LPCAT4

Summary

LPCAT4 (lysophosphatidylcholine acyltransferase 4, HGNC:30059) is a protein-coding gene on chromosome 15q14, encoding Lysophospholipid acyltransferase LPCAT4 (Q643R3). Displays acyl-CoA-dependent lysophospholipid acyltransferase activity with a subset of lysophospholipids as substrates; converts lysophosphatidylethanolamine to phosphatidylethanolamine, lysophosphatidylcholine to phosphatidycholine, 1-alkenyl-lysophatidylethanolamine to 1-alken….

Members of the 1-acylglycerol-3-phosphate O-acyltransferase (EC 2.3.1.51) family, such as AGPAT7, catalyze the conversion of lysophosphatidic acid (LPA) to phosphatidic acid (PA), a precursor in the biosynthesis of all glycerolipids. Both LPA and PA are involved in signal transduction (Ye et al., 2005 [PubMed 16243729]).

Source: NCBI Gene 254531 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 83 total
• MANE Select transcript: NM_153613

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30059
Approved symbol	LPCAT4
Name	lysophosphatidylcholine acyltransferase 4
Location	15q14
Locus type	gene with protein product
Status	Approved
Aliases	FLJ10257, LPAAT-eta, LPEAT2, LPLAT10
Ensembl gene	ENSG00000176454
Ensembl biotype	protein_coding
OMIM	612039
Entrez	254531

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 5 protein_coding, 5 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 TEC

ENST00000314891, ENST00000562404, ENST00000562431, ENST00000563240, ENST00000563748, ENST00000566581, ENST00000567507, ENST00000569804, ENST00000623384, ENST00000927809, ENST00000927810, ENST00000927811, ENST00000954576

RefSeq mRNA: 1 — MANE Select: NM_153613 NM_153613

CCDS: CCDS32191

Canonical transcript exons

ENST00000314891 — 14 exons

Exon	Start	End
ENSE00001253149	34364013	34364073
ENSE00001253225	34363422	34363456
ENSE00001253341	34366987	34367196
ENSE00001379614	34364194	34364306
ENSE00001380482	34363661	34363719
ENSE00001388957	34362782	34362836
ENSE00003493967	34360111	34360209
ENSE00003524206	34362196	34362321
ENSE00003525596	34365559	34365701
ENSE00003540312	34362573	34362655
ENSE00003630257	34361400	34361532
ENSE00003655651	34359589	34359745
ENSE00003693023	34365008	34365228
ENSE00003714179	34358633	34359302

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.5757 / max 213.2970, expressed in 1789 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
149252	20.2421	1787
149251	0.3337	125

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right hemisphere of cerebellum	UBERON:0014890	99.48	gold quality
cerebellar hemisphere	UBERON:0002245	99.42	gold quality
cerebellar cortex	UBERON:0002129	99.40	gold quality
lower esophagus mucosa	UBERON:0035834	99.19	gold quality
cerebellum	UBERON:0002037	98.85	gold quality
right frontal lobe	UBERON:0002810	98.31	gold quality
mucosa of transverse colon	UBERON:0004991	98.27	gold quality
apex of heart	UBERON:0002098	97.73	gold quality
transverse colon	UBERON:0001157	97.49	gold quality
rectum	UBERON:0001052	97.38	gold quality
nucleus accumbens	UBERON:0001882	97.36	gold quality
Brodmann (1909) area 9	UBERON:0013540	97.35	gold quality
small intestine Peyer’s patch	UBERON:0003454	97.13	gold quality
esophagus mucosa	UBERON:0002469	96.93	gold quality
cingulate cortex	UBERON:0003027	96.85	gold quality
anterior cingulate cortex	UBERON:0009835	96.84	gold quality
lateral nuclear group of thalamus	UBERON:0002736	96.80	gold quality
caudate nucleus	UBERON:0001873	96.70	gold quality
putamen	UBERON:0001874	96.70	gold quality
ectocervix	UBERON:0012249	96.70	gold quality
cerebellar vermis	UBERON:0004720	96.51	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	96.44	gold quality
pons	UBERON:0000988	96.20	gold quality
mucosa of stomach	UBERON:0001199	96.18	gold quality
body of stomach	UBERON:0001161	96.01	gold quality
prefrontal cortex	UBERON:0000451	95.99	gold quality
primary visual cortex	UBERON:0002436	95.91	gold quality
small intestine	UBERON:0002108	95.82	gold quality
frontal pole	UBERON:0002795	95.80	gold quality
paraflocculus	UBERON:0005351	95.74	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	18.58
E-GEOD-93593	yes	6.61
E-MTAB-10137	no	8.59

