LPCAT2

Summary

LPCAT2 (lysophosphatidylcholine acyltransferase 2, HGNC:26032) is a protein-coding gene on chromosome 16q12.2, encoding Lysophosphatidylcholine acyltransferase 2 (Q7L5N7). Exhibits both acyltransferase and acetyltransferase activities.

This gene encodes a member of the lysophospholipid acyltransferase family. The encoded enzyme may function in two ways: to catalyze the biosynthesis of platelet-activating factor (1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine) from 1-O-alkyl-sn-glycero-3-phosphocholine, and to catalyze the synthesis of glycerophospholipid precursors from arachidonyl-CoA and lysophosphatidylcholine. The encoded protein may function in membrane biogenesis and production of platelet-activating factor in inflammatory cells. The enzyme may localize to the endoplasmic reticulum and the Golgi.

Source: NCBI Gene 54947 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 75 total — 1 pathogenic
• MANE Select transcript: NM_017839

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26032
Approved symbol	LPCAT2
Name	lysophosphatidylcholine acyltransferase 2
Location	16q12.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20481, AGPAT11, LysoPAFAT, LPLAT9
Ensembl gene	ENSG00000087253
Ensembl biotype	protein_coding
OMIM	612040
Entrez	54947

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 protein_coding, 5 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000262134, ENST00000562299, ENST00000563095, ENST00000564084, ENST00000565056, ENST00000566375, ENST00000566911, ENST00000566915, ENST00000929286, ENST00000929287, ENST00000947554

RefSeq mRNA: 1 — MANE Select: NM_017839 NM_017839

CCDS: CCDS10753

Canonical transcript exons

ENST00000262134 — 14 exons

Exon	Start	End
ENSE00000684433	55531914	55531974
ENSE00000684434	55532824	55532882
ENSE00000945384	55529835	55529947
ENSE00001045312	55525508	55525647
ENSE00001325434	55509072	55509352
ENSE00001432137	55528377	55528594
ENSE00002631458	55582914	55586666
ENSE00003464407	55545735	55545817
ENSE00003472182	55537578	55537632
ENSE00003515528	55534443	55534477
ENSE00003520330	55574631	55574729
ENSE00003603536	55549277	55549402
ENSE00003663622	55550949	55551102
ENSE00003692381	55579109	55579244

Expression profiles

Bgee: expression breadth ubiquitous, 241 present calls, max score 94.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.1207 / max 857.0120, expressed in 1624 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
154168	10.9566	1528
154169	10.7514	1381
154167	1.4127	731

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
caput epididymis	UBERON:0004358	94.40	gold quality
left lobe of thyroid gland	UBERON:0001120	94.09	gold quality
thyroid gland	UBERON:0002046	93.88	gold quality
right lobe of thyroid gland	UBERON:0001119	93.79	gold quality
monocyte	CL:0000576	93.78	gold quality
seminal vesicle	UBERON:0000998	93.45	gold quality
leukocyte	CL:0000738	93.19	gold quality
bone marrow	UBERON:0002371	93.02	gold quality
bone marrow cell	CL:0002092	92.98	gold quality
corpus epididymis	UBERON:0004359	92.94	gold quality
stromal cell of endometrium	CL:0002255	92.40	gold quality
calcaneal tendon	UBERON:0003701	92.40	gold quality
blood	UBERON:0000178	90.93	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	89.73	gold quality
mucosa of stomach	UBERON:0001199	89.42	gold quality
colonic epithelium	UBERON:0000397	89.26	gold quality
trabecular bone tissue	UBERON:0002483	89.19	gold quality
spinal cord	UBERON:0002240	88.33	gold quality
smooth muscle tissue	UBERON:0001135	88.19	gold quality
body of uterus	UBERON:0009853	88.01	gold quality
epithelial cell of pancreas	CL:0000083	88.00	gold quality
buccal mucosa cell	CL:0002336	87.03	silver quality
decidua	UBERON:0002450	86.93	gold quality
vermiform appendix	UBERON:0001154	86.69	gold quality
cauda epididymis	UBERON:0004360	86.33	gold quality
tibial nerve	UBERON:0001323	85.72	gold quality
endocervix	UBERON:0000458	85.67	gold quality
tendon	UBERON:0000043	85.41	gold quality
epithelium of mammary gland	UBERON:0003244	85.18	gold quality
mammary duct	UBERON:0001765	85.17	gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-GEOD-81383	yes	278.06
E-HCAD-35	yes	34.94
E-HCAD-25	yes	14.96
E-MTAB-9067	yes	11.16
E-ANND-3	yes	11.08
E-CURD-112	yes	6.03
E-MTAB-5061	no	3.70

