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 intramembrane carrier activity. Involved in phospholipid transport. Predicted to be located in cytosol.

Source: NCBI Gene 58488 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 39 total
• GTEx eGene: eQTL in 15 tissues, sQTL in 43 (q < 0.05)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.51 (unconstrained)
• 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: 24 — 14 protein_coding, 8 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000268896

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 3, TSL 2: 1, TSL 3: 3, TSL 5: 1

ENST00000268896, ENST00000325214, ENST00000417982, ENST00000571489, ENST00000572536, ENST00000573500, ENST00000576183, ENST00000576221, ENST00000984002, ENST00000984003, ENST00000984004, ENST00000984005, ENST00000984006, ENST00000984007, ENST00000984009, ENST00001029966, ENST00001029967, ENST00001120381, ENST00001120382, ENST00001120383, ENST00001128621, ENST00001128622, ENST00001128623, ENST00001134849

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.

Highest expression (Bgee): secondary oocyte, lobe of liver, liver, oocyte, lung.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PCTP is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 15 tissues and its splicing (sQTL) in 43 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 58 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Nerve Tibial	sqtl	8.3e-37	-1.26	17:55780783:A:G
Heart Atrial Appendage	sqtl	3.7e-31	-1.45	17:55777617:C:T
Muscle Skeletal	sqtl	3.9e-29	-1.23	17:55783518:C:A
Heart Left Ventricle	sqtl	3.8e-26	-1.51	17:55780783:A:G
Adipose Subcutaneous	sqtl	4.8e-25	-1.08	17:55783518:C:A
Cells Cultured fibroblasts	sqtl	9.4e-24	-1.09	17:55780783:A:G
Nerve Tibial	eqtl	1.3e-22	+0.45	17:55756162:T:C
Testis	sqtl	4.7e-22	+1.01	17:55775492:A:G
Colon Transverse	sqtl	1.7e-18	-0.85	17:55793290:G:A
Esophagus Muscularis	sqtl	2.7e-18	-1.10	17:55780783:A:G
Whole Blood	eqtl	1.7e-15	+0.22	17:55763333:G:A
Colon Sigmoid	sqtl	4.6e-14	-0.97	17:55780783:A:G
Breast Mammary Tissue	sqtl	1.4e-13	-1.04	17:55780783:A:G
Brain Caudate basal ganglia	sqtl	7.7e-13	-1.65	17:55777617:C:T
Lung	sqtl	1.9e-12	+0.53	17:55774750:T:C
Esophagus Gastroesophageal Junction	sqtl	6.0e-12	-1.10	17:55780783:A:G
Adipose Visceral Omentum	sqtl	3.8e-11	-0.86	17:55777617:C:T
Whole Blood	sqtl	5.7e-11	+0.44	17:55775684:G:A
Thyroid	sqtl	7.4e-11	-0.80	17:55793290:G:A
Artery Tibial	sqtl	1.1e-10	-0.90	17:55780783:A:G

