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	5833
Gene name	Phosphate cytidylyltransferase 2, ethanolamine
Gene symbol	PCYT2
Synonyms (NCBI Gene)	ETSPG82
Chromosome	17
Chromosome location	17q25.3
Summary	This gene encodes an enzyme that catalyzes the formation of CDP-ethanolamine from CTP and phosphoethanolamine in the Kennedy pathway of phospholipid synthesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs377278120	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs778113360	G>A,T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1204173741	G>A	Pathogenic	Missense variant, coding sequence variant, non coding transcript variant

118

Show/Hide all (118)

miRTarBase ID	miRNA	Experiments	Reference
MIRT017368	hsa-miR-335-5p	Microarray	18185580
MIRT052191	hsa-let-7b-5p	CLASH	23622248
MIRT720608	hsa-miR-4726-3p	HITS-CLIP	19536157
MIRT720607	hsa-miR-6789-3p	HITS-CLIP	19536157
MIRT720606	hsa-miR-566	HITS-CLIP	19536157
MIRT572354	hsa-miR-1911-3p	PAR-CLIP	20371350
MIRT572352	hsa-miR-4742-5p	PAR-CLIP	20371350
MIRT572353	hsa-miR-4645-5p	PAR-CLIP	20371350
MIRT572351	hsa-miR-4673	PAR-CLIP	20371350
MIRT572350	hsa-miR-4285	PAR-CLIP	20371350
MIRT572348	hsa-miR-4786-5p	PAR-CLIP	20371350
MIRT572349	hsa-miR-3960	PAR-CLIP	20371350
MIRT572347	hsa-miR-8072	PAR-CLIP	20371350
MIRT525703	hsa-miR-7108-3p	PAR-CLIP	22012620
MIRT525702	hsa-miR-1292-3p	PAR-CLIP	22012620
MIRT525701	hsa-miR-3130-3p	PAR-CLIP	22012620
MIRT525700	hsa-miR-4707-3p	PAR-CLIP	22012620
MIRT525699	hsa-miR-4632-3p	PAR-CLIP	22012620
MIRT720608	hsa-miR-4726-3p	HITS-CLIP	19536157
MIRT720607	hsa-miR-6789-3p	HITS-CLIP	19536157
MIRT720606	hsa-miR-566	HITS-CLIP	19536157
MIRT572354	hsa-miR-1911-3p	PAR-CLIP	20371350
MIRT572352	hsa-miR-4742-5p	PAR-CLIP	20371350
MIRT572353	hsa-miR-4645-5p	PAR-CLIP	20371350
MIRT572351	hsa-miR-4673	PAR-CLIP	20371350
MIRT572350	hsa-miR-4285	PAR-CLIP	20371350
MIRT572348	hsa-miR-4786-5p	PAR-CLIP	20371350
MIRT572349	hsa-miR-3960	PAR-CLIP	20371350
MIRT572347	hsa-miR-8072	PAR-CLIP	20371350
MIRT525703	hsa-miR-7108-3p	PAR-CLIP	22012620
MIRT525702	hsa-miR-1292-3p	PAR-CLIP	22012620
MIRT525701	hsa-miR-3130-3p	PAR-CLIP	22012620
MIRT525700	hsa-miR-4707-3p	PAR-CLIP	22012620
MIRT525699	hsa-miR-4632-3p	PAR-CLIP	22012620
MIRT1218972	hsa-miR-1	CLIP-seq
MIRT1218973	hsa-miR-1278	CLIP-seq
MIRT1218974	hsa-miR-206	CLIP-seq
MIRT1218975	hsa-miR-299-3p	CLIP-seq
MIRT1218976	hsa-miR-3151	CLIP-seq
MIRT1218977	hsa-miR-4283	CLIP-seq
MIRT1218978	hsa-miR-4447	CLIP-seq
MIRT1218979	hsa-miR-4472	CLIP-seq
MIRT1218980	hsa-miR-4489	CLIP-seq
MIRT1218981	hsa-miR-4656	CLIP-seq
MIRT1218982	hsa-miR-491-5p	CLIP-seq
MIRT1218983	hsa-miR-548k	CLIP-seq
