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Aliases for PCYT1A Gene

Aliases for PCYT1A Gene

  • Phosphate Cytidylyltransferase 1, Choline, Alpha 2 3 5
  • Phosphate Cytidylyltransferase 1, Choline, Alpha Isoform 2 2
  • CTP:Phosphocholine Cytidylyltransferase A 3 4
  • Phosphorylcholine Transferase A 3 4
  • EC 4 61
  • CCT-Alpha 3 4
  • CCT A 3 4
  • PCYT1 3 4
  • CTPCT 3 4
  • CT A 3 4
  • Choline-Phosphate Cytidylyltransferase A 3
  • EC 2.7.7 61
  • 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 Jejunoileitis. Among its related pathways are Metabolism and Ca, cAMP and Lipid Signaling. 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F196272 1.6 FANTOM5 Ensembl ENCODE 31.1 +13.9 13925 3.2 TBP HDAC1 PKNOX1 CBX3 ATF1 CREB3L1 ZBTB40 YY1 CBX5 FOS PCYT1A TM4SF19 ENSG00000228028 RNU6-910P TCTEX1D2 RNF168 NRROS UBXN7
GH03F196218 1.4 FANTOM5 Ensembl ENCODE 25.5 +67.9 67862 3.4 MXI1 PKNOX1 SIN3A ARID4B MAX BMI1 EBF1 ZIC2 EGR1 POLR2A PCYT1A ZDHHC19 UBXN7 ENSG00000228028 RNU7-18P TFRC UBXN7-AS1 SLC51A RNF168 NRROS
GH03F196344 1 FANTOM5 Ensembl 20.2 -57.1 -57144 1.4 POLR2A SMAD5 THRAP3 ZBTB33 GLI4 TM4SF19 PCYT1A SDHAP2 UBXN7 RNF168 NRROS GC03M196342 RNU6-910P GC03M196394 RNU6-1279P
GH03F196277 0.9 Ensembl ENCODE 19.6 +7.8 7759 4.5 ATF1 PKNOX1 ARNT ARID4B SIN3A GATA2 FOS JUNB PPARG MEF2D PCYT1A SLC51A ENSG00000228028 TM4SF19 RNU6-910P
GH03F196267 0.6 ENCODE 18.7 +19.6 19584 1.2 TAL1 ZMYM3 BACH1 GTF3C2 ZNF121 ZNF316 RFXANK NFYB ZNF143 NFE2 PCYT1A SDHAP2 LINC00969 ENSG00000230732 RNU6ATAC24P RNU6-910P TM4SF19 MUC20P1 UBXN7 TFRC
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

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

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

Selected DME Specific Peptides for PCYT1A Gene


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

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PCYT1A (PCYT1A)
  • Santa Cruz Biotechnology (SCBT) Antibodies for PCYT1A

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 TAS --
GO:0005516 calmodulin binding IEA --
GO:0008289 lipid binding IEA --
GO:0016740 transferase activity IEA --
GO:0016779 nucleotidyltransferase activity 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

Inhibitory RNA Products

Flow Cytometry 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:0005635 nuclear envelope IEA --
GO:0005737 cytoplasm IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane TAS --
GO:0005829 cytosol IEA --
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:0006629 lipid metabolic process IEA --
GO:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0006657 CDP-choline pathway ISS --
GO:0008654 phospholipid biosynthetic process IEA --
GO:0009058 biosynthetic process IEA --
genes like me logo Genes that share ontologies with PCYT1A: view

Drugs & Compounds for PCYT1A Gene

(5) 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 148
Lamivudine Approved, Investigational Pharma Enzyme, substrate Nucleoside analog reverse transcriptase inhibitor 613
Phosphoric acid Approved Pharma 0
Cytidine triphosphate Experimental Pharma 0

(16) 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:

Inhibitory RNA Products

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and SAGE 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, MaxQB, and MOPED for PCYT1A Gene

Protein tissue co-expression partners for PCYT1A Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCYT1A Gene:


SOURCE GeneReport for Unigene cluster for PCYT1A Gene:

