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Aliases for PCYT1A Gene

Aliases for PCYT1A Gene

  • Phosphate Cytidylyltransferase 1, Choline, Alpha 2 3 5
  • CTP:Phosphocholine Cytidylyltransferase A 3 4
  • Phosphorylcholine Transferase A 3 4
  • EC 4 63
  • CCT-Alpha 3 4
  • CCT A 3 4
  • PCYT1 3 4
  • CTPCT 3 4
  • CT A 3 4
  • Phosphate Cytidylyltransferase 1, Choline, Alpha Isoform 2
  • Phosphate Cytidylyltransferase 1 2
  • Alpha Isoform 2
  • EC 2.7.7 63
  • Choline 2
  • SMDCRD 3
  • CCTA 3
  • CTA 3
  • CT 3

External Ids for PCYT1A Gene

Previous HGNC Symbols for PCYT1A Gene

  • PCYT1

Previous GeneCards Identifiers for PCYT1A Gene

  • GC03M191886
  • GC03M196194
  • GC03M197368
  • GC03M197291
  • GC03M197453
  • GC03M195941
  • GC03M193264

Summaries for PCYT1A Gene

Entrez Gene Summary for PCYT1A Gene

  • 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]

GeneCards Summary for PCYT1A Gene

PCYT1A (Phosphate Cytidylyltransferase 1, Choline, Alpha) is a Protein Coding gene. Diseases associated with PCYT1A include Spondylometaphyseal Dysplasia With Cone-Rod Dystrophy and Cone-Rod Dystrophy. Among its related pathways are Glucose / Energy Metabolism and Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics. GO annotations related to this gene include protein homodimerization activity and choline-phosphate cytidylyltransferase activity. An important paralog of this gene is PCYT1B.

UniProtKB/Swiss-Prot for PCYT1A Gene

  • Controls phosphatidylcholine synthesis.

Gene Wiki entry for PCYT1A Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCYT1A Gene

Genomics for PCYT1A Gene

Regulatory Elements for PCYT1A Gene

Enhancers for PCYT1A Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCYT1A on UCSC Golden Path with GeneCards custom track

Promoters for PCYT1A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCYT1A on UCSC Golden Path with GeneCards custom track

Genomic Location for PCYT1A Gene

196,214,222 bp from pter
196,287,957 bp from pter
73,736 bases
Minus strand

Genomic View for PCYT1A Gene

Genes around PCYT1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCYT1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCYT1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCYT1A Gene

Proteins for PCYT1A Gene

  • Protein details for PCYT1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Choline-phosphate cytidylyltransferase A
    Protein Accession:
    Secondary Accessions:
    • A9LYK9
    • D3DXB1
    • Q86Y88

    Protein attributes for PCYT1A Gene

    367 amino acids
    Molecular mass:
    41731 Da
    Quaternary structure:
    • Homodimer.

neXtProt entry for PCYT1A Gene

Proteomics data for PCYT1A Gene at MOPED

Post-translational modifications for PCYT1A Gene

  • Monoubiquitinated by the SCF(FBXL2) complex, leading to proteasomal degradation.
  • The serine residues of the C-terminus are phosphorylated. The inactive soluble form is stabilized by phosphorylation, the active membrane bound form is promoted by anionic lipids or diacylglycerol, and is stabilized by dephosphorylation (By similarity).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for PCYT1A Gene

Protein Domains for PCYT1A Gene

Suggested Antigen Peptide Sequences for PCYT1A Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cytidylyltransferase family.
  • Belongs to the cytidylyltransferase family.
genes like me logo Genes that share domains with PCYT1A: view

No data available for Gene Families for PCYT1A Gene

Function for PCYT1A Gene

Molecular function for PCYT1A Gene

GENATLAS Biochemistry:
CTP phosphocholine cytidyltransferase,42kDa,including 2 isoforms alpha and beta,regulator of phosphatidylcholine
UniProtKB/Swiss-Prot CatalyticActivity:
CTP + phosphocholine = diphosphate + CDP-choline.
UniProtKB/Swiss-Prot EnzymeRegulation:
By phosphorylation.
UniProtKB/Swiss-Prot Function:
Controls phosphatidylcholine synthesis.