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting LPCAT4, 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-190A-3P	100.00	80.35	5520
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-6083	99.47	68.73	2393
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-410-3P	99.27	69.98	2457
HSA-MIR-4468	98.01	66.85	1187
HSA-MIR-10397-3P	97.78	65.70	601
HSA-MIR-7976	95.75	65.67	1186
HSA-MIR-874-3P	95.02	65.66	806

Literature-anchored findings (GeneRIF, showing 4)

• report the cloning and characterization of a novel human 1-acyl-sn-glycerol-3-phosphate acyltransferase member AGPAT7 (1-acyl-sn-glycerol-3-phosphate acyltransferase 7) gene, which was mapped to human chromosome 15q14 (PMID:16243729)
• LPEAT2 as an important enzyme in the biosynthesis of ethanolamine-containing phospholipids, especially in brain. (PMID:18458083)
• LPCAT4 is overexpressed and involved in the deregulation of PC(16:0/16:1) in colorectal cancer. (PMID:23815430)
• LPCAT4 Knockdown Alters Barrier Integrity and Cellular Bioenergetics in Human Urothelium. (PMID:36233185)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	lpcat4	ENSDARG00000035028
mus_musculus	Lpcat4	ENSMUSG00000027134
rattus_norvegicus	Lpcat4	ENSRNOG00000005058
drosophila_melanogaster	LPCAT	FBGN0052699

Paralogs (4): LPCAT2 (ENSG00000087253), GPAT3 (ENSG00000138678), LPCAT1 (ENSG00000153395), GPAT4 (ENSG00000158669)

Protein

Protein identifiers

Lysophospholipid acyltransferase LPCAT4 — Q643R3 (reviewed: Q643R3)

Alternative names: 1-acylglycerol-3-phosphate O-acyltransferase 7, 1-acylglycerophosphocholine O-acyltransferase, 1-acylglycerophosphoserine O-acyltransferase, 1-alkenylglycerophosphoethanolamine O-acyltransferase, 1-alkylglycerophosphocholine O-acetyltransferase, Acyltransferase-like 3, Lysophosphatidylcholine acyltransferase 4, Lysophosphatidylethanolamine acyltransferase 2, Plasmalogen synthase

All UniProt accessions (2): Q643R3, H3BMK4

UniProt curated annotations — full annotation on UniProt →

Function. Displays acyl-CoA-dependent lysophospholipid acyltransferase activity with a subset of lysophospholipids as substrates; converts lysophosphatidylethanolamine to phosphatidylethanolamine, lysophosphatidylcholine to phosphatidycholine, 1-alkenyl-lysophatidylethanolamine to 1-alkenyl-phosphatidylethanolamine, lysophosphatidylglycerol and alkyl-lysophosphatidylcholine to phosphatidylglycerol and alkyl-phosphatidylcholine, respectively. In contrast, has no lysophosphatidylinositol, glycerol-3-phosphate, diacylglycerol or lysophosphatidic acid acyltransferase activity. Prefers long chain acyl-CoAs (C16, C18) as acyl donors.

Subcellular location. Endoplasmic reticulum membrane.

Tissue specificity. Widely expressed with predominant level in brain.

Pathway. Lipid metabolism; phospholipid metabolism.

