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

Summary

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: mouse all
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Genomic context

Location:: 3q29

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (196234368..196287726, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (198953844..199007214, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (195961239..196014597, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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: CN376065 OMIM: 620680 GeneReviews: Not available	not available
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome MedGen: C1837073 OMIM: 608940 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH104251 (e-PCR)
- UniSTS:98576

STS-L28957 (e-PCR)
- UniSTS:78865

A007I23 (e-PCR)
- UniSTS:61287

SHGC-36945 (e-PCR)
- UniSTS:8577

SHGC-57653 (e-PCR)
- UniSTS:67295

STS-L28957 (e-PCR)
- UniSTS:6393

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 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 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
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

EC 2.7.7.15

NP_005008.2

EC 2.7.7.15

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

NG_042817.2 RefSeqGene

Range

5000..58358

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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