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

166 targeting LPCAT2, 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-3163	100.00	77.23	8605
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3924	100.00	72.09	2394
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-656-3P	100.00	72.15	2788
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-433-3P	99.98	69.37	1203

Literature-anchored findings (GeneRIF, showing 8)

• The enzyme acetyl-CoA:LYSO-PAF acetyltransferase catalyzes not only biosynthesis of PAF upon acute inflammatory stimulation but also incorporation of arachidonoyl-CoA to produce PAF precursor membrane glycerophospholipids for membrane biogenesis. (PMID:17182612)
• Our enzymatic assays strongly suggest that the cDNA previously identified as LPCAT2/lyso platelet-activating factor-acetyltransferase cDNA has AGPAT activity and thus we prefer to identify this clone as AGPAT11 as well. (PMID:20363836)
• LPCAT1 and -2 have, in addition to their known function in specialized cells, a ubiquitous role in LD-associated lipid metabolism (PMID:21498505)
• Data indicate a strong negative correlation between ALOX15, FADS2, and IL5RA expression with 2-arachidonoylglycerophosphocholine levels in dual asthmatic responses. (PMID:23844124)
• three of these five genes (CXCL14, ITGAX, and LPCAT2) harbored polymorphisms associated with aggressive disease development in a human GWAS cohort consisting of 1,172 prostate cancer patients. (PMID:25411967)
• Lysophosphatidylcholine acyltransferase 2 (LPCAT2) co-localises with TLR4 and regulates macrophage inflammatory gene expression in response to LPS. (PMID:32587324)
• Lysophospholipid Acyltransferase 9 Promotes Emphysema Formation via Platelet-activating Factor. (PMID:38377392)
• LPCAT2 inhibits colorectal cancer progression via the PRMT1/SLC7A11 axis. (PMID:38605214)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	lpcat2	ENSDARG00000053010
mus_musculus	Lpcat2	ENSMUSG00000033192
rattus_norvegicus	Lpcat2	ENSRNOG00000016643
drosophila_melanogaster	LPCAT	FBGN0052699

Paralogs (4): GPAT3 (ENSG00000138678), LPCAT1 (ENSG00000153395), GPAT4 (ENSG00000158669), LPCAT4 (ENSG00000176454)

Protein

Protein identifiers

Lysophosphatidylcholine acyltransferase 2 — Q7L5N7 (reviewed: Q7L5N7)

Alternative names: 1-acylglycerol-3-phosphate O-acyltransferase 11, 1-acylglycerophosphocholine O-acyltransferase, 1-alkenylglycerophosphocholine O-acyltransferase, 1-alkylglycerophosphocholine O-acetyltransferase, Acetyl-CoA:lyso-platelet-activating factor acetyltransferase, Acyltransferase-like 1, Lysophosphatidic acid acyltransferase alpha

All UniProt accessions (2): Q7L5N7, H3BU68

UniProt curated annotations — full annotation on UniProt →

Function. Exhibits both acyltransferase and acetyltransferase activities. Catalyzes the conversion of lysophosphatidylcholine (1-acyl-sn-glycero-3-phosphocholine or LPC) into phosphatidylcholine (1,2-diacyl-sn-glycero-3-phosphocholine or PC). Catalyzes the conversion 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid or LPA) into 1,2-diacyl-sn-glycerol-3-phosphate (phosphatidic acid or PA) by incorporating an acyl moiety at the sn-2 position of the glycerol backbone. Involved in platelet-activating factor (PAF) biosynthesis by catalyzing the conversion of the PAF precursor, 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF) into 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (PAF). Also converts lyso-PAF to 1-O-alkyl-2-acyl-sn-glycero-3-phosphocholine (PC), a major component of cell membranes and a PAF precursor. Under resting conditions, acyltransferase activity is preferred. Upon acute inflammatory stimulus, acetyltransferase activity is enhanced and PAF synthesis increases. Involved in the regulation of lipid droplet number and size.

Subcellular location. Endoplasmic reticulum membrane. Golgi apparatus membrane. Cell membrane. Lipid droplet.

Domain organisation. The HXXXXD motif is essential for acyltransferase activity.