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

RefSeq proteins (1): NP_705841* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002123	Plipid/glycerol_acylTrfase	Domain
IPR045252	LPCAT1-like	Domain

Pfam: PF01553

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)

Substrate kinetics (BRENDA)

25 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
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
1-ACYL-2-LYSOPHOSPHATIDYLETHANOLAMINE	0.08	1

Catalyzed reactions (Rhea), 12 shown:

• a 1-acyl-sn-glycero-3-phosphocholine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphocholine + CoA (RHEA:12937)
• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine + an acyl-CoA = a 1-O-(1Z-alkenyl)-2-acyl-sn-glycero-3-phosphoethanolamine + CoA (RHEA:16245)
• 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-phosphoethanolamine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phosphoethanolamine + CoA (RHEA:32995)
• a 1-acyl-sn-glycero-3-phospho-L-serine + an acyl-CoA = a 1,2-diacyl-sn-glycero-3-phospho-L-serine + CoA (RHEA:33191)
• a 1-acyl-sn-glycero-3-phosphocholine + (9Z)-octadecenoyl-CoA = a 1-acyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphocholine + CoA (RHEA:33359)
• 1-hexadecanoyl-sn-glycero-3-phospho-L-serine + (9Z)-octadecenoyl-CoA = 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-L-serine + CoA (RHEA:37531)
• a 1-acyl-sn-glycero-3-phosphoethanolamine + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA = 1-acyl-2-(5Z,8Z,11Z,14Z)-eicosatetraenoyl-sn-glycero-3-phosphoethanolamine + CoA (RHEA:37575)
• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine + (9Z)-octadecenoyl-CoA = 1-O-(1Z)-alkenyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphoethanolamine + CoA (RHEA:37631)
• a 1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine + (5Z,8Z,11Z,14Z)-eicosatetraenoyl-CoA = 1-O-(1Z)-alkenyl-2-(5Z,8Z,11Z,14Z)-eicosatetraenoyl-sn-glycero-3-phosphoethanolamine + CoA (RHEA:37635)
• 1-octadecanoyl-sn-glycero-3-phospho-(1’-sn-glycerol) + (9Z)-octadecenoyl-CoA = 1-octadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phospho-(1’-sn-glycerol) + CoA (RHEA:37647)
• a 1-acyl-sn-glycero-3-phosphoethanolamine + (9Z)-octadecenoyl-CoA = 1-acyl-2-(9Z)-octadecenoyl-sn-glycero-3-phosphoethanolamine + CoA (RHEA:37731)

UniProt features (7 total): transmembrane region 2, chain 1, region of interest 1, short sequence motif 1, compositionally biased region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q643R3-F1	83.78	0.51

Functional residue map

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

Glycosylation sites (1): 152

Function

Pathways and Gene Ontology

Reactome pathways

9 pathways

ID	Pathway
R-HSA-1482788	Acyl chain remodelling of PC
R-HSA-1482801	Acyl chain remodelling of PS
R-HSA-1482839	Acyl chain remodelling of PE
R-HSA-1482925	Acyl chain remodelling of PG
R-HSA-1483166	Synthesis of PA
R-HSA-1430728	Metabolism
R-HSA-1483206	Glycerophospholipid biosynthesis
R-HSA-1483257	Phospholipid metabolism
R-HSA-556833	Metabolism of lipids

MSigDB gene sets: 157 (showing top): GOBP_PHOSPHATIDYLSERINE_ACYL_CHAIN_REMODELING, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, MATTIOLI_MGUS_VS_PCL, chr15q14, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, USF_C, GOBP_PHOSPHATIDYLGLYCEROL_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, DOANE_RESPONSE_TO_ANDROGEN_DN, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS

GO Biological Process (8): phospholipid metabolic process (GO:0006644), phosphatidic acid biosynthetic process (GO:0006654), phosphatidylglycerol acyl-chain remodeling (GO:0036148), phosphatidylserine acyl-chain remodeling (GO:0036150), phosphatidylcholine acyl-chain remodeling (GO:0036151), phosphatidylethanolamine acyl-chain remodeling (GO:0036152), lipid metabolic process (GO:0006629), phospholipid biosynthetic process (GO:0008654)

