Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5130
Gene name	Phosphate cytidylyltransferase 1A, choline
Gene symbol	PCYT1A
Synonyms (NCBI Gene)	CCTACCTalphaCGL5CTCTACTPCTPCYT1SMDCRD
Chromosome	3
Chromosome location	3q29
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

Show/Hide all (12)

SNP ID	Visualize variation	Clinical significance	Consequence
rs540053239	C>G,T	Pathogenic	Synonymous variant, missense variant, coding sequence variant
rs587777189	G>A	Pathogenic	Missense variant, coding sequence variant
rs587777190	G>C	Pathogenic	Missense variant, coding sequence variant
rs587777191	C>T	Pathogenic	Missense variant, coding sequence variant
rs587777192	G>A,T	Pathogenic	Stop gained, coding sequence variant, synonymous variant
rs587777193	G>-,GG	Pathogenic	Coding sequence variant, frameshift variant
rs587777194	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs587777195	A>G	Pathogenic	Missense variant, coding sequence variant
rs587777196	->C	Pathogenic	Coding sequence variant, frameshift variant
rs762145853	->T	Likely-pathogenic	Frameshift variant, coding sequence variant
rs765196598	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1057518600	->CT	Likely-pathogenic	Frameshift variant, coding sequence variant

135

Show/Hide all (135)

