PCTP

Summary

PCTP (phosphatidylcholine transfer protein, HGNC:8752) is a protein-coding gene on chromosome 17q22, encoding Phosphatidylcholine transfer protein (Q9UKL6). Catalyzes the transfer of phosphatidylcholine between membranes.

Enables phosphatidylcholine binding activity and phosphatidylcholine transporter activity. Involved in phospholipid transport. Predicted to be located in cytosol.

Source: NCBI Gene 58488 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 38 total
• Druggable target: yes
• MANE Select transcript: NM_021213

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8752
Approved symbol	PCTP
Name	phosphatidylcholine transfer protein
Location	17q22
Locus type	gene with protein product
Status	Approved
Aliases	STARD2
Ensembl gene	ENSG00000141179
Ensembl biotype	protein_coding
OMIM	606055
Entrez	58488

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000268896, ENST00000325214, ENST00000417982, ENST00000571489, ENST00000572536, ENST00000573500, ENST00000576183, ENST00000576221

RefSeq mRNA: 4 — MANE Select: NM_021213 NM_001102402, NM_001330377, NM_001330378, NM_021213

CCDS: CCDS11588, CCDS45741, CCDS82165, CCDS82166

Canonical transcript exons

ENST00000268896 — 6 exons

Exon	Start	End
ENSE00001247504	55771106	55771185
ENSE00002640421	55776035	55777374
ENSE00002969634	55751051	55751244
ENSE00003464574	55774792	55774859
ENSE00003545537	55767335	55767452
ENSE00003595692	55773724	55773895

Expression profiles

Bgee: expression breadth ubiquitous, 257 present calls, max score 97.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.8730 / max 133.8733, expressed in 1803 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161792	6.5276	1721
161791	6.3635	1742
161790	1.4028	812
161793	1.1300	713
161794	0.4492	216

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.13	gold quality
right lobe of liver	UBERON:0001114	95.23	gold quality
liver	UBERON:0002107	94.46	gold quality
oocyte	CL:0000023	93.86	gold quality
right lung	UBERON:0002167	92.71	gold quality
monocyte	CL:0000576	91.96	gold quality
mononuclear cell	CL:0000842	91.43	gold quality
leukocyte	CL:0000738	91.23	gold quality
mucosa of transverse colon	UBERON:0004991	91.22	gold quality
placenta	UBERON:0001987	89.85	gold quality
sural nerve	UBERON:0015488	89.47	gold quality
rectum	UBERON:0001052	89.38	gold quality
blood	UBERON:0000178	88.82	gold quality
tibial nerve	UBERON:0001323	88.41	gold quality
colonic mucosa	UBERON:0000317	88.10	gold quality
nephron tubule	UBERON:0001231	87.98	gold quality
adult mammalian kidney	UBERON:0000082	87.85	gold quality
mucosa of sigmoid colon	UBERON:0004993	87.75	gold quality
tibia	UBERON:0000979	87.69	gold quality
palpebral conjunctiva	UBERON:0001812	87.60	gold quality
transverse colon	UBERON:0001157	87.47	gold quality
lower lobe of lung	UBERON:0008949	87.35	gold quality
visceral pleura	UBERON:0002401	87.14	gold quality
seminal vesicle	UBERON:0000998	87.04	gold quality
large intestine	UBERON:0000059	86.67	gold quality
colon	UBERON:0001155	86.60	gold quality
granulocyte	CL:0000094	86.55	gold quality
heart left ventricle	UBERON:0002084	86.50	gold quality
upper lobe of left lung	UBERON:0008952	86.24	gold quality
parietal pleura	UBERON:0002400	86.23	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	14.74

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PPARA

miRNA regulators (miRDB)

94 targeting PCTP, 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-3162-3P	100.00	65.37	363
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4789-5P	99.98	70.76	2721
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-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-3688-3P	99.97	72.02	2834
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4487	99.96	64.58	1252
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-8087	99.90	69.55	1351
HSA-MIR-3681-3P	99.88	70.46	2254
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-4659A-3P	99.80	72.62	4248

Literature-anchored findings (GeneRIF, showing 7)

