PCYT1B

Summary

PCYT1B (phosphate cytidylyltransferase 1B, choline, HGNC:8755) is a protein-coding gene on chromosome Xp22.11, encoding Choline-phosphate cytidylyltransferase B (Q9Y5K3). Catalyzes the key rate-limiting step in the CDP-choline pathway for phosphatidylcholine biosynthesis.

The protein encoded by this gene belongs to the cytidylyltransferase family. It is involved in the regulation of phosphatidylcholine biosynthesis. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 9468 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 45 total
• MANE Select transcript: NM_004845

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8755
Approved symbol	PCYT1B
Name	phosphate cytidylyltransferase 1B, choline
Location	Xp22.11
Locus type	gene with protein product
Status	Approved
Aliases	CCT-beta, CTB, CCTbeta
Ensembl gene	ENSG00000102230
Ensembl biotype	protein_coding
OMIM	300948
Entrez	9468

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000356768, ENST00000379144, ENST00000379145, ENST00000496020

RefSeq mRNA: 3 — MANE Select: NM_004845 NM_001163264, NM_001163265, NM_004845

CCDS: CCDS14213, CCDS55391, CCDS55392

Canonical transcript exons

ENST00000379144 — 8 exons

Exon	Start	End
ENSE00000667338	24618985	24619084
ENSE00000863231	24607745	24607861
ENSE00000863234	24646989	24647347
ENSE00001250483	24590023	24590174
ENSE00001479871	24558087	24562505
ENSE00003597095	24587241	24587319
ENSE00003605925	24579316	24579458
ENSE00003624788	24575130	24575318

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 86.55.

FANTOM5 (CAGE): breadth broad, TPM avg 2.1184 / max 86.1217, expressed in 426 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
198751	0.7057	296
198748	0.5298	242
198750	0.2818	150
198755	0.2744	87
198749	0.1599	86
198754	0.1477	71
198753	0.0191	10

Top tissues by expression

258 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
ventricular zone	UBERON:0003053	86.55	gold quality
cortical plate	UBERON:0005343	83.34	gold quality
ganglionic eminence	UBERON:0004023	82.01	gold quality
prefrontal cortex	UBERON:0000451	80.47	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	79.97	gold quality
amygdala	UBERON:0001876	79.18	gold quality
nucleus accumbens	UBERON:0001882	78.94	gold quality
left testis	UBERON:0004533	78.61	gold quality
cingulate cortex	UBERON:0003027	78.49	gold quality
spinal cord	UBERON:0002240	78.33	gold quality
anterior cingulate cortex	UBERON:0009835	78.32	gold quality
right testis	UBERON:0004534	78.08	gold quality
testis	UBERON:0000473	77.86	gold quality
corpus callosum	UBERON:0002336	77.85	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.62	gold quality
neocortex	UBERON:0001950	77.28	gold quality
temporal lobe	UBERON:0001871	77.18	gold quality
frontal cortex	UBERON:0001870	77.14	gold quality
caudate nucleus	UBERON:0001873	77.14	gold quality
putamen	UBERON:0001874	77.05	gold quality
right frontal lobe	UBERON:0002810	77.02	gold quality
cerebellar vermis	UBERON:0004720	76.67	gold quality
entorhinal cortex	UBERON:0002728	76.55	gold quality
telencephalon	UBERON:0001893	76.54	gold quality
vena cava	UBERON:0004087	76.48	silver quality
dorsolateral prefrontal cortex	UBERON:0009834	76.26	gold quality
cerebral cortex	UBERON:0000956	76.22	gold quality
Ammon’s horn	UBERON:0001954	76.05	gold quality
Brodmann (1909) area 9	UBERON:0013540	75.51	gold quality
sperm	CL:0000019	75.23	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

140 targeting PCYT1B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6798-5P	100.00	65.77	699
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-512-3P	99.97	67.35	1049
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-1236-3P	99.94	68.04	1695
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-6780A-5P	99.88	66.69	2776
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-544A	99.84	68.66	1965

Literature-anchored findings (GeneRIF, showing 5)