miRTarBase ID	miRNA	Experiments	Reference
MIRT032475	hsa-let-7b-5p	Proteomics	18668040
MIRT050150	hsa-miR-26a-5p	CLASH	23622248
MIRT719105	hsa-miR-520g-3p	HITS-CLIP	19536157
MIRT719104	hsa-miR-520h	HITS-CLIP	19536157
MIRT719103	hsa-miR-1226-3p	HITS-CLIP	19536157
MIRT719102	hsa-miR-622	HITS-CLIP	19536157
MIRT719101	hsa-miR-6849-3p	HITS-CLIP	19536157
MIRT719100	hsa-miR-186-3p	HITS-CLIP	19536157
MIRT719099	hsa-miR-4264	HITS-CLIP	19536157
MIRT719098	hsa-miR-150-5p	HITS-CLIP	19536157
MIRT719097	hsa-miR-532-3p	HITS-CLIP	19536157
MIRT719096	hsa-miR-2116-3p	HITS-CLIP	19536157
MIRT719095	hsa-miR-4713-5p	HITS-CLIP	19536157
MIRT551731	hsa-miR-6890-5p	PAR-CLIP	21572407
MIRT551730	hsa-miR-3155a	PAR-CLIP	21572407
MIRT551729	hsa-miR-3155b	PAR-CLIP	21572407
MIRT551728	hsa-miR-484	PAR-CLIP	21572407
MIRT551727	hsa-miR-1273f	PAR-CLIP	21572407
MIRT551726	hsa-miR-193b-5p	PAR-CLIP	21572407
MIRT551725	hsa-miR-6801-5p	PAR-CLIP	21572407
MIRT551724	hsa-miR-6832-5p	PAR-CLIP	21572407
MIRT551723	hsa-miR-197-3p	PAR-CLIP	21572407
MIRT551722	hsa-miR-3170	PAR-CLIP	21572407
MIRT551721	hsa-miR-6855-5p	PAR-CLIP	21572407
MIRT551720	hsa-miR-5587-5p	PAR-CLIP	21572407
MIRT551719	hsa-miR-5096	PAR-CLIP	21572407
MIRT460196	hsa-miR-1321	PAR-CLIP	23592263
MIRT460195	hsa-miR-4739	PAR-CLIP	23592263
MIRT460194	hsa-miR-4756-5p	PAR-CLIP	23592263
MIRT460193	hsa-miR-5681a	PAR-CLIP	23592263
MIRT460192	hsa-miR-5004-5p	PAR-CLIP	23592263
MIRT460191	hsa-miR-7154-3p	PAR-CLIP	23592263
MIRT460190	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT460189	hsa-miR-1302	PAR-CLIP	23592263
MIRT460188	hsa-miR-4298	PAR-CLIP	23592263
MIRT460187	hsa-miR-6778-5p	PAR-CLIP	23592263
MIRT719105	hsa-miR-520g-3p	HITS-CLIP	19536157
MIRT719104	hsa-miR-520h	HITS-CLIP	19536157
MIRT719103	hsa-miR-1226-3p	HITS-CLIP	19536157
MIRT719102	hsa-miR-622	HITS-CLIP	19536157
MIRT719101	hsa-miR-6849-3p	HITS-CLIP	19536157
MIRT719100	hsa-miR-186-3p	HITS-CLIP	19536157
MIRT719099	hsa-miR-4264	HITS-CLIP	19536157
MIRT719098	hsa-miR-150-5p	HITS-CLIP	19536157
MIRT719097	hsa-miR-532-3p	HITS-CLIP	19536157
MIRT719096	hsa-miR-2116-3p	HITS-CLIP	19536157
MIRT719095	hsa-miR-4713-5p	HITS-CLIP	19536157
MIRT551731	hsa-miR-6890-5p	PAR-CLIP	21572407
MIRT551730	hsa-miR-3155a	PAR-CLIP	21572407
MIRT551729	hsa-miR-3155b	PAR-CLIP	21572407
MIRT551728	hsa-miR-484	PAR-CLIP	21572407
MIRT551727	hsa-miR-1273f	PAR-CLIP	21572407
MIRT551726	hsa-miR-193b-5p	PAR-CLIP	21572407
MIRT551725	hsa-miR-6801-5p	PAR-CLIP	21572407
MIRT551724	hsa-miR-6832-5p	PAR-CLIP	21572407
MIRT551723	hsa-miR-197-3p	PAR-CLIP	21572407
MIRT551722	hsa-miR-3170	PAR-CLIP	21572407
MIRT551721	hsa-miR-6855-5p	PAR-CLIP	21572407
MIRT551720	hsa-miR-5587-5p	PAR-CLIP	21572407
MIRT551719	hsa-miR-5096	PAR-CLIP	21572407
MIRT460196	hsa-miR-1321	PAR-CLIP	23592263
MIRT460195	hsa-miR-4739	PAR-CLIP	23592263
MIRT460194	hsa-miR-4756-5p	PAR-CLIP	23592263
MIRT460193	hsa-miR-5681a	PAR-CLIP	23592263
MIRT460192	hsa-miR-5004-5p	PAR-CLIP	23592263
MIRT460191	hsa-miR-7154-3p	PAR-CLIP	23592263
MIRT460190	hsa-miR-7106-5p	PAR-CLIP	23592263
MIRT460189	hsa-miR-1302	PAR-CLIP	23592263
MIRT460188	hsa-miR-4298	PAR-CLIP	23592263
MIRT460187	hsa-miR-6778-5p	PAR-CLIP	23592263
MIRT1218833	hsa-miR-1275	CLIP-seq
MIRT1218834	hsa-miR-129-3p	CLIP-seq
MIRT1218835	hsa-miR-18a	CLIP-seq
MIRT1218836	hsa-miR-18b	CLIP-seq
MIRT1218837	hsa-miR-2278	CLIP-seq
MIRT1218838	hsa-miR-2355-5p	CLIP-seq
MIRT1218839	hsa-miR-2467-3p	CLIP-seq
MIRT1218840	hsa-miR-3121-5p	CLIP-seq
MIRT1218841	hsa-miR-3124-3p	CLIP-seq
MIRT1218842	hsa-miR-3147	CLIP-seq
MIRT1218843	hsa-miR-3189-3p	CLIP-seq
MIRT1218844	hsa-miR-3591-5p	CLIP-seq
MIRT1218845	hsa-miR-3674	CLIP-seq
MIRT1218846	hsa-miR-3678-3p	CLIP-seq
MIRT1218847	hsa-miR-3679-3p	CLIP-seq
MIRT1218848	hsa-miR-4255	CLIP-seq
MIRT1218849	hsa-miR-4263	CLIP-seq
MIRT1218850	hsa-miR-4425	CLIP-seq
MIRT1218851	hsa-miR-4464	CLIP-seq
MIRT1218852	hsa-miR-4521	CLIP-seq
MIRT1218853	hsa-miR-4665-5p	CLIP-seq
MIRT1218854	hsa-miR-4690-5p	CLIP-seq
MIRT1218855	hsa-miR-4694-3p	CLIP-seq
MIRT1218856	hsa-miR-4735-3p	CLIP-seq
MIRT1218857	hsa-miR-4748	CLIP-seq
MIRT1218858	hsa-miR-4778-3p	CLIP-seq
MIRT1218859	hsa-miR-4803	CLIP-seq
MIRT1218860	hsa-miR-494	CLIP-seq
MIRT1218861	hsa-miR-511	CLIP-seq
MIRT1218862	hsa-miR-522	CLIP-seq
MIRT1218863	hsa-miR-615-5p	CLIP-seq
MIRT2063319	hsa-miR-1286	CLIP-seq
MIRT2063320	hsa-miR-1910	CLIP-seq
MIRT1218838	hsa-miR-2355-5p	CLIP-seq
MIRT2063321	hsa-miR-2964a-5p	CLIP-seq
MIRT1218840	hsa-miR-3121-5p	CLIP-seq
MIRT1218841	hsa-miR-3124-3p	CLIP-seq
MIRT1218844	hsa-miR-3591-5p	CLIP-seq
MIRT2063322	hsa-miR-361-3p	CLIP-seq
MIRT2063323	hsa-miR-3614-5p	CLIP-seq
MIRT1218845	hsa-miR-3674	CLIP-seq
MIRT1218847	hsa-miR-3679-3p	CLIP-seq
MIRT2063324	hsa-miR-3940-5p	CLIP-seq
MIRT1218848	hsa-miR-4255	CLIP-seq
MIRT2063325	hsa-miR-4436a	CLIP-seq
MIRT2063326	hsa-miR-4438	CLIP-seq
MIRT1218851	hsa-miR-4464	CLIP-seq
MIRT2063327	hsa-miR-4507	CLIP-seq
MIRT2063328	hsa-miR-4687-3p	CLIP-seq
MIRT2063329	hsa-miR-4722-5p	CLIP-seq
MIRT1218857	hsa-miR-4748	CLIP-seq
MIRT1218858	hsa-miR-4778-3p	CLIP-seq
MIRT1218861	hsa-miR-511	CLIP-seq
MIRT2063330	hsa-miR-668	CLIP-seq
MIRT2063319	hsa-miR-1286	CLIP-seq
MIRT1218841	hsa-miR-3124-3p	CLIP-seq
MIRT2063324	hsa-miR-3940-5p	CLIP-seq
MIRT2063325	hsa-miR-4436a	CLIP-seq
MIRT2063326	hsa-miR-4438	CLIP-seq
MIRT2063327	hsa-miR-4507	CLIP-seq
MIRT2063328	hsa-miR-4687-3p	CLIP-seq
MIRT2063329	hsa-miR-4722-5p	CLIP-seq
MIRT1218844	hsa-miR-3591-5p	CLIP-seq
MIRT1218851	hsa-miR-4464	CLIP-seq
MIRT1218857	hsa-miR-4748	CLIP-seq

