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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PCYT1A
phosphate cytidylyltransferase 1A, choline
Chromosome 3 Β· 3q29
NCBI Gene: 5130Ensembl: ENSG00000161217.13HGNC: HGNC:8754UniProt: B4E322
73PubMed Papers
22Diseases
0Drugs
14Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
endoplasmic reticulumphosphatidylcholine biosynthetic processCDP-choline pathwayendoplasmic reticulum membraneSpondylometaphyseal dysplasia - cone-rod dystrophyspondylometaphyseal dysplasia-cone-rod dystrophy syndromelipodystrophy, congenital generalized, type 5neurodegenerative disease
✦AI Summary

PCYT1A (phosphate cytidylyltransferase 1A, choline) encodes the rate-limiting enzyme in the CDP-choline pathway for phosphatidylcholine (PC) biosynthesis 1. The enzyme catalyzes a crucial step in the Kennedy pathway for de novo PC synthesis, with high expression observed in retinal MΓΌller glial cells 1. PCYT1A plays essential roles in cellular membrane integrity and lipid metabolism. The protein is activated during autophagy and facilitates autophagosome formation by incorporating newly synthesized choline phospholipids into autophagosomal membranes 2. In immune function, PCYT1A-mediated glycerophospholipid metabolism licenses IgE-mediated mast cell degranulation and contributes to allergic disease pathophysiology 3. Genetic variants in PCYT1A are associated with spina bifida risk, with certain SNPs showing twofold increased disease risk 4. PCYT1A deficiency causes inherited retinal dystrophies through disruption of fatty acid metabolism and induction of ferroptosis in photoreceptor cells 1. The gene is also implicated in polycystic ovary syndrome through epigenetic silencing and subsequent lipidome alterations 5. These findings establish PCYT1A as a critical regulator of phospholipid metabolism with significant roles in development, immunity, and disease pathogenesis.

Sources cited
1
PCYT1A encodes the rate-limiting enzyme in CDP-choline pathway and causes retinal dystrophies when deficient
PMID: 38858683
2
PCYT1A is activated during autophagy and required for autophagosome formation
PMID: 31517566
3
PCYT1A-mediated glycerophospholipid metabolism facilitates mast cell degranulation and allergic diseases
PMID: 40397574
4
PCYT1A genetic variants are associated with spina bifida risk
PMID: 17184542
5
PCYT1A epigenetic silencing is associated with polycystic ovary syndrome and lipidome alterations
PMID: 33521992
Disease Associationsβ“˜22
Spondylometaphyseal dysplasia - cone-rod dystrophyOpen Targets
0.78Strong
spondylometaphyseal dysplasia-cone-rod dystrophy syndromeOpen Targets
0.76Strong
lipodystrophy, congenital generalized, type 5Open Targets
0.47Moderate
neurodegenerative diseaseOpen Targets
0.46Moderate
Leber congenital amaurosisOpen Targets
0.45Moderate
genetic disorderOpen Targets
0.41Moderate
cholestasis, progressive familial intrahepatic, 6Open Targets
0.38Weak
Insulin resistanceOpen Targets
0.19Weak
congenital generalized lipodystrophyOpen Targets
0.19Weak
Retinal dystrophyOpen Targets
0.17Weak
ankylosing spondylitisOpen Targets
0.12Weak
neoplasmOpen Targets
0.10Weak
Alzheimer diseaseOpen Targets
0.09Suggestive
hepatocellular carcinomaOpen Targets
0.08Suggestive
laryngeal squamous cell carcinomaOpen Targets
0.07Suggestive
esophageal squamous cell carcinomaOpen Targets
0.06Suggestive
pulmonary tuberculosisOpen Targets
0.05Suggestive
Abnormality of the skeletal systemOpen Targets
0.05Suggestive
Testicular Germ Cell TumorOpen Targets