• Human phosphate cytidylyltransferase 1, choline, beta is a novel CaOx crystal growth inhibitor. (PMID:19595683)
• PCYT1B, a placental-specific enzyme post-translationally modifying neurokinin B, is essential for the pathogenic role of CRP in preeclampsia through activation of the neurokinin 3 receptor. (PMID:25452470)
• CCT contributes to phospholipid compositional homeostasis. [Review] (PMID:26165797)
• Genetic Polymorphisms of LPCAT1, CHPT1 and PCYT1B and Risk of Neonatal Respiratory Distress Syndrome among a Chinese Han Population. (PMID:31964590)
• Differential dephosphorylation of CTP:phosphocholine cytidylyltransferase upon translocation to nuclear membranes and lipid droplets. (PMID:32186954)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	pcyt1ba	ENSDARG00000058162
danio_rerio	pcyt1bb	ENSDARG00000104207
mus_musculus	Pcyt1b	ENSMUSG00000035246
rattus_norvegicus	AABR07038849.1	ENSRNOG00000051341
drosophila_melanogaster	Pcyt2	FBGN0035231
drosophila_melanogaster	Pcyt1	FBGN0041342
caenorhabditis_elegans		WBGENE00017241
caenorhabditis_elegans	Y18H1A.11	WBGENE00021215

Paralogs (2): PCYT1A (ENSG00000161217), PCYT2 (ENSG00000185813)

Protein

Protein identifiers

Choline-phosphate cytidylyltransferase B — Q9Y5K3 (reviewed: Q9Y5K3)

Alternative names: CCT-beta, CTP:phosphocholine cytidylyltransferase B, Phosphorylcholine transferase B

All UniProt accessions (2): Q9Y5K3, F2Z2B1

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Homodimer.

Subcellular location. Cytoplasm. Endoplasmic reticulum Endoplasmic reticulum.

Tissue specificity. Highly expressed in testis, placenta, brain, ovary, liver and fetal lung. Expressed in brain, liver and fetal lung.

Post-translational modifications. Phosphorylated. Extensively phosphorylated.

Pathway. Phospholipid metabolism; phosphatidylcholine biosynthesis; phosphatidylcholine from phosphocholine: step 1/2.

Similarity. Belongs to the cytidylyltransferase family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9Y5K3-1	2, Beta-2	yes
Q9Y5K3-2	1, Beta-1
Q9Y5K3-3	3
Q9Y5K3-4	4

RefSeq proteins (3): NP_001156736, NP_001156737, NP_004836* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004821	Cyt_trans-like	Domain
IPR014729	Rossmann-like_a/b/a_fold	Homologous_superfamily
IPR041723	CCT	Domain
IPR045049	Pcy1-like	Family

Pfam: PF01467

Catalyzed reactions (Rhea), 1 shown:

• phosphocholine + CTP + H(+) = CDP-choline + diphosphate (RHEA:18997)

UniProt features (37 total): modified residue 14, binding site 13, splice variant 4, region of interest 2, compositionally biased region 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y5K3-F1	76.71	0.45

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (13): 151; 168; 169; 173; 195; 196; 197; 200; 84; 85; 92; 122 …

Post-translational modifications (14): 315, 319, 322, 323, 329, 331, 335, 345, 346, 349, 350, 355, 360, 362

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-1483191	Synthesis of PC

MSigDB gene sets: 183 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, MYAATNNNNNNNGGC_UNKNOWN, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, ACTACCT_MIR196A_MIR196B, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, AAGCCAT_MIR135A_MIR135B, AP4_Q6, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_MALE_GAMETE_GENERATION, AAAYRNCTG_UNKNOWN, CAGCTG_AP4_Q5, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, EFC_Q6, FOXD3_01

GO Biological Process (9): ovarian follicle development (GO:0001541), phosphatidylcholine biosynthetic process (GO:0006656), CDP-choline pathway (GO:0006657), spermatogenesis (GO:0007283), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654), biosynthetic process (GO:0009058), phosphatidylcholine metabolic process (GO:0046470), organophosphate biosynthetic process (GO:0090407)

GO Molecular Function (6): choline-phosphate cytidylyltransferase activity (GO:0004105), phosphatidylcholine binding (GO:0031210), identical protein binding (GO:0042802), catalytic activity (GO:0003824), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779)