Pathway. Lipid metabolism; phospholipid metabolism.

Similarity. Belongs to the 1-acyl-sn-glycerol-3-phosphate acyltransferase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q7L5N7-1	1	yes
Q7L5N7-2	2

RefSeq proteins (1): NP_060309* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002048	EF_hand_dom	Domain
IPR002123	Plipid/glycerol_acylTrfase	Domain
IPR011992	EF-hand-dom_pair	Homologous_superfamily
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR045252	LPCAT1-like	Domain

Pfam: PF01553, PF13499

Enzyme classification (BRENDA):

• EC 2.3.1.23 — 1-acylglycerophosphocholine O-acyltransferase (BRENDA: 25 organisms, 283 substrates, 101 inhibitors, 64 Km, 2 kcat entries)
• EC 2.3.1.51 — 1-acylglycerol-3-phosphate O-acyltransferase (BRENDA: 39 organisms, 381 substrates, 31 inhibitors, 32 Km, 4 kcat entries)
• EC 2.3.1.67 — 1-alkylglycerophosphocholine O-acetyltransferase (BRENDA: 7 organisms, 47 substrates, 133 inhibitors, 17 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

34 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
OLEOYL-COA	0.0004–0.152	15
1-ACYL-SN-GLYCERO-3-PHOSPHOCHOLINE	0.0017–0.107	9
ACETYL-COA	0.067–0.274	9
1-ACYL-SN-GLYCEROL 3-PHOSPHATE	0.0053–0.125	8
OLEOYL-COA	0.0027–0.0215	8
PALMITOYL-COA	0.0014–0.012	8
ARACHIDONOYL-COA	0.0032–0.7156	6
1-OLEOYL-SN-GLYCEROL 3-PHOSPHATE	0.0048–0.018	5
PALMITOYL-COA	0.0027–0.0413	4
STEAROYL-COA	0.0021–0.232	4
1-PALMITOYL-SN-GLYCERO-3-PHOSPHOCHOLINE	0.0018–0.0081	3
1-PALMITOYL-LYSOPHOSPHATIDYLCHOLINE	0.0023–0.7219	2
DOCOSAHEXANOYL-COA	0.0031–0.0132	2
LINOLEOYL-COA	0.0035–0.2014	2
LYSOPHOSPHATIDYLCHOLINE	0.0131–0.027	2

Catalyzed reactions (Rhea), 12 shown:

• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphocholine + an acyl-CoA = a 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphocholine + CoA (RHEA:10344)
• a 1-acyl-sn-glycero-3-phosphocholine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphocholine + CoA (RHEA:12937)
• a 1-O-alkyl-sn-glycero-3-phosphocholine + acetyl-CoA = a 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + CoA (RHEA:18461)
• a 1-acyl-sn-glycero-3-phosphate + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphate + CoA (RHEA:19709)
• 1-hexadecanoyl-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate + CoA (RHEA:33187)
• 1-hexadecanoyl-sn-glycero-3-phosphocholine + (9Z)-octadecenoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + CoA (RHEA:35991)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1,2-di-(9Z-octadecenoyl)-sn-glycero-3-phosphate + CoA (RHEA:37131)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + hexadecanoyl-CoA = 1-(9Z)-octadecenoyl-2-hexadecanoyl-sn-glycero-3-phosphate + CoA (RHEA:37143)
• 1-heptadecanoyl-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1-heptadecanoyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphate + CoA (RHEA:37151)
• heptadecanoyl-CoA + 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate = 1-(9Z)-octadecenoyl-2-heptadecanoyl-sn-glycero-3-phosphate + CoA (RHEA:37155)
• 1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + (9Z,12Z)-octadecadienoyl-CoA = 1-(9Z)-octadecenoyl-2-(9Z,12Z)-octadecadienoyl-sn-glycero-3-phosphate + CoA (RHEA:37159)
• 1-octadecanoyl-sn-glycero-3-phosphate + (9Z)-octadecenoyl-CoA = 1-octadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphate + CoA (RHEA:37163)

UniProt features (23 total): binding site 10, topological domain 2, compositionally biased region 2, domain 2, short sequence motif 2, chain 1, transmembrane region 1, splice variant 1, sequence variant 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7L5N7-F1	82.05	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 (10): 404; 406; 408; 410; 415; 441; 443; 445; 447; 452