Show/Hide all (2)

Transcription factor	Regulation	Reference
ZNF143	Activation	14702349
ZNF76	Activation	14702349

Show/Hide all (46)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0004105	Function	Choline-phosphate cytidylyltransferase activity	IBA
GO:0004105	Function	Choline-phosphate cytidylyltransferase activity	IDA	10480912
GO:0004105	Function	Choline-phosphate cytidylyltransferase activity	IEA
GO:0004105	Function	Choline-phosphate cytidylyltransferase activity	ISS
GO:0004105	Function	Choline-phosphate cytidylyltransferase activity	TAS	7918629
GO:0005515	Function	Protein binding	IPI	28514442, 32296183, 33961781
GO:0005516	Function	Calmodulin binding	IEA
GO:0005634	Component	Nucleus	IDA	10480912
GO:0005634	Component	Nucleus	IEA
GO:0005635	Component	Nuclear envelope	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA	10480912
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IDA	10480912
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	ISS
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005829	Component	Cytosol	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006656	Process	Phosphatidylcholine biosynthetic process	IDA	10480912
GO:0006656	Process	Phosphatidylcholine biosynthetic process	IEA
GO:0006656	Process	Phosphatidylcholine biosynthetic process	IEA
GO:0006656	Process	Phosphatidylcholine biosynthetic process	ISS
GO:0006657	Process	CDP-choline pathway	IDA	10480912
GO:0006657	Process	CDP-choline pathway	IEA
GO:0006657	Process	CDP-choline pathway	ISS
GO:0008289	Function	Lipid binding	IEA
GO:0008654	Process	Phospholipid biosynthetic process	IEA
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0031210	Function	Phosphatidylcholine binding	IBA
GO:0031210	Function	Phosphatidylcholine binding	IEA
GO:0042100	Process	B cell proliferation	IEA
GO:0042100	Process	B cell proliferation	ISS
GO:0042587	Component	Glycogen granule	IEA
GO:0042587	Component	Glycogen granule	ISS
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0042803	Function	Protein homodimerization activity	IEA
GO:0045190	Process	Isotype switching	IEA
GO:0045190	Process	Isotype switching	ISS
GO:0046470	Process	Phosphatidylcholine metabolic process	IEA
GO:0090407	Process	Organophosphate biosynthetic process	IEA
GO:0140678	Function	Molecular function inhibitor activity	IEA

MIM	HGNC	e!Ensembl
123695	8754	ENSG00000161217

P49585

Protein name

Choline-phosphate cytidylyltransferase A (EC 2.7.7.15) (CCT-alpha) (CTP:phosphocholine cytidylyltransferase A) (CCT A) (CT A) (Phosphorylcholine transferase A)

Protein function

Catalyzes the key rate-limiting step in the CDP-choline pathway for phosphatidylcholine biosynthesis.

