1, choline, alpha
Description	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]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nPCYT1A encodes the rate‐limiting enzyme CTP:phosphocholine cytidylyltransferase‐α, which is essential for the de novo biosynthesis of phosphatidylcholine (PC), a major component of cellular membranes. Functional studies show that loss‐of‐function mutations in PCYT1A disrupt PC production and underlie diverse human disorders. For example, biallelic mutations have been linked to spondylometaphyseal dysplasia with cone–rod dystrophy, congenital lipodystrophy with severe fatty liver, low HDL cholesterol levels, and even isolated retinal dystrophy, highlighting its critical role in both skeletal, metabolic, and visual system homeostasis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "4"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAt the molecular level, PCYT1A activity is tightly regulated through interactions with cellular membranes and through conformational changes that are modulated by phosphorylation events. Detailed in vitro studies reveal that the enzyme’s catalytic domain and membrane‐binding regions undergo structural transitions—mediated by changes in phosphorylation status and membrane association—that are essential for its activation. In stressed or nutrient‐deprived states, such as during autophagy or in response to lung injury, PCYT1A is upregulated to replenish PC pools needed for the formation and maintenance of organelle membranes, including those of autophagosomes, thereby preserving cellular homeostasis."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "5", "end_ref": "10"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its catalytic role in PC synthesis, genetic and epigenetic studies implicate PCYT1A in broader developmental and pathological processes. Polymorphisms in this gene have been associated with a reduced risk of nonsyndromic cleft lip with or without cleft palate, as well as with maternal complications such as intrauterine fetal death and altered serum betaine levels. Moreover, altered expression of PCYT1A—resulting from promoter hypermethylation—has been observed in conditions such as polycystic ovary syndrome, while in lung adenocarcinoma high PCYT1A expression correlates with suppressed mTORC1 signaling and less aggressive tumor behavior. These findings emphasize that PCYT1A not only drives essential membrane lipid synthesis but also plays a key role in regulating cellular metabolism and growth in a tissue‐ and context‐specific manner."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "11", "end_ref": "15"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Guilherme L Yamamoto, Wagner A R Baratela, Tatiana F Almeida, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations in PCYT1A cause spondylometaphyseal dysplasia with cone-rod dystrophy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Hum Genet (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ajhg.2013.11.022"}], "href": "https://doi.org/10.1016/j.ajhg.2013.11.022"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24387991"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24387991"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Felicity Payne, Koini Lim, Amandine Girousse, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations disrupting the Kennedy phosphatidylcholine pathway in humans with congenital lipodystrophy and fatty liver disease."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1408523111"}], "href": "https://doi.org/10.1073/pnas.1408523111"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24889630"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24889630"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Rosemary B Cornell, Neale D Ridgway "}, {"type": "b", "children": [{"type": "t", "text": "CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Prog Lipid Res (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.plipres.2015.07.001"}], "href": "https://doi.org/10.1016/j.plipres.2015.07.001"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26165797"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26165797"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Francesco Testa, Mariaelena Filippelli, Raffaella Brunetti-Pierri, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations in the PCYT1A gene are responsible for isolated forms of retinal dystrophy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur J Hum Genet (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ejhg.2017.23"}], "href": "https://doi.org/10.1038/ejhg.2017.23"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28272537"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28272537"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Lian Li, Li Shen, Hua She, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nitric oxide-induced activation of NF-κB-mediated NMDA-induced CTP:phosphocholine cytidylyltransferase alpha expression inhibition in A549 cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Cell Biol Toxicol (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s10565-010-9168-0"}], "href": "https://doi.org/10.1007/s10565-010-9168-0"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20661636"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20661636"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Rosemary B Cornell, Svetla G Taneva, Melissa K Dennis, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Disease-linked mutations in the phosphatidylcholine regulatory enzyme CCTα impair enzymatic activity and fold stability."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.RA118.006457"}], "href": "https://doi.org/10.1074/jbc.RA118.006457"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30559292"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30559292"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Svetla G Taneva, Jaeyong Lee, Daniel G Knowles, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Interdomain communication in the phosphatidylcholine regulatory enzyme, CCTα, relies on a modular αE helix."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.RA119.009849"}], "href": "https://doi.org/10.1074/jbc.RA119.009849"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31488547"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31488547"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Daniel G Knowles, Jaeyong Lee, Svetla G Taneva, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Remodeling of the interdomain allosteric linker upon membrane binding of CCTα pulls its active site close to the membrane surface."