MIRT1218984	hsa-miR-548n	CLIP-seq
MIRT1218985	hsa-miR-613	CLIP-seq
MIRT1218986	hsa-miR-1287	CLIP-seq
MIRT1218987	hsa-miR-1343	CLIP-seq
MIRT1218988	hsa-miR-146a	CLIP-seq
MIRT1218989	hsa-miR-146b-5p	CLIP-seq
MIRT1218990	hsa-miR-1587	CLIP-seq
MIRT1218991	hsa-miR-185	CLIP-seq
MIRT1218992	hsa-miR-1912	CLIP-seq
MIRT1218993	hsa-miR-1972	CLIP-seq
MIRT1218994	hsa-miR-198	CLIP-seq
MIRT1218995	hsa-miR-3135b	CLIP-seq
MIRT1218996	hsa-miR-3144-5p	CLIP-seq
MIRT1218997	hsa-miR-3169	CLIP-seq
MIRT1218998	hsa-miR-3613-5p	CLIP-seq
MIRT1218999	hsa-miR-3618	CLIP-seq
MIRT1219000	hsa-miR-3650	CLIP-seq
MIRT1219001	hsa-miR-3667-3p	CLIP-seq
MIRT1219002	hsa-miR-378g	CLIP-seq
MIRT1219003	hsa-miR-3919	CLIP-seq
MIRT1219004	hsa-miR-3925-5p	CLIP-seq
MIRT1219005	hsa-miR-4257	CLIP-seq
MIRT1219006	hsa-miR-4297	CLIP-seq
MIRT1219007	hsa-miR-4306	CLIP-seq
MIRT1219008	hsa-miR-4311	CLIP-seq
MIRT1219009	hsa-miR-4438	CLIP-seq
MIRT1218978	hsa-miR-4447	CLIP-seq
MIRT1218979	hsa-miR-4472	CLIP-seq
MIRT1219010	hsa-miR-4488	CLIP-seq
MIRT1219011	hsa-miR-4492	CLIP-seq
MIRT1219012	hsa-miR-4498	CLIP-seq
MIRT1219013	hsa-miR-4515	CLIP-seq
MIRT1219014	hsa-miR-4632	CLIP-seq
MIRT1219015	hsa-miR-4644	CLIP-seq
MIRT1218981	hsa-miR-4656	CLIP-seq
MIRT1219016	hsa-miR-4675	CLIP-seq
MIRT1219017	hsa-miR-4697-5p	CLIP-seq
MIRT1219018	hsa-miR-4717-5p	CLIP-seq
MIRT1219019	hsa-miR-4741	CLIP-seq
MIRT1219020	hsa-miR-4755-3p	CLIP-seq
MIRT1219021	hsa-miR-541	CLIP-seq
MIRT1219022	hsa-miR-601	CLIP-seq
MIRT1219023	hsa-miR-654-5p	CLIP-seq
MIRT1219024	hsa-miR-762	CLIP-seq
MIRT1219025	hsa-miR-765	CLIP-seq
MIRT1219026	hsa-miR-885-3p	CLIP-seq
MIRT1219010	hsa-miR-4488	CLIP-seq
MIRT2063349	hsa-miR-4511	CLIP-seq
MIRT1219017	hsa-miR-4697-5p	CLIP-seq
MIRT1219020	hsa-miR-4755-3p	CLIP-seq
MIRT2063350	hsa-miR-548b-3p	CLIP-seq
MIRT2291782	hsa-miR-2682	CLIP-seq
MIRT2291783	hsa-miR-4269	CLIP-seq
MIRT2291784	hsa-miR-449c	CLIP-seq
MIRT2291785	hsa-miR-485-5p	CLIP-seq
MIRT2291786	hsa-miR-940	CLIP-seq
MIRT2589466	hsa-miR-1225-3p	CLIP-seq
MIRT2589467	hsa-miR-3064-5p	CLIP-seq
MIRT1218995	hsa-miR-3135b	CLIP-seq
MIRT2589468	hsa-miR-331-3p	CLIP-seq
MIRT1219001	hsa-miR-3667-3p	CLIP-seq
MIRT1219006	hsa-miR-4297	CLIP-seq
MIRT2589469	hsa-miR-604	CLIP-seq
MIRT2589470	hsa-miR-647	CLIP-seq
MIRT2589466	hsa-miR-1225-3p	CLIP-seq
MIRT2589467	hsa-miR-3064-5p	CLIP-seq
MIRT1218995	hsa-miR-3135b	CLIP-seq
MIRT2589468	hsa-miR-331-3p	CLIP-seq
MIRT1219001	hsa-miR-3667-3p	CLIP-seq
MIRT1219006	hsa-miR-4297	CLIP-seq
MIRT2589469	hsa-miR-604	CLIP-seq
MIRT2589470	hsa-miR-647	CLIP-seq

Show/Hide all (2)

Transcription factor	Regulation	Reference
NFKB1	Unknown	18583706
RELA	Unknown	18583706