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01467	CTP_transf_like	80 → 208	Cytidylyltransferase-like	Domain

Tissue specificity

TISSUE SPECIFICITY: Brain, placenta, liver, fetal and adult lung. {ECO:0000269|PubMed:10480912}.

Sequence

MDAQCSAKVNARKRRKEAPGPNGATEEDGVPSKVQRCAVGLRQPAPFSDEIEVDFSKPYV
RVTMEEASRGTPCERPVRVYADGIFDLFHSGHARALMQAKNLFPNTYLIVGVCSDELTHN
FKGFTVMNENERYDAVQHCRYVDEVVRNAPWTLTPEFLAEHRIDFVAHDDIPYSSAGSDD
VYKHIKEAGMFAPTQRTEGISTSDIITRIVRDYDVYARRNLQRGYTAKELNVSFINEKKY
HLQERVDKVKKKVKDVEEKSKEFVQKVEEKSIDLIQKWEEKSREFIGSFLEMFGPEGALK
HMLKEGKGRMLQAISPKQSPSSSPTRERSPSPSFRWPFSGKTSPPCSPANLSRHKAAAYD
ISEDEED

Sequence length

367

Interactions

View interactions

	KEGG		Reactome
	Phosphonate and phosphinate metabolism Glycerophospholipid metabolism Metabolic pathways Choline metabolism in cancer		Synthesis of PC

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Lipodystrophy, congenital generalized, type 5	Pathogenic	rs1398190721	RCV003493360
Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome	Pathogenic; Likely pathogenic	rs1724289595, rs1285004802, rs587777189, rs587777190, rs587777191, rs540053239, rs587777194, rs587777195, rs2474015361	RCV001335225 RCV005860224 RCV000087314 RCV000087315 RCV000087316 RCV000087319 RCV000087320 RCV000087321 RCV003140446

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Gastric cancer	Uncertain significance	rs375663930	RCV005923891
Leber congenital amaurosis	Conflicting classifications of pathogenicity	rs1577358031	RCV001199491
Ovarian serous cystadenocarcinoma	Uncertain significance	rs372728478	RCV005922860
PCYT1A-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity	rs373884509, rs138930531, rs142952629, rs201929666, rs533990347, rs201702214, rs142799242	RCV003920964 RCV003960888 RCV003940842 RCV003942871 RCV003923155 RCV003936236 RCV004758775
Retinal dystrophy	Uncertain significance; Likely benign	rs375529354, rs199831548, rs771371499	RCV004815440 RCV004818201 RCV004815286

Show/Hide Text Mining Associations (27)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Bone Diseases Developmental	Associate	29122926
Carcinoma Non Small Cell Lung	Associate	24692084
Carcinoma Squamous Cell	Associate	24692084
Cone Rod Dystrophies	Associate	24387991, 28272537
Eye Abnormalities	Associate	29122926
Fatty Liver	Associate	28272537
Lipodystrophy	Associate	28272537
Lung Neoplasms	Associate	23171216
Lymphatic Metastasis	Stimulate	31413263
Lymphoma	Associate	28686226
Lymphoma B Cell	Inhibit	28686226
Lymphoma Large B Cell Diffuse	Associate	28686226
Muscular Dystrophies	Associate	24387991
Muscular Dystrophy Congenital Megaconial Type	Associate	24387991
Neoplasms	Stimulate	28686226
Neoplasms	Associate	37958610
Neoplasms Squamous Cell	Stimulate	31413263
Orofacial Cleft 1	Associate	29855589
Pyruvate Carboxylase Deficiency Disease	Associate	38280862
Retinal Dystrophies	Associate	28272537
Spinal Dysraphism	Associate	17184542
Spondylometaphyseal Dysplasia with Cone Rod Dystrophy	Associate	28272537
Squamous Cell Carcinoma of Head and Neck	Associate	24692084
Stomach Neoplasms	Associate	34504059
Strudwick syndrome	Associate	24387991, 28272537
Urinary Bladder Neoplasms	Associate	29475387
Velopharyngeal Insufficiency	Associate	29855589

PCYT1A (phosphate cytidylyltransferase 1A, choline)