LCAT

gene
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Summary

LCAT (lecithin-cholesterol acyltransferase, HGNC:6522) is a protein-coding gene on chromosome 16q22.1, encoding Phosphatidylcholine-sterol acyltransferase (P04180). Central enzyme in the extracellular metabolism of plasma lipoproteins.

This gene encodes the extracellular cholesterol esterifying enzyme, lecithin-cholesterol acyltransferase. The esterification of cholesterol is required for cholesterol transport. Mutations in this gene have been found to cause fish-eye disease as well as LCAT deficiency.

Source: NCBI Gene 3931 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): LCAT deficiency (Definitive, GenCC) — +2 more curated relationships
  • GWAS associations: 21
  • Clinical variants (ClinVar): 352 total — 19 pathogenic, 15 likely-pathogenic
  • Phenotypes (HPO): 21
  • Druggable target: yes
  • MANE Select transcript: NM_000229

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6522
Approved symbolLCAT
Namelecithin-cholesterol acyltransferase
Location16q22.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000213398
Ensembl biotypeprotein_coding
OMIM606967
Entrez3931

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000264005, ENST00000570369, ENST00000570396, ENST00000570980, ENST00000573538, ENST00000573846, ENST00000575277, ENST00000575467, ENST00000576450

RefSeq mRNA: 1 — MANE Select: NM_000229 NM_000229

CCDS: CCDS10854

Canonical transcript exons

ENST00000264005 — 6 exons

ExonStartEnd
ENSE000006921686794305667943212
ENSE000013080706793975067940478
ENSE000034780426794267167942766
ENSE000035645386794286167942976
ENSE000036006016794236367942587
ENSE000038939236794394867944120

Expression profiles

Bgee: expression breadth ubiquitous, 194 present calls, max score 99.12.

FANTOM5 (CAGE): breadth broad, TPM avg 1.4337 / max 324.4416, expressed in 183 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
1578341.4337183

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lobe of liverUBERON:000111499.12gold quality
right hemisphere of cerebellumUBERON:001489096.16gold quality
tibial nerveUBERON:000132396.14gold quality
left lobe of thyroid glandUBERON:000112096.11gold quality
apex of heartUBERON:000209896.05gold quality
liverUBERON:000210796.01gold quality
right lobe of thyroid glandUBERON:000111995.80gold quality
ascending aortaUBERON:000149695.68gold quality
right coronary arteryUBERON:000162595.64gold quality
thoracic aortaUBERON:000151595.55gold quality
endocervixUBERON:000045895.54gold quality
body of uterusUBERON:000985395.49gold quality
lower esophagus muscularis layerUBERON:003583395.13gold quality
lower esophagusUBERON:001347395.10gold quality
left coronary arteryUBERON:000162694.93gold quality
esophagogastric junction muscularis propriaUBERON:003584194.92gold quality
right lungUBERON:000216794.81gold quality
cerebellar hemisphereUBERON:000224594.78gold quality
descending thoracic aortaUBERON:000234594.76gold quality
upper lobe of left lungUBERON:000895294.76gold quality
cerebellar cortexUBERON:000212994.66gold quality
metanephros cortexUBERON:001053394.49gold quality
left uterine tubeUBERON:000130394.45gold quality
aortaUBERON:000094794.33gold quality
thyroid glandUBERON:000204694.30gold quality
omental fat padUBERON:001041494.07gold quality
coronary arteryUBERON:000162194.03gold quality
peritoneumUBERON:000235893.99gold quality
muscle layer of sigmoid colonUBERON:003580593.89gold quality
mucosa of stomachUBERON:000119993.83gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.57

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PAX3, SP1, SP3, STAT3

Literature-anchored findings (GeneRIF, showing 40)