Show/Hide all (18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0004306	Function	Ethanolamine-phosphate cytidylyltransferase activity	IBA
GO:0004306	Function	Ethanolamine-phosphate cytidylyltransferase activity	IEA
GO:0004306	Function	Ethanolamine-phosphate cytidylyltransferase activity	IMP	31637422
GO:0004306	Function	Ethanolamine-phosphate cytidylyltransferase activity	TAS	9083101
GO:0005515	Function	Protein binding	IPI	28514442, 32296183, 32814053, 33961781
GO:0005737	Component	Cytoplasm	IBA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IBA
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IEA
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IMP	28052917, 29500230
GO:0006646	Process	Phosphatidylethanolamine biosynthetic process	IMP	31637422
GO:0008654	Process	Phospholipid biosynthetic process	IEA
GO:0008654	Process	Phospholipid biosynthetic process	TAS	9083101
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0090407	Process	Organophosphate biosynthetic process	IEA

MIM	HGNC	e!Ensembl
602679	8756	ENSG00000185813

Q99447

Protein name

Ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14) (CTP:phosphoethanolamine cytidylyltransferase) (Phosphorylethanolamine transferase)

Protein function

Ethanolamine-phosphate cytidylyltransferase that catalyzes the second step in the synthesis of phosphatidylethanolamine (PE) from ethanolamine via the CDP-ethanolamine pathway (PubMed:31637422, PubMed:9083101). Phosphatidylethanolamine is a domi

PDB

3ELB , 4XSV

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01467	CTP_transf_like	26 → 152	Cytidylyltransferase-like	Domain
PF01467	CTP_transf_like	217 → 333	Cytidylyltransferase-like	Domain

Tissue specificity

TISSUE SPECIFICITY: Strongest expression in liver, heart, and skeletal muscle. {ECO:0000269|PubMed:9083101}.

Sequence

MIRNGRGAAGGAEQPGPGGRRAVRVWCDGCYDMVHYGHSNQLRQARAMGDYLIVGVHTDE
EIAKHKGPPVFTQEERYKMVQAIKWVDEVVPAAPYVTTLETLDKYNCDFCVHGNDITLTV
DGRDTYEEVKQAGRYRECKRTQGVSTTDLVGRMLLVTKAHHSSQEMSSEYREYADSFGKC
PGGRNPWTGVSQFLQTSQKIIQFASGKEPQPGETVIYVAGAFDLFHIGHVDFLEKVHRLA
ERPYIIAGLHFDQEVNHYKGKNYPIMNLHERTLSVLACRYVSEVVIGAPYAVTAELLSHF
KVDLVCHGKTEIIPDRDGSDPYQEPKRRGIFRQIDSGSNLTTDLIVQRIITNRLEYEARN
QKKEAKELAFLEAARQQAAQPLGERDGDF

Sequence length

389

Interactions

View interactions

	KEGG		Reactome
	Phosphonate and phosphinate metabolism Glycerophospholipid metabolism Metabolic pathways		Synthesis of PE

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ovarian serous cystadenocarcinoma	Pathogenic	rs953415774	RCV005936627	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spastic paraplegia 82, autosomal recessive	Likely pathogenic; Pathogenic	rs1436764763, rs2510047496, rs751856962, rs953415774, rs763945631, rs2510045525, rs778113360, rs377278120	RCV003388197 RCV003320450 RCV003388298 RCV003881730 RCV003881731 RCV003994676 RCV001003407 RCV001003408 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (1)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
AUTOSOMAL RECESSIVE SPASTIC PARAPLEGIA TYPE 82	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (15)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	38157930	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	GENOMICS_ENGLAND_DG	22764088, 31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	BEFREE	31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	GENOMICS_ENGLAND_DG	22764088, 31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental regression	Developmental regression	GENOMICS_ENGLAND_DG	22764088, 31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	GENOMICS_ENGLAND_DG	22764088, 31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	BEFREE	31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Insulin Resistance	Diabetes mellitus, type 2	Pubtator	29986096	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	22764088, 31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	22339418		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	31577958		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	31577958		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia, Hereditary	Spastic paraplegia	BEFREE	31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Spastic tetraparesis	Spastic tetraparesis	GENOMICS_ENGLAND_DG	22764088, 31637422		★★★★★ ★☆☆☆☆ Found in Text Mining only
Testicular Germ Cell Tumor	Testicular germ cell tumor	Pubtator	34621245	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

PCYT2 (phosphate cytidylyltransferase 2, ethanolamine)