Enzyme Numbers (IUBMB) for PCYT1A Gene

Gene Ontology (GO) - Molecular Function for PCYT1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004105 choline-phosphate cytidylyltransferase activity ISS,TAS --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with PCYT1A: view
genes like me logo Genes that share phenotypes with PCYT1A: view

Human Phenotype Ontology for PCYT1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PCYT1A Gene

MGI Knock Outs for PCYT1A:

Animal Model Products

  • Taconic Biosciences Mouse Models for PCYT1A

CRISPR Products

No data available for Transcription Factor Targets and HOMER Transcription for PCYT1A Gene

Localization for PCYT1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCYT1A Gene

Cytoplasm, cytosol. Membrane; Peripheral membrane protein. Note=It can interconvert between an inactive cytosolic form and an active membrane-bound form. {ECO:0000250}.

Subcellular locations from

Jensen Localization Image for PCYT1A Gene COMPARTMENTS Subcellular localization image for PCYT1A gene
Compartment Confidence
cytosol 5
endoplasmic reticulum 5
nucleus 4
mitochondrion 1
plasma membrane 1

Gene Ontology (GO) - Cellular Components for PCYT1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042587 glycogen granule ISS --
genes like me logo Genes that share ontologies with PCYT1A: view

Pathways & Interactions for PCYT1A Gene

genes like me logo Genes that share pathways with PCYT1A: view

Pathways by source for PCYT1A Gene

UniProtKB/Swiss-Prot P49585-PCY1A_HUMAN

  • Pathway: Phospholipid metabolism; phosphatidylcholine biosynthesis; phosphatidylcholine from phosphocholine: step 1/2.

SIGNOR curated interactions for PCYT1A Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for PCYT1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006644 phospholipid metabolic process TAS --
GO:0006657 CDP-choline pathway ISS --
genes like me logo Genes that share ontologies with PCYT1A: view

Drugs & Compounds for PCYT1A Gene

(6) Drugs for PCYT1A Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Target, product of 139
Lamivudine Approved, Investigational Pharma Enzyme, substrate Nucleoside analog reverse transcriptase inhibitor 601
Cytidine triphosphate Experimental Pharma 0
Diphosphate Experimental Pharma 0
Phosphocholine Experimental Pharma 0

(15) Additional Compounds for PCYT1A Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Audes
  • CDP-Choline
  • Cereb
  • Choline 5'-cytidine diphosphate
  • Choline cytidine diphosphate
Diglycerides Group A
  • 1,2-Dimyristoyl-rac-glycerol
  • DAG(14:0/14:0)
  • DAG(28:0)
  • DG(14:0/14:0)
  • DG(28:0)
Diglycerides Group B
  • 1-Palmitoleoyl-2-arachidonyl-sn-glycerol
  • DAG(16:1/20:0)
  • DAG(16:1n7/20:0)
  • DAG(16:1w7/20:0)
  • DAG(36:1)
Diglycerides Group C
  • 1-Myristoyl-3-stearoyl-sn-glycerol
  • 1-Tetradecanoyl-3-octadecanoyl-sn-glycerol
  • DAG(14:0/0:0/18:0)
  • DAG(32:0)
  • DG(32:0)
genes like me logo Genes that share compounds with PCYT1A: view

Transcripts for PCYT1A Gene

Unigene Clusters for PCYT1A Gene

Phosphate cytidylyltransferase 1, choline, alpha:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PCYT1A Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c
SP1: - - - - -
SP2: - - - -
SP3: - - -
SP4: - - -
SP5: - - - - -
SP6: -
SP8: - - - -
SP9: -

Relevant External Links for PCYT1A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCYT1A Gene

mRNA expression in normal human tissues for PCYT1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PCYT1A Gene

This gene is overexpressed in Whole Blood (x4.3).

Protein differential expression in normal tissues from HIPED for PCYT1A Gene

This gene is overexpressed in Breast (52.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PCYT1A Gene

SOURCE GeneReport for Unigene cluster for PCYT1A Gene Hs.135997

genes like me logo Genes that share expression patterns with PCYT1A: view

Protein tissue co-expression partners for PCYT1A Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for PCYT1A Gene