• crystal structures of human PC-TP in complex with dilinoleoyl-PtdCho or palmitoyl-linoleoyl-PtdCho reveal that a single well-ordered PtdCho molecule occupies a centrally located tunnel (PMID:12055623)
• phosphatidylcholine transfer protein gene variants are associated with LDL-peak particle size (PMID:17266964)
• Yeast two-hybrid screening using libraries prepared from mouse liver and embryo identified Them2 (thioesterase superfamily member 2) and the homeodomain transcription factor Pax3 (paired box gene 3), respectively, as PC-TP-interacting proteins. (PMID:17704541)
• PC-TP contributes to the racial difference in PAR4-mediated platelet activation. (PMID:24216752)
• Mutations in PCTP gene is associated with prostate cancer (PMID:26585945)
• Identified the variant rs2912553 as contributing to racially differential expression of PCTP. (PMID:28251237)
• PCTP contributes to human platelet activation by enhancing dense granule secretion. (PMID:33770537)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pctp	ENSDARG00000073985
mus_musculus	Pctp	ENSMUSG00000020553
rattus_norvegicus	Pctp	ENSRNOG00000002425

Paralogs (2): STARD7 (ENSG00000084090), STARD10 (ENSG00000214530)

Protein

Protein identifiers

Phosphatidylcholine transfer protein — Q9UKL6 (reviewed: Q9UKL6)

Alternative names: START domain-containing protein 2, StAR-related lipid transfer protein 2

All UniProt accessions (6): Q9UKL6, I3L2M9, I3L3H0, I3L4Z8, J3QT99, Q549N3

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the transfer of phosphatidylcholine between membranes. Binds a single lipid molecule.

Subunit / interactions. Interacts with ACOT13/THEM2.

Subcellular location. Cytoplasm.

Tissue specificity. Highest expression in liver, placenta, testis, kidney and heart. Low levels in brain and lung. No expression detected in thymus.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UKL6-1	1	yes
Q9UKL6-2	2

RefSeq proteins (4): NP_001095872, NP_001317306, NP_001317307, NP_067036* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002913	START_lipid-bd_dom	Domain
IPR023393	START-like_dom_sf	Homologous_superfamily
IPR041950	STARD2_START	Domain
IPR051213	START_lipid_transfer	Family

Pfam: PF01852

UniProt features (29 total): strand 10, helix 6, binding site 3, turn 2, modified residue 2, chain 1, domain 1, sequence conflict 1, splice variant 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
7U9D	X-RAY DIFFRACTION	2.18
1LN1	X-RAY DIFFRACTION	2.4
1LN2	X-RAY DIFFRACTION	2.9
1LN3	X-RAY DIFFRACTION	2.9

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UKL6-F1	93.59	0.90

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 (3): 72; 78; 157

Post-translational modifications (2): 1, 139

Mutagenesis-validated functional residues (1):

Position	Phenotype
63	reduces activity by 20%.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1483191	Synthesis of PC
R-HSA-77289	Mitochondrial Fatty Acid Beta-Oxidation

MSigDB gene sets: 215 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, CEBPB_01, GOBP_ORGANOPHOSPHATE_ESTER_TRANSPORT, CEBP_Q2, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, KESHELAVA_MULTIPLE_DRUG_RESISTANCE, MODULE_480, GOBP_MULTICELLULAR_ORGANISMAL_LEVEL_HOMEOSTASIS, REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION, GOBP_PHOSPHOLIPID_TRANSPORT, LIU_CMYB_TARGETS_UP, ACEVEDO_LIVER_CANCER_UP

GO Biological Process (3): lipid transport (GO:0006869), phospholipid transport (GO:0015914), negative regulation of cold-induced thermogenesis (GO:0120163)

GO Molecular Function (4): phosphatidylcholine intramembrane carrier activity (GO:0008525), phosphatidylcholine binding (GO:0031210), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (2): cytosol (GO:0005829), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	1
Fatty acid metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cellular anatomical structure	2
transport	1
lipid localization	1
lipid transport	1
organophosphate ester transport	1
negative regulation of multicellular organismal process	1
cold-induced thermogenesis	1
regulation of cold-induced thermogenesis	1
intramembrane lipid carrier activity	1
phospholipid binding	1
cation binding	1
quaternary ammonium group binding	1
cytoplasm	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