GO Molecular Function (12): 1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841), lysophosphatidic acid acyltransferase activity (GO:0042171), 2-acylglycerol-3-phosphate O-acyltransferase activity (GO:0047144), 1-alkenylglycerophosphoethanolamine O-acyltransferase activity (GO:0047166), 1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184), 1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192), lysophospholipid acyltransferase activity (GO:0071617), 1-acylglycerophosphoethanolamine O-acyltransferase activity (GO:0106262), 1-acylglycerophosphoserine O-acyltransferase activity (GO:0106263), obsolete O-acyltransferase activity (GO:0008374), transferase activity (GO:0016740), acyltransferase activity (GO:0016746)

GO Cellular Component (3): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Glycerophospholipid biosynthesis	5
Phospholipid metabolism	1
Metabolism of lipids	1
Metabolism	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
acyltransferase activity, transferring groups other than amino-acyl groups	5
phosphatidylcholine metabolic process	2
lysophosphatidic acid acyltransferase activity	2
lipid metabolic process	1
organophosphate metabolic process	1
phosphatidic acid metabolic process	1
glycerophospholipid biosynthetic process	1
phosphatidylglycerol metabolic process	1
phosphatidylserine metabolic process	1
primary metabolic process	1
phospholipid metabolic process	1
lipid biosynthetic process	1
organophosphate biosynthetic process	1
acylglycerol O-acyltransferase activity	1
lysophospholipid acyltransferase activity	1
O-acetyltransferase activity	1
catalytic activity	1
transferase activity	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
cellular anatomical structure	1

Protein interactions and networks

STRING

1274 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LPCAT4	LCLAT1	Q6UWP7	660
LPCAT4	LPCAT3	Q6P1A2	649
LPCAT4	AGPAT1	Q99943	646
LPCAT4	AGPAT3	Q9NRZ7	636
LPCAT4	MBOAT2	Q6ZWT7	630
LPCAT4	AGPAT5	Q9NUQ2	624
LPCAT4	AASDH	Q4L235	603
LPCAT4	AGPAT4	Q9NRZ5	601
LPCAT4	AGPAT2	O15120	541
LPCAT4	MBOAT1	Q6ZNC8	506
LPCAT4	TAFAZZIN	Q16635	498
LPCAT4	AUP1	Q9Y679	471
LPCAT4	GPAT2	Q6NUI2	453
LPCAT4	TMC4	Q7Z404	444
LPCAT4	MBOAT7	Q96N66	440

IntAct

52 interactions, top by confidence:

A	B	Type	Score
HAVCR2	TCAF2	psi-mi:“MI:0914”(association)	0.530
LPCAT4	DUSP14	psi-mi:“MI:0914”(association)	0.530
TNFSF8	LGALS8	psi-mi:“MI:0914”(association)	0.530
LDLRAD1	ADAM10	psi-mi:“MI:0914”(association)	0.530
SLC6A8	ILVBL	psi-mi:“MI:0914”(association)	0.530
ERBB2	LPCAT4	psi-mi:“MI:0915”(physical association)	0.370
CFTR	LPCAT4	psi-mi:“MI:0915”(physical association)	0.370
SCGB2A2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
TMEM25	FUZ	psi-mi:“MI:0914”(association)	0.350
CHRM4	GEMIN2	psi-mi:“MI:0914”(association)	0.350
	TMEM223	psi-mi:“MI:0914”(association)	0.350
KCNA2	TMEM129	psi-mi:“MI:0914”(association)	0.350
IGHM	ESYT2	psi-mi:“MI:0914”(association)	0.350
TTMP	TMEM223	psi-mi:“MI:0914”(association)	0.350
TTYH1	TMEM223	psi-mi:“MI:0914”(association)	0.350
TSPAN15	TMEM223	psi-mi:“MI:0914”(association)	0.350
RAMP2	GXYLT2	psi-mi:“MI:0914”(association)	0.350
HCST	TMEM120B	psi-mi:“MI:0914”(association)	0.350
TSPAN10	KLRG2	psi-mi:“MI:0914”(association)	0.350
LRRC25	POTEF	psi-mi:“MI:0914”(association)	0.350
PCDHGC4		psi-mi:“MI:0914”(association)	0.350
TMEM59	GPR89A	psi-mi:“MI:0914”(association)	0.350
GPR12	TLCD2	psi-mi:“MI:0914”(association)	0.350
TMEM25	NME4	psi-mi:“MI:0914”(association)	0.350
CHRM4	TNPO2	psi-mi:“MI:0914”(association)	0.350
CD3D	CLGN	psi-mi:“MI:0914”(association)	0.350