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

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
(Pan troglodytes)
Mammalia PCYT1A 34
  • 99.84 (n)
(Canis familiaris)
Mammalia PCYT1A 34 35
  • 92.46 (n)
(Bos Taurus)
Mammalia PCYT1A 34 35
  • 91.87 (n)
(Mus musculus)
Mammalia Pcyt1a 34 16 35
  • 89.74 (n)
(Rattus norvegicus)
Mammalia Pcyt1a 34
  • 89.37 (n)
(Monodelphis domestica)
Mammalia PCYT1A 35
  • 55 (a)
(Ornithorhynchus anatinus)
Mammalia PCYT1A 35
  • 54 (a)
(Gallus gallus)
Aves PCYT1A 34 35
  • 80.6 (n)
(Anolis carolinensis)
Reptilia PCYT1A 35
  • 88 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pcyt1a 34
  • 76.2 (n)
Str.1627 34
African clawed frog
(Xenopus laevis)
Amphibia pcyt1a-prov 34
(Danio rerio)
Actinopterygii pcyt1ab 35
  • 75 (a)
pcyt1aa 34 35
  • 73.44 (n)
fruit fly
(Drosophila melanogaster)
Insecta Cct1 36 34 35
  • 63.21 (n)
Cct2 36 35
  • 57 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002263 34
  • 56.61 (n)
(Caenorhabditis elegans)
Secernentea Y18H1A.11 34 35
  • 54 (n)
F08C6.2 36
  • 47 (a)
F28A10.10 36 35
  • 46 (a)
pcyt-1 35
  • 37 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PCT1 35
  • 31 (a)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.5008 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9202 35
  • 54 (a)
Species where no ortholog for PCYT1A was found in the sources mined by GeneCards:
  • 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

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
rs540053239 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940], Pathogenic 196,241,987(+) TAGCC(C/G/T)CTCTG reference, synonymous-codon, missense
rs587777189 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940], Pathogenic 196,248,245(+) TCTTC(A/G)CTTGC reference, missense
rs587777190 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940], Pathogenic 196,247,405(+) CCAGG(C/G)CGCAT reference, missense
rs587777191 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940], Pathogenic 196,248,246(+) CTTCG(C/T)TTGCA reference, missense
rs587777194 Spondylometaphyseal dysplasia with cone-rod dystrophy (SMDCRD) [MIM:608940], Pathogenic 196,247,468(+) ATTCT(C/T)GTTCA reference, missense

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

Variant ID Type Subtype PubMed ID
dgv2689n106 CNV duplication 24896259
esv2658720 CNV deletion 23128226
esv2759213 CNV gain+loss 17122850
esv3330620 CNV duplication 20981092
esv3341217 CNV duplication 20981092
esv3599276 CNV loss 21293372
esv3599277 CNV gain 21293372
esv3599278 CNV gain 21293372
esv3599279 CNV gain 21293372
nsv1008512 CNV gain 25217958
nsv1009811 CNV gain 25217958
nsv1117050 CNV deletion 24896259
nsv1146811 CNV duplication 26484159
nsv518925 CNV loss 19592680
nsv593071 CNV gain 21841781
nsv950310 CNV duplication 24416366
nsv997797 CNV gain 25217958

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for PCYT1A Gene

MalaCards: The human disease database

(4) 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 retinal dystrophy-2
sengers syndrome
  • mitochondrial dna depletion syndrome 10
- 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 64
  2. Mutations in PCYT1A Cause Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy. (PMID: 24387991) Yamamoto G.L. … Bertola D.R. (Am. J. Hum. Genet. 2014) 3 4 64
  3. Mutations in PCYT1A, Encoding a Key Regulator of Phosphatidylcholine Metabolism, Cause Spondylometaphyseal Dysplasia with Cone-Rod Dystrophy. (PMID: 24387990) Hoover-Fong J. … Pauli R.M. (Am. J. Hum. Genet. 2014) 3 4 64
  4. Associations of folate and choline metabolism gene polymorphisms with orofacial clefts. (PMID: 19737740) Mostowska A. … Jagodzinski P.P. (J. Med. Genet. 2010) 3 46 64
  5. Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts. (PMID: 20662904) Mostowska A. … Jagodzinski P.P. (Eur. J. Oral Sci. 2010) 3 46 64

Products for PCYT1A Gene