0.04Suggestive
acute kidney injuryOpen Targets
0.04Suggestive
Lipodystrophy, congenital generalized, 5UniProt
Spondylometaphyseal dysplasia with cone-rod dystrophyUniProt
Pathogenic Variants14
NM_001312673.2(PCYT1A):c.223C>T (p.Arg75Ter)Pathogenic
not provided|Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 75
NM_001312673.2(PCYT1A):c.448C>G (p.Pro150Ala)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 150
NM_001312673.2(PCYT1A):c.669G>C (p.Arg223Ser)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 223
NM_001312673.2(PCYT1A):c.296C>T (p.Ala99Val)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome|Inborn genetic diseases|not provided
β˜…β˜…β˜†β˜†2022β†’ Residue 99
NM_001312673.2(PCYT1A):c.413A>G (p.His138Arg)Likely pathogenic
Lipodystrophy, congenital generalized, type 5
β˜…β˜†β˜†β˜†2025β†’ Residue 138
NM_001312673.2(PCYT1A):c.60dup (p.Pro21fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 21
NM_001312673.2(PCYT1A):c.935dup (p.Ala313fs)Likely pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜†β˜†β˜†2022β†’ Residue 313
NM_001312673.2(PCYT1A):c.850G>T (p.Glu284Ter)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜†β˜†β˜†2018β†’ Residue 284
NM_001312673.2(PCYT1A):c.374C>T (p.Thr125Met)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2016β†’ Residue 125
NM_001312673.2(PCYT1A):c.955_956dup (p.Ser319fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2016β†’ Residue 319
NM_001312673.2(PCYT1A):c.295G>A (p.Ala99Thr)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜†β˜†β˜†β†’ Residue 99
NM_001312673.2(PCYT1A):c.385G>A (p.Glu129Lys)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜†β˜†β˜†β†’ Residue 129
NM_001312673.2(PCYT1A):c.571T>C (p.Phe191Leu)Pathogenic
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome
β˜…β˜†β˜†β˜†β†’ Residue 191
NM_001312673.2(PCYT1A):c.424G>A (p.Val142Met)Pathogenic
Lipodystrophy, congenital generalized, type 5
β˜†β˜†β˜†β˜†2024β†’ Residue 142
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Related Genes
MAPK3Protein interaction99%SELENOIProtein interaction92%PHOSPHO1Protein interaction91%MAPK9Protein interaction91%PCYT1BProtein interaction79%MAPK8Protein interaction75%
Tissue Expression6 tissues
Heart
100%
Lung
48%
Liver
31%
Ovary
28%
Brain
28%
Bone Marrow
21%
Gene Interaction Network
Click a node to explore
PCYT1AMAPK3SELENOIPHOSPHO1MAPK9PCYT1BMAPK8
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P49585
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.93LoF Tolerant
pLIβ“˜
0.02Tolerant
Observed/Expected LoF0.55 [0.34–0.93]
RankingsWhere PCYT1A stands among ~20K protein-coding genes
  • #6,494of 20,598
    Most Researched73
  • #2,514of 5,498
    Most Pathogenic Variants14
  • #8,650of 17,882
    Most Constrained (LOEUF)0.93
Genes detectedPCYT1A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Metabolic control of T
PMID: 34234346
Nature Β· 2021
1.00
2
Chaiqin chengqi decoction treatment mitigates hypertriglyceridemia-associated acute pancreatitis by modulating liver-mediated glycerophospholipid metabolism.
PMID: 39217651
Phytomedicine Β· 2024
0.90
3
NSUN2 modified by SUMO-2/3 promotes gastric cancer progression and regulates mRNA m5C methylation.
PMID: 34504059
Cell Death Dis Β· 2021
0.80
4
PCYT1A deficiency disturbs fatty acid metabolism and induces ferroptosis in the mouse retina.
PMID: 38858683
BMC Biol Β· 2024
0.70
5
CHKA and PCYT1A gene polymorphisms, choline intake and spina bifida risk in a California population.
PMID: 17184542
BMC Med Β· 2006
0.60