BioGRID (74): LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), SPG7 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), DUSP14 (Affinity Capture-MS), DSG4 (Affinity Capture-MS), USP33 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Affinity Capture-MS), LPCAT4 (Two-hybrid)

ESM2 similar proteins: A0A061IR73, A0A7N9VSG0, A7YSY2, D3KCC4, D3ZU57, D4A2B7, O08644, O15197, O19179, O43542, O75064, O95382, P0C0K6, P0C0K7, P51840, P52785, P52824, P54777, Q02846, Q05932, Q13470, Q13608, Q1HG60, Q3ZBE0, Q4KM32, Q5JZY3, Q643R3, Q6MG64, Q6NVG1, Q6ZPS2, Q76MJ5, Q7TNJ2, Q80SX8, Q8BYG9, Q8IZY2, Q8NFF5, Q8R5G7, Q8TDZ2, Q8WWN8, Q91V24

Diamond homologs: P0C1Q3, Q0KHU5, Q1HAQ0, Q1LWG4, Q28C60, Q3TFD2, Q4V8A1, Q502J0, Q643R3, Q6DCK1, Q6NVG1, Q7L5N7, Q8BYI6, Q8L7R3, Q8NF37, Q9D5U0, Q9HW50, Q8S8S2, O73761, P43080, P46065, Q16982, Q8VBV8, G5EDN6, P48451, Q24214, Q3HRN9, P0A257, P0A258, P26647, A0AAR7, B3DLU1, B3VSB7, F8VPZ3, M9PD06, O73763, O81445, P05933, P21457, P22728

SIGNOR signaling

4 interactions.

A	Effect	B	Mechanism
LPCAT4	“up-regulates quantity”	1,2-diacyl-sn-glycero-3-phosphocholine	“chemical modification”
LPCAT4	“up-regulates quantity”	“coenzyme A(4-)”	“chemical modification”
LPCAT4	“down-regulates quantity”	1-O-acyl-sn-glycero-3-phosphocholine	“chemical modification”
LPCAT4	“down-regulates quantity”	acyl-CoA(4-)	“chemical modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1779 predictions. Top by Δscore:

Variant	Effect	Δscore
15:34359587:A:AC	donor_gain	1.0000
15:34359588:C:CC	donor_gain	1.0000
15:34359588:CAG:C	donor_gain	1.0000
15:34359588:CAGA:C	donor_gain	1.0000
15:34359588:CAGAG:C	donor_gain	1.0000
15:34359615:G:A	donor_gain	1.0000
15:34359741:AAGAG:A	acceptor_gain	1.0000
15:34359742:AGAG:A	acceptor_gain	1.0000
15:34359743:GAG:G	acceptor_gain	1.0000
15:34359744:AG:A	acceptor_gain	1.0000
15:34359745:GCTTG:G	acceptor_loss	1.0000
15:34359746:C:CC	acceptor_gain	1.0000
15:34359747:T:C	acceptor_gain	1.0000
15:34359747:T:TC	acceptor_gain	1.0000
15:34360105:CATTA:C	donor_loss	1.0000
15:34360106:ATTAC:A	donor_loss	1.0000
15:34360107:TTACC:T	donor_loss	1.0000
15:34360108:TACC:T	donor_loss	1.0000
15:34360109:ACCT:A	donor_loss	1.0000
15:34360110:CCTC:C	donor_loss	1.0000
15:34360215:G:C	acceptor_gain	1.0000
15:34361399:CCTG:C	donor_gain	1.0000
15:34361529:CAGC:C	acceptor_gain	1.0000
15:34361544:T:C	acceptor_gain	1.0000
15:34361544:T:TC	acceptor_gain	1.0000
15:34362571:A:AC	donor_gain	1.0000
15:34362572:C:CA	donor_gain	1.0000
15:34362572:CTGTG:C	donor_gain	1.0000
15:34362656:C:CC	acceptor_gain	1.0000
15:34364191:CA:C	donor_loss	1.0000

AlphaMissense

3344 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:34363712:G:C	F220L	1.000
15:34363712:G:T	F220L	1.000
15:34363714:A:G	F220L	1.000
15:34364202:A:G	W195R	1.000
15:34364202:A:T	W195R	1.000
15:34365044:A:G	S148P	1.000
15:34365085:T:A	D134V	1.000
15:34362591:A:T	V289D	0.999
15:34362654:A:G	F268S	0.999
15:34362811:A:G	S258P	0.999
15:34362813:G:T	A257D	0.999
15:34363444:A:G	W242R	0.999
15:34363444:A:T	W242R	0.999
15:34363686:A:T	V229D	0.999
15:34363689:G:T	P228H	0.999
15:34363713:A:G	F220S	0.999
15:34363714:A:T	F220I	0.999
15:34364017:T:A	K216N	0.999
15:34364017:T:G	K216N	0.999
15:34364020:G:C	F215L	0.999
15:34364020:G:T	F215L	0.999
15:34364021:A:G	F215S	0.999
15:34364022:A:G	F215L	0.999
15:34364055:C:A	G204C	0.999
15:34364055:C:G	G204R	0.999
15:34364060:G:T	P202H	0.999
15:34364062:A:C	F201L	0.999
15:34364062:A:T	F201L	0.999
15:34364064:A:G	F201L	0.999
15:34364200:C:A	W195C	0.999

dbSNP variants (sampled 300 via entrez): RS1000223760 (15:34362937 G>A,T), RS1000306184 (15:34366644 G>A), RS1000799747 (15:34364800 A>C,G), RS1000888359 (15:34360281 C>T), RS1000923738 (15:34358192 C>T), RS1001208167 (15:34358642 ATC>A), RS1001217642 (15:34365477 C>A,G,T), RS1001639622 (15:34358965 GT>G,GTT), RS1001862568 (15:34364866 T>C), RS1002162686 (15:34358808 T>C), RS1002215330 (15:34364136 G>T), RS1002246388 (15:34364566 A>G), RS1002449711 (15:34358470 G>A,C), RS1002661053 (15:34362030 T>C), RS1003248191 (15:34362708 C>T)

Disease associations

OMIM: gene MIM:612039 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008595_90	Cognitive ability, years of educational attainment or schizophrenia (pleiotropy)	8.000000e-10

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004337	intelligence
EFO:0004784	self reported educational attainment

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression, affects expression	5
sodium arsenite	decreases expression, increases abundance, increases expression	3
entinostat	decreases expression, affects cotreatment	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
avobenzone	increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	decreases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Vorinostat	decreases expression	1
Acetaminophen	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Atrazine	increases expression	1
Carbamazepine	affects expression	1
Catechin	affects cotreatment, increases expression	1
Cisplatin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Hydralazine	affects cotreatment, increases expression	1
Ivermectin	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment, decreases expression	1
Malathion	increases expression	1
Methyl Methanesulfonate	decreases expression	1

Clinical trials (associated diseases)

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