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

showing 100 of 281 tissues 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
cardiac ventricle	UBERON:0002082	86.20	gold quality
upper lobe of lung	UBERON:0008948	86.20	gold quality
duodenum	UBERON:0002114	86.15	gold quality
apex of heart	UBERON:0002098	86.12	gold quality
gastrocnemius	UBERON:0001388	86.10	gold quality
intestine	UBERON:0000160	85.97	gold quality
bone marrow	UBERON:0002371	85.94	gold quality
corpus epididymis	UBERON:0004359	85.94	gold quality
jejunal mucosa	UBERON:0000399	85.93	gold quality
muscle of leg	UBERON:0001383	85.78	gold quality
cortex of kidney	UBERON:0001225	85.69	gold quality
kidney	UBERON:0002113	85.69	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.62	gold quality
islet of Langerhans	UBERON:0000006	85.54	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.35	gold quality
esophagus squamous epithelium	UBERON:0006920	85.29	gold quality
mucosa of stomach	UBERON:0001199	85.04	gold quality
lung	UBERON:0002048	84.99	gold quality
body of stomach	UBERON:0001161	84.84	gold quality
pleura	UBERON:0000977	84.77	gold quality
right atrium auricular region	UBERON:0006631	84.47	gold quality
heart	UBERON:0000948	84.45	gold quality
small intestine Peyer’s patch	UBERON:0003454	84.34	gold quality
kidney epithelium	UBERON:0004819	84.33	gold quality
biceps brachii	UBERON:0001507	84.23	gold quality
small intestine	UBERON:0002108	84.21	gold quality
omental fat pad	UBERON:0010414	84.15	gold quality
skeletal muscle organ	UBERON:0014892	84.15	gold quality
muscle organ	UBERON:0001630	84.14	gold quality
peritoneum	UBERON:0002358	84.13	gold quality
adipose tissue of abdominal region	UBERON:0007808	84.12	gold quality
renal glomerulus	UBERON:0000074	83.94	gold quality
endometrium	UBERON:0001295	83.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.74	gold quality
calcaneal tendon	UBERON:0003701	83.74	gold quality
cardiac atrium	UBERON:0002081	83.70	gold quality
metanephric glomerulus	UBERON:0004736	83.68	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	83.67	gold quality
mucosa of urinary bladder	UBERON:0001259	83.56	silver quality
epithelium of esophagus	UBERON:0001976	83.54	gold quality
stomach	UBERON:0000945	83.39	gold quality
spleen	UBERON:0002106	83.37	gold quality
bone marrow cell	CL:0002092	83.29	gold quality
adipose tissue	UBERON:0001013	83.01	gold quality
decidua	UBERON:0002450	82.88	gold quality
urinary bladder	UBERON:0001255	82.84	gold quality
connective tissue	UBERON:0002384	82.83	gold quality
fundus of stomach	UBERON:0001160	82.80	gold quality
metanephros	UBERON:0000081	82.79	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	82.74	gold quality
tendon	UBERON:0000043	82.70	gold quality
pancreas	UBERON:0001264	82.68	gold quality
subcutaneous adipose tissue	UBERON:0002190	82.27	gold quality
body of pancreas	UBERON:0001150	82.06	gold quality
upper leg skin	UBERON:0004262	81.95	gold quality
lower esophagus muscularis layer	UBERON:0035833	81.94	gold quality
lower esophagus	UBERON:0013473	81.93	gold quality
gall bladder	UBERON:0002110	81.89	gold quality
mammalian vulva	UBERON:0000997	81.62	gold quality
trabecular bone tissue	UBERON:0002483	81.52	gold quality
left testis	UBERON:0004533	81.52	gold quality
jejunum	UBERON:0002115	81.50	gold quality
esophagus	UBERON:0001043	81.33	gold quality
caecum	UBERON:0001153	81.29	gold quality
endocervix	UBERON:0000458	81.19	gold quality
vermiform appendix	UBERON:0001154	81.17	gold quality
testis	UBERON:0000473	81.07	gold quality
esophagus mucosa	UBERON:0002469	80.99	gold quality
right testis	UBERON:0004534	80.97	gold quality
left coronary artery	UBERON:0001626	80.89	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

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Liver	tissue	91.6	medium
Kidney	tissue	27.7	high
Placenta	tissue	27.0	high
Epididymis	tissue	26.7	high
Rectum	tissue	22.4	high
Seminal vesicle	tissue	21.7	medium
Colon	tissue	21.6	high
Tongue	tissue	18.0
Duodenum	tissue	17.0	high
Small intestine	tissue	15.6	medium
Heart muscle	tissue	15.4	high
Adipose tissue	tissue	14.4	not detected
Skeletal muscle	tissue	14.3	medium
Stomach 1	tissue	13.3	medium
Lung	tissue	13.2	medium
Parathyroid gland	tissue	12.5	medium
Urinary bladder	tissue	12.5	medium
Testis	tissue	11.4	high
Breast	tissue	11.0	medium
Bone marrow	tissue	10.8	medium
Salivary gland	tissue	10.2	high
Spleen	tissue	10.1	medium
Smooth muscle	tissue	10.0	medium
Appendix	tissue	9.8	medium
Pancreas	tissue	9.7	medium
Cervix	tissue	9.3	medium
Lymph node	tissue	9.3	medium
Gallbladder	tissue	9.1	high
Prostate	tissue	9.0	medium
Esophagus	tissue	8.5	high
Fallopian tube	tissue	8.4	medium
Tonsil	tissue	8.3	medium
Ovary	tissue	8.0	medium
Pituitary gland	tissue	7.6
Vagina	tissue	7.6	medium
Choroid plexus	tissue	7.2
Thyroid gland	tissue	7.0	medium
Adrenal gland	tissue	6.8	medium
Postcentral gyrus	tissue	6.7
Endometrium 1	tissue	6.5	medium
Locus coeruleus	tissue	6.5
Nucleus accumbens	tissue	6.1
Hippocampus	tissue	6.0	medium
Thymus	tissue	5.5
Retina	tissue	3.9
Skin 1	tissue	3.0	medium
Caudate putamen	tissue	1.7
Spinal cord	tissue	1.5
Frontal cortex	tissue	1.3
Substantia nigra	tissue	1.1
Superior colliculi	tissue	1.0
Pons	tissue	0.8
Midbrain	tissue	0.8
Medulla oblongata	tissue	0.8
Thalamus	tissue	0.8
Cerebral cortex	tissue	0.6	high
Basal ganglia	tissue	0.6	high
Putamen	tissue	0.6
Temporal cortex	tissue	0.6
Amygdala	tissue	0.5