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-1482788	Acyl chain remodelling of PC

MSigDB gene sets: 203 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, MODULE_511, MODULE_493, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS

GO Biological Process (7): platelet activating factor biosynthetic process (GO:0006663), phosphatidylcholine acyl-chain remodeling (GO:0036151), membrane organization (GO:0061024), lipid metabolic process (GO:0006629), phospholipid metabolic process (GO:0006644), glycerophospholipid metabolic process (GO:0006650), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (12): 1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841), calcium ion binding (GO:0005509), lysophosphatidic acid acyltransferase activity (GO:0042171), 2-acylglycerol-3-phosphate O-acyltransferase activity (GO:0047144), plasmalogen synthase activity (GO:0047159), 1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184), 1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192), protein binding (GO:0005515), obsolete O-acyltransferase activity (GO:0008374), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), metal ion binding (GO:0046872)

GO Cellular Component (9): Golgi membrane (GO:0000139), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), Golgi stack (GO:0005795), lipid droplet (GO:0005811), plasma membrane (GO:0005886), Golgi apparatus (GO:0005794), membrane (GO:0016020), organelle subcompartment (GO:0031984)

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
phospholipid metabolic process	2
lysophosphatidic acid acyltransferase activity	2
acyltransferase activity, transferring groups other than amino-acyl groups	2
cytoplasm	2
endomembrane system	2
intracellular membrane-bounded organelle	2
cellular anatomical structure	2
ether lipid biosynthetic process	1
platelet activating factor metabolic process	1
glycerophospholipid biosynthetic process	1
phosphatidylcholine metabolic process	1
cellular component organization	1
primary metabolic process	1
lipid metabolic process	1
organophosphate metabolic process	1
glycerolipid metabolic process	1
lipid biosynthetic process	1
organophosphate biosynthetic process	1
acylglycerol O-acyltransferase activity	1
metal ion binding	1
lysophospholipid acyltransferase activity	1
O-acetyltransferase activity	1
binding	1
catalytic activity	1
transferase activity	1
cation binding	1
Golgi apparatus	1
bounding membrane of organelle	1
organelle membrane	1
nuclear outer membrane-endoplasmic reticulum membrane network	1
endoplasmic reticulum subcompartment	1
Golgi apparatus subcompartment	1
intracellular membraneless organelle	1
membrane	1
cell periphery	1
membrane-bounded organelle	1
intracellular organelle	1

Protein interactions and networks

STRING

1498 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LPCAT2	AGPAT2	O15120	878
LPCAT2	PLA2G7	Q13093	719
LPCAT2	LPCAT3	Q6P1A2	715
LPCAT2	CHPT1	Q8WUD6	638
LPCAT2	BSCL2	Q96G97	614
LPCAT2	MBOAT2	Q6ZWT7	591
LPCAT2	A0A2R8Y471	A0A2R8Y471	575
LPCAT2	CEPT1	Q9Y6K0	540
LPCAT2	AGPAT4	Q9NRZ5	537
LPCAT2	ZNF22	P17026	533
LPCAT2	AGPAT3	Q9NRZ7	511
LPCAT2	CAPNS2	Q96L46	505
LPCAT2	GPAT2	Q6NUI2	502
LPCAT2	AGPAT5	Q9NUQ2	496
LPCAT2	PTAFR	P25105	464

IntAct

65 interactions, top by confidence:

A	B	Type	Score
LPCAT2	MFSD14B	psi-mi:“MI:0915”(physical association)	0.560
LPCAT2	KCNJ6	psi-mi:“MI:0915”(physical association)	0.560
LPCAT2	RHBDD1	psi-mi:“MI:0915”(physical association)	0.560
LPCAT2	HSD17B13	psi-mi:“MI:0915”(physical association)	0.560
LPCAT2	ERGIC3	psi-mi:“MI:0915”(physical association)	0.560
LPCAT2	RETREG3	psi-mi:“MI:0915”(physical association)	0.560
MFSD14B	LPCAT2	psi-mi:“MI:0915”(physical association)	0.560
KCNJ6	LPCAT2	psi-mi:“MI:0915”(physical association)	0.560
EBP	LPCAT2	psi-mi:“MI:0915”(physical association)	0.560
HLA-DPA1	TYW5	psi-mi:“MI:0914”(association)	0.530
HEATR1	DUSP14	psi-mi:“MI:0914”(association)	0.530
TMEM9	ESYT2	psi-mi:“MI:0914”(association)	0.530
SLC39A4	TMEM120B	psi-mi:“MI:0914”(association)	0.530
STK16	UNC119B	psi-mi:“MI:0914”(association)	0.530
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
ARMC6	SLC27A2	psi-mi:“MI:0914”(association)	0.530
MVK	LPCAT2	psi-mi:“MI:0915”(physical association)	0.400
LPCAT2	CREB3	psi-mi:“MI:0915”(physical association)	0.370
M2	ESYT2	psi-mi:“MI:0914”(association)	0.350
POMK	ESYT2	psi-mi:“MI:0914”(association)	0.350
RHOA	TAX1BP3	psi-mi:“MI:0914”(association)	0.350
IQCB1	PCP4L1	psi-mi:“MI:0914”(association)	0.350
	SDCBP	psi-mi:“MI:0914”(association)	0.350
MGARP	BTAF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (90): LPCAT2 (Affinity Capture-MS), LPCAT2 (Affinity Capture-MS), LPCAT2 (Affinity Capture-MS), LPCAT2 (Two-hybrid), LPCAT2 (Affinity Capture-MS), LPCAT2 (Proximity Label-MS), ERGIC3 (Two-hybrid), FAM134C (Two-hybrid), RHBDD1 (Two-hybrid), EBP (Two-hybrid), HIATL1 (Two-hybrid), KCNJ6 (Two-hybrid), HSD17B13 (Two-hybrid), LPCAT2 (Affinity Capture-MS), LPCAT2 (Proximity Label-MS)

ESM2 similar proteins: A0A0M4FCN7, A7M6E7, A7M6E8, B4G0F3, B8BKI7, C6JS30, E0CTF3, F4JJJ3, K7K424, K7PEY4, O23617, O48780, O80437, O80738, Q0VCR6, Q0WUI9, Q1LWG4, Q2R483, Q4V9F0, Q5FVP8, Q5XF03, Q5ZJD8, Q6P342, Q6PAZ3, Q70VZ8, Q7L5N7, Q8BYI6, Q8K3K7, Q8L7M0, Q8S8S2, Q94A08, Q94AH8, Q96MH6, Q96PD7, Q9ASU1, Q9C6L5, Q9CAY3, Q9D1E8, Q9D850, Q9DCV3

Diamond homologs: A0AAR7, A0JM59, A5D9H7, A5PMR2, A5PN09, A6H8I0, A6NNY8, A6QNM7, A6QR55, A6ZY34, A7TGY3, A7Z056, A8HAL1, B1WBD7, B2GUX4, B2GUZ1, B2RQC2, B3LGK1, D3ZU96, E1B9W9, F8VPZ3, M9PD06, O22207, O57429, O60139, O75604, O88623, O94966, P0C8Z3, P25296, P32571, P35123, P35125, P39538, P39944, P40818, P43080, P46065, P51784, Q01988

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
LPCAT2	“up-regulates quantity”	1,2-diacyl-sn-glycero-3-phosphocholine	“chemical modification”
LPCAT2	“up-regulates quantity”	“coenzyme A(4-)”	“chemical modification”
LPCAT2	“down-regulates quantity”	1-O-acyl-sn-glycero-3-phosphocholine	“chemical modification”
LPCAT2	“down-regulates quantity”	acyl-CoA(4-)	“chemical modification”
MAPKAPK2	“up-regulates activity”	LPCAT2	phosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	48
Likely benign	7
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
625853	NM_017839.5(LPCAT2):c.172-6188G>A	Pathogenic

SpliceAI

2613 predictions. Top by Δscore:

Variant	Effect	Δscore
16:55528591:GGCA:G	donor_gain	1.0000
16:55528592:GCA:G	donor_gain	1.0000
16:55528592:GCAG:G	donor_gain	1.0000
16:55528595:G:GG	donor_gain	1.0000
16:55529833:A:AG	acceptor_gain	1.0000
16:55529834:G:GG	acceptor_gain	1.0000
16:55529943:CCCAG:C	donor_loss	1.0000
16:55529945:CAG:C	donor_loss	1.0000
16:55529946:AGG:A	donor_loss	1.0000
16:55529947:GG:G	donor_loss	1.0000
16:55529948:G:GC	donor_loss	1.0000
16:55529949:T:G	donor_loss	1.0000
16:55531818:A:AG	acceptor_gain	1.0000
16:55531819:A:G	acceptor_gain	1.0000
16:55545813:GCAGA:G	donor_gain	1.0000
16:55545816:GA:G	donor_gain	1.0000
16:55545817:AG:A	donor_loss	1.0000
16:55545818:G:GG	donor_gain	1.0000
16:55545819:TAAG:T	donor_loss	1.0000
16:55545820:AAGT:A	donor_loss	1.0000
16:55549271:TTTTA:T	acceptor_loss	1.0000
16:55549274:TA:T	acceptor_loss	1.0000
16:55549275:A:AG	acceptor_gain	1.0000
16:55549276:G:GA	acceptor_loss	1.0000
16:55549276:G:GG	acceptor_gain	1.0000
16:55549276:GA:G	acceptor_gain	1.0000
16:55549398:TTGAA:T	donor_gain	1.0000
16:55549400:GAA:G	donor_gain	1.0000
16:55549401:AA:A	donor_gain	1.0000
16:55549402:AG:A	donor_loss	1.0000

AlphaMissense

3531 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:55549314:G:C	D325H	1.000
16:55509311:T:C	F44L	0.999
16:55509313:C:A	F44L	0.999
16:55509313:C:G	F44L	0.999
16:55531970:A:C	K233N	0.999
16:55531970:A:T	K233N	0.999
16:55545802:G:C	R307P	0.999
16:55549315:A:C	D325A	0.999
16:55549315:A:T	D325V	0.999
16:55549316:C:A	D325E	0.999
16:55549316:C:G	D325E	0.999
16:55509309:C:A	P43H	0.998
16:55509312:T:C	F44S	0.998
16:55509312:T:G	F44C	0.998
16:55529885:T:C	S194P	0.998
16:55531923:T:C	F218L	0.998
16:55531925:C:A	F218L	0.998
16:55531925:C:G	F218L	0.998
16:55531932:G:C	G221R	0.998
16:55534461:T:A	W261R	0.998
16:55534461:T:C	W261R	0.998
16:55549314:G:T	D325Y	0.998
16:55549315:A:G	D325G	0.998
16:55549319:C:G	C326W	0.998
16:55549324:T:C	L328S	0.998
16:55528501:C:G	H146D	0.997
16:55528517:A:T	D151V	0.997
16:55529859:T:A	V185D	0.997
16:55529919:G:C	R205P	0.997
16:55531933:G:A	G221D	0.997

dbSNP variants (sampled 300 via entrez): RS1000017028 (16:55525038 A>C), RS1000166669 (16:55585092 G>A), RS1000173844 (16:55554166 A>G), RS1000324958 (16:55546721 G>A,T), RS1000335872 (16:55539103 A>G), RS1000367809 (16:55532096 A>C), RS1000442201 (16:55539717 A>G), RS1000452097 (16:55539436 C>T), RS1000500178 (16:55552352 G>A), RS1000674082 (16:55538152 T>G), RS1000676964 (16:55547180 T>C), RS1000786663 (16:55586313 A>G), RS1000970140 (16:55510945 C>T), RS1001054535 (16:55545023 C>G,T), RS1001173426 (16:55555929 C>T)

Disease associations

OMIM: gene MIM:612040 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): multicentric osteolysis-nodulosis-arthropathy spectrum (MONDO:0018298)

Orphanet (2): Torg-Winchester syndrome (Orphanet:3460), Multicentric osteolysis-nodulosis-arthropathy spectrum (Orphanet:371428)

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001856_19	Thyroid hormone levels	5.000000e-08
GCST001856_23	Thyroid hormone levels	1.000000e-06
GCST004029_33	Angiotensin-converting enzyme inhibitor intolerance	3.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004730	hormone measurement
EFO:0005325	response to angiotensin-converting enzyme inhibitor

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases methylation, affects cotreatment, increases expression, affects expression	8
Benzo(a)pyrene	increases methylation, decreases expression, increases expression	3
Tretinoin	increases expression, decreases expression	3
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
bisphenol A	affects cotreatment, increases expression	1
trichostatin A	increases expression	1
sulforaphane	increases expression	1
cobaltous chloride	decreases expression	1
butyraldehyde	increases expression	1
manganese chloride	increases expression, increases abundance	1
potassium chromate(VI)	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
entinostat	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
torcetrapib	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Cadmium	decreases expression, increases abundance	1
Cisplatin	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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