Orthologs for PCYT1A Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PCYT1A Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PCYT1A 35
  • 91.87 (n)
  • 96.4 (a)
  • 86 (a)
(Canis familiaris)
Mammalia PCYT1A 35
  • 92.46 (n)
  • 96.46 (a)
  • 96 (a)
(Mus musculus)
Mammalia Pcyt1a 35
  • 89.74 (n)
  • 96.19 (a)
Pcyt1a 16
Pcyt1a 36
  • 96 (a)
(Pan troglodytes)
Mammalia PCYT1A 35
  • 99.84 (n)
  • 99.51 (a)
(Rattus norvegicus)
Mammalia Pcyt1a 35
  • 89.37 (n)
  • 96.46 (a)
(Monodelphis domestica)
Mammalia PCYT1A 36
  • 55 (a)
(Ornithorhynchus anatinus)
Mammalia PCYT1A 36
  • 54 (a)
(Gallus gallus)
Aves PCYT1A 35
  • 80.6 (n)
  • 89.34 (a)
  • 89 (a)
(Anolis carolinensis)
Reptilia PCYT1A 36
  • 88 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcyt1a 35
  • 76.2 (n)
  • 85.83 (a)
Str.1627 35
African clawed frog
(Xenopus laevis)
Amphibia pcyt1a-prov 35
(Danio rerio)
Actinopterygii pcyt1aa 35
  • 73.44 (n)
  • 81.04 (a)
pcyt1aa 36
  • 78 (a)
pcyt1ab 36
  • 75 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cct1 37
  • 57 (a)
Cct2 37
  • 57 (a)
Cct1 35
  • 63.21 (n)
  • 61.92 (a)
Cct1 36
  • 34 (a)
Cct2 36
  • 46 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002263 35
  • 56.61 (n)
  • 55.93 (a)
(Caenorhabditis elegans)
Secernentea F08C6.2 37
  • 47 (a)
F28A10.10 37
  • 46 (a)
Y18H1A.11 35
  • 54 (n)
  • 54.15 (a)
F28A10.10 36
  • 50 (a)
pcyt-1 36
  • 37 (a)
Y18H1A.11 36
  • 47 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PCT1 36
  • 31 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.5008 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9202 36
  • 54 (a)
Species with no ortholog for PCYT1A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PCYT1A Gene

Gene Tree for PCYT1A (if available)
Gene Tree for PCYT1A (if available)

Paralogs for PCYT1A Gene

Paralogs for PCYT1A Gene Pseudogenes for PCYT1A Gene

genes like me logo Genes that share paralogs with PCYT1A: view

Variants for PCYT1A Gene

Sequence variations from dbSNP and Humsavar for PCYT1A Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
VAR_071083 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)
VAR_071084 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)
VAR_071085 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)
VAR_071086 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)
VAR_071087 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD)

Structural Variations from Database of Genomic Variants (DGV) for PCYT1A Gene

Variant ID Type Subtype PubMed ID
dgv1549e1 CNV Complex 17122850
nsv878175 CNV Loss 21882294
dgv5372n71 CNV Gain 21882294
dgv5373n71 CNV Gain 21882294
nsv878182 CNV Loss 21882294
esv2658720 CNV Deletion 23128226
nsv518925 CNV Loss 19592680

Variation tolerance for PCYT1A Gene

Residual Variation Intolerance Score: 50.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.88; 35.07% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCYT1A Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCYT1A Gene

Disorders for PCYT1A Gene

MalaCards: The human disease database

(3) MalaCards diseases for PCYT1A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spondylometaphyseal dysplasia with cone-rod dystrophy
  • smd-crd
cone-rod dystrophy
  • cone-rod dystrophy 5
urethral stricture
- elite association - COSMIC cancer census association via MalaCards


  • Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940]: A disorder characterized by postnatal growth deficiency resulting in profound short stature, rhizomelia with bowing of the lower extremities, platyspondyly with anterior vertebral protrusions, progressive metaphyseal irregularity and cupping with shortened tubular bones, and early-onset progressive visual impairment associated with a pigmentary maculopathy and electroretinographic evidence of cone-rod dysfunction. {ECO:0000269 PubMed:24387990, ECO:0000269 PubMed:24387991}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PCYT1A

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PCYT1A: view

No data available for Genatlas for PCYT1A Gene

Publications for PCYT1A Gene

  1. Primary structure and expression of a human CTP:phosphocholine cytidylyltransferase. (PMID: 7918629) Kalmar G.B. … Cornell R.B. (Biochim. Biophys. Acta 1994) 2 3 4 67
  2. CHKA and PCYT1A gene polymorphisms, choline intake and spina bifida risk in a California population. (PMID: 17184542) Enaw J.O. … Finnell R.H. (BMC Med 2006) 3 25
  3. Distribution of CTP:phosphocholine cytidylyltransferase (CCT) isoforms. Identification of a new CCTbeta splice variant. (PMID: 10480912) Lykidis A. … Jackowski S. (J. Biol. Chem. 1999) 3 23
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  5. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. (PMID: 26496610) Hein M.Y. … Mann M. (Cell 2015) 3

Products for PCYT1A Gene

Sources for PCYT1A Gene