586 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCTP	ACOT13	Q9NPJ3	940
PCTP	STARD4	Q96DR4	940
PCTP	STARD3	Q14849	938
PCTP	STARD5	P59094	937
PCTP	STARD6	P59095	926
PCTP	SLC38A5	Q8WUX1	837
PCTP	CERT1	Q9Y5P4	799
PCTP	STAR	P49675	790
PCTP	PAX3	P23760	706
PCTP	ACOT11	Q8WXI4	613
PCTP	ACOT12	Q8WYK0	566
PCTP	STARD8	Q92502	553
PCTP	SCP2	P22307	514
PCTP	STARD9	Q9P2P6	508
PCTP	STARD10	Q9Y365	467

IntAct

11 interactions, top by confidence:

A	B	Type	Score
PCTP	AGTRAP	psi-mi:“MI:0915”(physical association)	0.560
AGTRAP	PCTP	psi-mi:“MI:0915”(physical association)	0.560
RAB5A	ATE1	psi-mi:“MI:0914”(association)	0.530
PCTP	RANGRF	psi-mi:“MI:0915”(physical association)	0.400
	PCTP	psi-mi:“MI:0915”(physical association)	0.400
	HLA-C	psi-mi:“MI:0914”(association)	0.350
PCTP	TPPP	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): PCTP (Two-hybrid), VAPA (Affinity Capture-MS), PCTP (Affinity Capture-RNA), RANGRF (Affinity Capture-MS), PCTP (Affinity Capture-MS), RAD23B (Affinity Capture-MS), TPPP (Affinity Capture-MS), UBB (Affinity Capture-MS), PCTP (Co-fractionation), PCTP (Co-fractionation), ACOT13 (Reconstituted Complex), PAX3 (Reconstituted Complex), ACOT13 (Affinity Capture-Western), PAX3 (Affinity Capture-Western)

ESM2 similar proteins: A1A4M6, A2A259, A2AIG8, O14734, O15527, O43502, O54783, O55229, O70293, O73884, O95294, P02720, P43250, P47844, P53808, P53809, Q3UFY7, Q5R8P9, Q6AYP7, Q6AYT9, Q6EV97, Q6GV29, Q6NUN0, Q6WZ17, Q6WZ18, Q6WZ19, Q6WZ20, Q86VF5, Q8BGA8, Q8BVM4, Q8R2J9, Q8TCT0, Q8VCE6, Q8VHQ9, Q924H5, Q969T7, Q96A70, Q9CXP4, Q9D142, Q9EPQ7

Diamond homologs: P02720, P53808, P53809, Q8R1R3, Q9NQZ5, Q9UKL6, Q54N86

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	29
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1137 predictions. Top by Δscore:

Variant	Effect	Δscore
17:55751308:G:GT	donor_gain	1.0000
17:55767332:T:G	acceptor_gain	1.0000
17:55767333:A:AG	acceptor_gain	1.0000
17:55767334:G:GA	acceptor_gain	1.0000
17:55767334:GA:G	acceptor_gain	1.0000
17:55767334:GAA:G	acceptor_gain	1.0000
17:55767451:AGGTG:A	donor_loss	1.0000
17:55767452:GGTG:G	donor_loss	1.0000
17:55767453:G:GG	donor_gain	1.0000
17:55767453:GTGA:G	donor_loss	1.0000
17:55767454:T:A	donor_loss	1.0000
17:55771104:A:AG	acceptor_gain	1.0000
17:55771105:G:GG	acceptor_gain	1.0000
17:55773895:GGT:G	donor_loss	1.0000
17:55773896:GTA:G	donor_loss	1.0000
17:55773897:T:G	donor_loss	1.0000
17:55774786:CTCTA:C	acceptor_loss	1.0000
17:55774787:TCTAG:T	acceptor_loss	1.0000
17:55774788:CTA:C	acceptor_loss	1.0000
17:55774789:TA:T	acceptor_loss	1.0000
17:55774790:A:AC	acceptor_loss	1.0000
17:55774790:A:AG	acceptor_gain	1.0000
17:55774791:G:GT	acceptor_gain	1.0000
17:55774791:GT:G	acceptor_gain	1.0000
17:55774791:GTT:G	acceptor_gain	1.0000
17:55774791:GTTT:G	acceptor_gain	1.0000
17:55774791:GTTTT:G	acceptor_gain	1.0000
17:55774856:CAAGG:C	donor_loss	1.0000
17:55774857:AAG:A	donor_loss	1.0000
17:55774860:GT:G	donor_loss	1.0000