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Posterior thalamic nucleus (10.8), Habenula (9.8), Medial dorsal thalamic nucleus (9.5), Pulvinar (9.3), Ventromedial nucleus (9.3).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PPARA

miRNA regulators (miRDB)

Targeting PCTP by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 94 miRNAs:

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

Functional genomics

gnomAD constraint: pLI 4.91e-07, LOEUF 1.51, missense Z -0.569 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000268896 — one region, missense o/e 1.07.

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)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:107375) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 12 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal lipid homeostasis	1
abnormal macrophage physiology	1
gallstones	1
increased cholesterol level	1
decreased cholesterol level	1
abnormal bile secretion	1
abnormal bile composition	1
abnormal bile salt level	1
abnormal phospholipid level	1
abnormal gallbladder physiology	1
abnormal bile canaliculus morphology	1
increased macrophage apoptosis	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Bos taurus	P02720	80.7%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
ANKFN1	protein-coding	162282
NOG	protein-coding	9241
TMEM100	protein-coding	55273

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. Cytosol.

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

Catalyzed reactions (Rhea)

• a 1,2-diacyl-sn-glycero-3-phosphocholine(in) = a 1,2-diacyl-sn-glycero-3-phosphocholine(out) (RHEA:38571)

UniProt features (30 total): strand 10, helix 7, 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 by resolution:

PDB	Title	Method	Resolution (Å)
7U9D	Crystal Structure of Human Phosphatidylcholine Transfer Protein in Complex with …	X-RAY DIFFRACTION	2.18
1LN1	Crystal Structure of Human Phosphatidylcholine Transfer Protein in Complex with …	X-RAY DIFFRACTION	2.4
1LN2	Crystal Structure of Human Phosphatidylcholine Transfer Protein in Complex with …	X-RAY DIFFRACTION	2.9
1LN3	Structure of Human Phosphatidylcholine Transfer Protein in Complex with …	X-RAY DIFFRACTION	2.9

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Metabolic proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoli; nucleoplasm

Antibody reliability (HPA): IH approved · IF approved

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)

Position	Role
72	a 1,2-diacyl-sn-glycero-3-phosphocholine
78	a 1,2-diacyl-sn-glycero-3-phosphocholine
157	a 1,2-diacyl-sn-glycero-3-phosphocholine

Post-translational modifications (2)

Type	Positions
N-acetylmethionine	1
Phosphoserine	139

Mutagenesis-validated functional residues (1)

Position	Phenotype
63	reduces activity by 20%.

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 7; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

7 pathways:

ID	Pathway	Evidence
R-HSA-77289	Mitochondrial Fatty Acid Beta-Oxidation	curated
R-HSA-1483191	Synthesis of PC	curated
R-HSA-8978868	Fatty acid metabolism	—
R-HSA-1483206	Glycerophospholipid biosynthesis	—
R-HSA-1430728	Metabolism	—
R-HSA-556833	Metabolism of lipids	—
R-HSA-1483257	Phospholipid metabolism	—

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 (4): phosphatidylcholine biosynthetic process (GO:0006656), 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

5 top-level categories:

Category	Pathways
Metabolism of lipids	2
Glycerophospholipid biosynthesis	1
Fatty acid metabolism	1
Phospholipid metabolism	1
Metabolism	1