GO Cellular Component (3): cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
female gonad development	1
anatomical structure development	1
phosphatidylcholine metabolic process	1
glycerophospholipid biosynthetic process	1
choline kinase activity	1
diacylglycerol cholinephosphotransferase activity	1
phosphatidylcholine biosynthetic process	1
developmental process involved in reproduction	1
male gamete generation	1
primary metabolic process	1
phospholipid metabolic process	1
lipid biosynthetic process	1
organophosphate biosynthetic process	1
metabolic process	1
glycerophospholipid metabolic process	1
biosynthetic process	1
organophosphate metabolic process	1
cytidylyltransferase activity	1
phospholipid binding	1
cation binding	1
quaternary ammonium group binding	1
protein binding	1
molecular_function	1
catalytic activity	1
transferase activity, transferring phosphorus-containing groups	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1

Protein interactions and networks

STRING

1164 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCYT1B	CHKA	P35790	953
PCYT1B	CHPT1	Q8WUD6	795
PCYT1B	CEPT1	Q9Y6K0	770
PCYT1B	CHKB	Q9Y259	700
PCYT1B	PEMT	Q9UBM1	625
PCYT1B	SELENOI	Q9C0D9	568
PCYT1B	CATIP	Q7Z7H3	507
PCYT1B	CDS2	O95674	489
PCYT1B	VWC2L	B2RUY7	486
PCYT1B	LPCAT1	Q8NF37	469
PCYT1B	GPCPD1	Q9NPB8	464
PCYT1B	ETNK2	Q9NVF9	452
PCYT1B	TAF7L	Q5H9L4	449
PCYT1B	ISYNA1	Q9NPH2	446
PCYT1B	KLHL15	Q96M94	445

IntAct

8 interactions, top by confidence:

A	B	Type	Score
VKORC1L1	PCYT1A	psi-mi:“MI:0914”(association)	0.740
	CCDC22	psi-mi:“MI:0914”(association)	0.350
PCYT1A	RAB3GAP1	psi-mi:“MI:0914”(association)	0.350
BBS1	PCYT1A	psi-mi:“MI:0914”(association)	0.350
LRRC4C	PCYT1A	psi-mi:“MI:0914”(association)	0.350
PCYT1A	GNL1	psi-mi:“MI:0914”(association)	0.350
RAP1GDS1	MRAS	psi-mi:“MI:0914”(association)	0.350
SMPD2	A2ML1	psi-mi:“MI:0914”(association)	0.350

BioGRID (21): PCYT1B (Affinity Capture-MS), PCYT1B (Co-crystal Structure), PCYT1B (Two-hybrid), PCYT1A (Two-hybrid), TMEM43 (Two-hybrid), VKORC1L1 (Two-hybrid), PCYT1B (Affinity Capture-MS), PCYT1B (Co-crystal Structure), PCYT1B (Co-crystal Structure), PCYT1B (Affinity Capture-MS), PCYT1B (Affinity Capture-MS), PCYT1B (Affinity Capture-MS), PDE6C (Co-fractionation), SLC36A4 (Co-fractionation), TSHZ3 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A0A0D1CFF0, A0A0D1CRD0, A0A0D1DZV5, A2WYE9, B7F7B9, B8NHD6, D0Z5N4, F4JLK2, G2WWH6, I1RQE2, M9MH90, O04932, O22060, O59761, O94532, P04712, P30298, P31922, P31927, P31928, P49031, P49036, Q02331, Q04564, Q09109, Q0JGK4, Q11076, Q41607, Q42652, Q43845, Q43876, Q5B7I6, Q67WN8, Q6ZHZ1, Q74ZH9, Q75BF1, Q811Q9, Q86ME2, Q8RY24, Q94BT0

Diamond homologs: A1W0D6, A7H2L7, A8FMK8, C5A1S7, D3RZA9, D5EBS7, F4JJE0, O58466, O74975, O88637, P13259, P19836, P27623, P33412, P49583, P49584, P49585, P49586, P49587, Q55BZ4, Q5EA75, Q5HTW1, Q6TG09, Q811Q9, Q8RKI6, Q8SQW6, Q8TXT2, Q8U1T9, Q922E4, Q99447, Q9QZC4, Q9UTI6, Q9UZ37, Q9Y5K3, Q9ZV56, Q9ZVI9, B5I9H4, B6YXC8, C6A439, D3DZ18

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

45 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1262 predictions. Top by Δscore:

Variant	Effect	Δscore
X:24562506:C:CC	acceptor_gain	1.0000
X:24575126:ATACC:A	donor_loss	1.0000
X:24575127:TACCC:T	donor_loss	1.0000
X:24575128:A:AC	donor_gain	1.0000
X:24575128:AC:A	donor_gain	1.0000
X:24575129:C:CA	donor_loss	1.0000
X:24575129:C:CC	donor_gain	1.0000
X:24575129:CC:C	donor_gain	1.0000
X:24575318:CCTGG:C	acceptor_gain	1.0000
X:24575319:C:CC	acceptor_gain	1.0000
X:24575322:G:GC	acceptor_gain	1.0000
X:24575328:G:C	acceptor_gain	1.0000
X:24575328:G:GC	acceptor_gain	1.0000
X:24575329:T:C	acceptor_gain	1.0000
X:24575329:T:TC	acceptor_gain	1.0000
X:24575330:T:C	acceptor_gain	1.0000
X:24575330:T:TC	acceptor_gain	1.0000
X:24575334:A:T	acceptor_gain	1.0000
X:24579314:A:AC	donor_gain	1.0000
X:24579315:C:CC	donor_gain	1.0000
X:24579454:CATCC:C	acceptor_gain	1.0000
X:24579456:TCC:T	acceptor_gain	1.0000
X:24579456:TCCC:T	acceptor_loss	1.0000
X:24579457:CCC:C	acceptor_gain	1.0000
X:24579458:CCTGT:C	acceptor_loss	1.0000
X:24579459:C:CC	acceptor_gain	1.0000
X:24587246:T:TA	donor_gain	1.0000
X:24590018:AGTAC:A	donor_loss	1.0000
X:24590019:GTA:G	donor_loss	1.0000
X:24590020:TA:T	donor_loss	1.0000

AlphaMissense

2432 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:24575193:C:A	W278C	1.000
X:24575193:C:G	W278C	1.000
X:24575195:A:G	W278R	1.000
X:24575195:A:T	W278R	1.000
X:24579329:A:T	V232D	1.000
X:24579335:A:G	L230P	1.000
X:24579353:C:A	G224V	1.000
X:24579353:C:T	G224E	1.000
X:24579354:C:A	G224W	1.000
X:24579354:C:G	G224R	1.000
X:24579354:C:T	G224R	1.000
X:24579355:T:A	R223S	1.000
X:24579355:T:G	R223S	1.000
X:24579356:C:A	R223I	1.000
X:24579356:C:G	R223T	1.000
X:24579362:A:G	L221P	1.000
X:24579364:G:C	N220K	1.000
X:24579364:G:T	N220K	1.000
X:24579366:T:C	N220D	1.000
X:24579368:C:G	R219P	1.000
X:24579369:G:T	R219S	1.000
X:24579371:C:G	R218P	1.000
X:24579374:G:T	A217D	1.000
X:24579392:C:G	R211P	1.000
X:24579395:A:T	V210D	1.000
X:24579398:A:T	I209N	1.000
X:24579407:A:T	I206N	1.000
X:24579417:A:G	S203P	1.000
X:24579419:G:A	T202I	1.000
X:24579436:T:A	R196S	1.000

dbSNP variants (sampled 300 via entrez): RS1000071336 (X:24629346 G>A), RS1000077749 (X:24671754 C>A), RS1000087263 (X:24582951 A>G), RS1000154002 (X:24577537 C>T), RS1000169456 (X:24632947 C>T), RS1000176284 (X:24611442 G>A), RS1000245244 (X:24620711 A>G), RS1000302021 (X:24637940 A>G), RS1000367498 (X:24564225 C>A,T), RS1000379731 (X:24646754 C>A), RS1000410871 (X:24647468 C>A,T), RS1000416883 (X:24568706 C>A,G), RS1000487455 (X:24575846 T>C), RS1000532477 (X:24597575 A>T), RS1000551579 (X:24610028 G>T)

Disease associations

OMIM: gene MIM:300948 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression	4
sodium arsenite	affects binding, increases reaction, decreases methylation, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
OTX015	decreases expression	1
mivebresib	decreases expression	1
methylmercuric chloride	increases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
dorsomorphin	affects cotreatment, decreases expression, increases expression	1
(+)-JQ1 compound	decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	affects cotreatment, increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Caffeine	increases phosphorylation	1
Doxorubicin	decreases expression	1
Lipopolysaccharides	affects cotreatment, increases expression	1
Dronabinol	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.