AlphaMissense

1402 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:55771182:A:C	R112S	0.987
17:55771182:A:T	R112S	0.987
17:55767427:A:C	R78S	0.985
17:55767427:A:T	R78S	0.985
17:55773889:A:C	S169R	0.983
17:55773891:C:A	S169R	0.983
17:55773891:C:G	S169R	0.983
17:55767434:T:A	W81R	0.982
17:55767434:T:C	W81R	0.982
17:55767436:G:C	W81C	0.982
17:55767436:G:T	W81C	0.982
17:55767358:A:C	K55N	0.981
17:55767358:A:T	K55N	0.981
17:55773860:T:C	L159P	0.980
17:55767426:G:C	R78T	0.975
17:55773787:G:C	A135P	0.975
17:55774852:C:A	A191D	0.974
17:55776050:T:C	F199L	0.974
17:55776052:C:A	F199L	0.974
17:55776052:C:G	F199L	0.974
17:55771181:G:C	R112T	0.973
17:55774828:T:C	I183T	0.973
17:55774855:C:A	A192D	0.971
17:55751231:G:C	R43P	0.970
17:55771183:G:C	D113H	0.970
17:55771181:G:T	R112I	0.969
17:55767437:G:C	D82H	0.968
17:55767353:T:C	Y54H	0.967
17:55773737:G:C	R118P	0.967
17:55767438:A:C	D82A	0.966

dbSNP variants (sampled 300 via entrez): RS1000019255 (17:55749502 G>A,T), RS1000055262 (17:55749909 T>C), RS1000109238 (17:55802398 G>A,C), RS1000109749 (17:55835269 T>A), RS1000201635 (17:55792644 G>A), RS1000216279 (17:55798929 G>A), RS1000259493 (17:55752608 T>A), RS1000267519 (17:55752270 A>G), RS1000306997 (17:55834486 C>T), RS1000312870 (17:55798628 C>T), RS1000319803 (17:55841534 T>C), RS1000347542 (17:55847992 A>G), RS1000358085 (17:55822559 GAAAGAGGATAA>G), RS1000409664 (17:55828478 A>G), RS1000411111 (17:55847368 T>C)

Disease associations

OMIM: gene MIM:606055 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001290_3	Height	6.000000e-09
GCST007576_289	Chronotype	1.000000e-10
GCST008839_263	Height	5.000000e-11
GCST009391_867	Metabolite levels	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008328	chronotype measurement
EFO:0010534	suberic acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4523490 (SINGLE PROTEIN)

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

ChEMBL bioactivities

12 potent at pChembl≥5 of 24 total, top 12 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.64	IC50	2300	nM	CHEMBL4570603
5.64	IC50	2300	nM	CHEMBL4591876
5.50	IC50	3200	nM	CHEMBL4538653
5.50	IC50	3200	nM	CHEMBL4527673
5.44	IC50	3600	nM	CHEMBL4522144
5.40	IC50	4000	nM	CHEMBL4519651
5.39	IC50	4100	nM	CHEMBL4521758
5.39	IC50	4100	nM	CHEMBL4577274
5.30	IC50	5000	nM	CHEMBL4557336
5.30	Kd	5000	nM	CHEMBL4553666
5.19	IC50	6500	nM	CHEMBL4553666
5.10	IC50	8000	nM	CHEMBL4523027

CTD chemical–gene interactions

40 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	3
Cyclosporine	decreases expression	3
Nickel	decreases expression	2
Cadmium Chloride	increases abundance, increases expression, decreases expression	2
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	increases expression	1
perfluorooctane sulfonic acid	increases expression	1
pentabromodiphenyl ether	decreases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
bisphenol S	decreases methylation	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Calcitriol	increases expression, affects cotreatment	1
Capsaicin	decreases expression	1
Cisplatin	increases expression	1
Clofibrate	affects localization	1
Coumestrol	decreases expression	1
Doxorubicin	decreases expression	1
Phenobarbital	affects expression	1
Smoke	decreases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Dihydrotestosterone	increases expression	1

ChEMBL screening assays

12 unique, capped per target: 12 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL4482712	Binding	Inhibition of N-terminal His-tagged human PC-TP expressed in Escherichia coli using NBD-PC and donor and acceptor small unilamellar vesicles by fluorescence quench assay	Phosphatidylcholine transfer protein inhibitors

Clinical trials (associated diseases)

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