GO top-level categories

17 GO namespaces:

Category	Terms
binding	2
cellular anatomical structure	2
phosphatidylcholine metabolic process	1
glycerophospholipid biosynthetic process	1
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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 10 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
phospholipid transport	BP	direct assay
phosphatidylcholine binding	MF	direct assay
phosphatidylcholine intramembrane carrier activity	MF	direct assay

Protein interactions and networks

STRING

showing 15 of 452 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCTP	STARD5	P59094	930
PCTP	STARD6	P59095	927
PCTP	STARD4	Q96DR4	914
PCTP	STARD3	Q14849	907
PCTP	SLC38A5	Q8WUX1	835
PCTP	STAR	P49675	749
PCTP	CERT1	Q9Y5P4	674
PCTP	ACOT13	Q9NPJ3	661
PCTP	ACOT11	Q8WXI4	571
PCTP	STARD9	Q9P2P6	544
PCTP	STARD8	Q92502	536
PCTP	ACOT12	Q8WYK0	497
PCTP	STARD10	Q9Y365	488
PCTP	STXBP4	Q6ZWJ1	483
PCTP	SCP2	P22307	444

IntAct

Human interaction partners of PCTP in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

3 partners by confidence:

Partner	Interaction type	MIscore	Records
AGTRAP	physical association	0.560	3
RANGRF	physical association	0.400	1
TPPP	association	0.350	1

BioGRID (14 interactions; top human partners by supporting records): ACOT13 (Reconstituted Complex; 2 records), PAX3 (Reconstituted Complex; 2 records), AGO2 (Affinity Capture-RNA), AGTRAP (Two-hybrid), LMCD1 (Co-fractionation), RAB5A (Affinity Capture-MS), RAD23B (Affinity Capture-MS), RANGRF (Affinity Capture-MS), RAP1A (Co-fractionation), TPPP (Affinity Capture-MS), UBB (Affinity Capture-MS), VAPA (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for PCTP: 39 ClinVar records (0 pathogenic / likely pathogenic); 4 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	3
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 39 predictions of 669):

Position(s)	Effect	Δscore	Sites
17:55767332	acceptor_gain	1.0000
17:55767453–55767454	donor_loss	1.0000	5
17:55773896–55773897	donor_loss	1.0000	4
17:55774790–55774791	acceptor_loss	1.0000	5
17:55774860–55774861	donor_loss	1.0000	5
17:55751245–55751246	donor_loss	0.9900	6
17:55751446	donor_gain	0.9900
17:55767333–55767334	acceptor_loss	0.9900	6
17:55771104–55771105	acceptor_loss	0.9900	5
17:55771150	donor_gain	0.9900

AlphaMissense

372 missense substitutions predicted likely pathogenic (of 1,402 scored), across 110 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
D82	8	0.945	0.968
D113	8	0.925	0.970
D177	8	0.907	0.954
W81	7	0.958	0.982
W30	7	0.892	0.953
W101	7	0.884	0.964
F199	7	0.881	0.974
W186	7	0.807	0.949
F172	7	0.795	0.964
D74	7	0.777	0.844
R112	6	0.948	0.987
R78	6	0.926	0.985
P184	6	0.896	0.955
K55	6	0.884	0.981
V152	6	0.870	0.943
F13	6	0.844	0.941
M173	6	0.789	0.883
W190	6	0.784	0.861
P106	6	0.747	0.826
Y54	5	0.922	0.967

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Renal Clear Cell Carcinoma (TCGA)	favorable	3.2e-06
Head and Neck Squamous Cell Carcinoma (TCGA)	unfavorable	1.41e-05

Disease associations

OMIM: gene MIM:606055 | disease phenotypes:

GWAS associations

4 associations:

Study	Trait	p-value
GCST008839_413	Height	5e-11
GCST007576_127	Chronotype	1e-10
GCST001290_3	Height	6e-9
GCST009391_892	Metabolite levels	6e-6

EFO canonical traits (from GWAS)

2 canonical traits:

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 (CPIC guideline: no)

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	increases expression, affects expression	3
Cyclosporine	decreases expression	3
Nickel	decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases 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	increases reaction, affects binding	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)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for PCTP across ~30M SureChEMBL compounds — explore on Sugi Predict.