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.RA119.009850"}], "href": "https://doi.org/10.1074/jbc.RA119.009850"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31488548"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31488548"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Gabriela Andrejeva, Sharon Gowan, Gigin Lin, et al. "}, {"type": "b", "children": [{"type": "a", "children": [{"type": "t", "text": "i"}], "href": "i"}, {"type": "t", "text": "De novo"}, {"type": "a", "children": [{"type": "t", "text": "/i"}], "href": "/i"}, {"type": "t", "text": " phosphatidylcholine synthesis is required for autophagosome membrane formation and maintenance during autophagy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Autophagy (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/15548627.2019.1659608"}], "href": "https://doi.org/10.1080/15548627.2019.1659608"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "31517566"}], "href": "https://pubmed.ncbi.nlm.nih.gov/31517566"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Lambert Yue, Michael J McPhee, Kevin Gonzalez, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Biol Cell (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1091/mbc.E20-01-0014"}], "href": "https://doi.org/10.1091/mbc.E20-01-0014"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32186954"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32186954"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Adrianna Mostowska, Kamil K Hozyasz, Barbara Biedziak, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Eur J Oral Sci (2010)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1111/j.1600-0722.2010.00757.x"}], "href": "https://doi.org/10.1111/j.1600-0722.2010.00757.x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20662904"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20662904"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Krzysztof Drews, Agata Różycka, Magdalena Barlik, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Polymorphic variants of genes involved in choline pathway and the risk of intrauterine fetal death."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Ginekol Pol (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.5603/GP.a2017.0039"}], "href": "https://doi.org/10.5603/GP.a2017.0039"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28509322"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28509322"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Agata Chmurzynska, Agnieszka Seremak-Mrozikiewicz, Anna M Malinowska, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PEMT rs12325817 and PCYT1A rs7639752 polymorphisms are associated with betaine but not choline concentrations in pregnant women."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nutr Res (2018)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.nutres.2018.04.018"}], "href": "https://doi.org/10.1016/j.nutres.2018.04.018"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30055775"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30055775"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "Jing Yu, Changtao Wu, Qi Wu, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PCYT1A suppresses proliferation and migration via inhibiting mTORC1 pathway in lung adenocarcinoma."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Biochem Biophys Res Commun (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.bbrc.2020.05.164"}], "href": "https://doi.org/10.1016/j.bbrc.2020.05.164"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32703435"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32703435"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Zhanrui Mao, Ting Li, Hui Zhao, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Methylome and transcriptome profiling revealed epigenetic silencing of LPCAT1 and PCYT1A associated with lipidome alterations in polycystic ovary syndrome."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Cell Physiol (2021)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1002/jcp.30309"}], "href": "https://doi.org/10.1002/jcp.30309"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "33521992"}], "href": "https://pubmed.ncbi.nlm.nih.gov/33521992"}]}]}]}
Synonyms	SMDCRD, CTA, PCYT1, CTPCT, CCTA
Proteins	PCY1A_HUMAN
NCBI Gene ID	5130
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PCYT1A has 8,952 functional associations with biological entities spanning 9 categories (molecular profile, organism, functional term, phrase or reference, disease, phenotype or trait, chemical, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 128 datasets.

Click the + buttons to view associations for PCYT1A from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PCYT1A Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PCYT1A gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of PCYT1A gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PCYT1A gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of PCYT1A gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PCYT1A gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	Biocarta Pathways	pathways involving PCYT1A protein from the Biocarta Pathways dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of PCYT1A gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PCYT1A gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PCYT1A gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of PCYT1A gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of PCYT1A gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with PCYT1A protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with PCYT1A gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PCYT1A gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PCYT1A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of PCYT1A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations	phenotypes associated with PCYT1A gene from the curated ClinVar Gene-Phenotype Associations dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of PCYT1A gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PCYT1A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing PCYT1A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing PCYT1A protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with PCYT1A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with PCYT1A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of PCYT1A gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PCYT1A gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with PCYT1A gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with PCYT1A gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of PCYT1A protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving PCYT1A gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving PCYT1A gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PCYT1A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with PCYT1A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with PCYT1A gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with PCYT1A gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	DrugBank Drug Targets	interacting drugs for PCYT1A protein from the curated DrugBank Drug Targets dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at PCYT1A gene from the ENCODE Histone Modification Site Profiles dataset.
	ENCODE Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PCYT1A gene from the ENCODE Transcription Factor Binding Site Profiles dataset.
	ENCODE Transcription Factor Targets	transcription factors binding the promoter of PCYT1A gene in ChIP-seq datasets from the ENCODE Transcription Factor Targets dataset.
	ESCAPE Omics Signatures of Genes and Proteins for Stem Cells	PubMedIDs of publications reporting gene signatures containing PCYT1A from the ESCAPE Omics Signatures of Genes and Proteins for Stem Cells dataset.
	GAD Gene-Disease Associations	diseases associated with PCYT1A gene in GWAS and other genetic association datasets from the GAD Gene-Disease Associations dataset.