  • The lecithin:cholesterol acyltransferase (LCAT) activity in cord blood was extremely low. (PMID:11882335)
  • Results suggest that LCAT may take part in the detoxification of oxidants even after the loss of its cholesterol esterification function. (PMID:11966470)
  • IL-6 induced activation of full-length LCAT promoter activity. A minimal IL-6 response element mapped within the distal promoter and was sufficient to mediate the IL-6 response (PMID:12032172)
  • In conclusion, 12% of Hypoalphalipoproteinemia subjects were found to carry mutations in apo A-I, LCAT, or GBA genes (PMID:12048121)
  • The results suggest that as follicle maturation progresses, Toc and Asc concentrations increase in follicular fluid, thus protecting LCAT from oxidative damage and loss of activity (PMID:12051518)
  • Endotoxin-lipoprotein complex formation as a factor in atherogenesis: associations with hyperlipidemia and with lecithin:cholesterol acyltransferase activity (PMID:12139471)
  • comparison of 5 natural point mutations of apo A-I illustrates that a specific sequence between amino acids 110 and 162 is required for LCAT activation (PMID:12573451)
  • 608T polymorphism of LCAT gene was associated with higher plasma HDL-C level in Coronary Arteriosclerosis patients. (PMID:12673583)
  • Familial lecithin:cholesterol acyltransferase (LCAT) deficiency, arising from mutation, is associated with complete absence of Lecithin:cholesterol acyltransferase (LCAT) activity. (PMID:12957688)
  • Postprandial chylomicrons may play an important role in promoting reverse cholesterol transport in vivo by serving as the preferred ultimate vehicle for transporting cholesterol released from cell membranes to the liver via LCAT and CETP. (PMID:15102891)
  • T13M mutation of LCAT gene causes fish-eye disease. (PMID:15115696)
  • tested whether rare sequence variants of ABCA1, APOA1, and LCAT collectively contribute to variation in plasma levels of high density lipoprotein cholesterol; nonsynonymous sequence variants were significantly more common in individuals with low HDL-C (PMID:15297675)
  • role of LCAT in estradiol-2 esterification and its involvement in antioxidant protection of HDL (PMID:15472210)
  • Selective LCAT-mediated reactivity with pre-beta 1-high density lipoprotein represents a novel mechanism increasing the efficiency of reverse cholesterol transport. (PMID:15544352)
  • Deficiency is manifested by fish eye disease. (PMID:15936482)
  • the inheritance of a mutated LCAT genotype causes a gene-dose-dependent alteration in the plasma lipid/lipoprotein profile, which is remarkably similar between subjects classified as LCAT deficiency or fish eye disease (PMID:15994445)
  • a novel G–>A mutation in exon 6 of LCAT gene, which resulted in an amino acid substitution of valine for methionine in familial LCAT deficiency (PMID:16051254)
  • Mutation underlies increased carotid artery intima-media thickness, which suggests that LCAT protects against atherosclerosis. (PMID:16061733)
  • analysis of mutations in the LCAT gene that result in an intermediate phenotype between LCAT-deficiency and fish-eye disease (case report) (PMID:16216249)
  • Decreased LDL in LCAT-deficiency is attributable to increased catabolism caused by rapid catabolism of abnormal LDL and upregulation of LDL receptor pathway. Decreased catabolism of LpX contributes to its accumulation in LCAT-deficiency. (Lipoprotein X) (PMID:16543491)
  • Redistribution of charged residues in mutant LCAT may be a major factor responsible for the dramatically reduced activity of the enzyme with HDL and reconstituted high density lipoprotein (rHDL). (PMID:16780378)
  • The LCAT 608C/T polymorphism is possibly a predisposing factor in atherosclerotic cerebral infarction happening of Chinese Han population. (PMID:16883530)
  • HDL particles generated by this pathway may account at least for some of the atheroprotective functions of apolipoprotein E (PMID:17206937)
  • Apolipoprotein A=I activation affects the kinetics of the LCAT reaction (PMID:17216278)
  • decreased cholesterol-total cholesterol ratio in the plasma of human apolipoprotein A-I transgenic Scavenger Receptors, Class B, Type I-/- mice is attributed to a reduction in LCAT reactivity with sphingomyelin-enriched HDL particles (PMID:17272829)
  • analysis of mutations in LCAT in two patients with severe LCAT deficiency [case report] (PMID:17526537)
  • The study establishes that apoA-I(Leu141Arg)Pisa and apoA-I(Leu159Arg)FIN inhibit an early step in the biogenesis of HDL due to inefficient esterification of the cholesterol of the prebeta1-HDL particles by the endogenous LCAT. (PMID:17711302)
  • Multiple linear regression analysis confirmed the independent association of cellular cholesterol efflux to plasma with cholesteryl ester transfer protein genotype (PMID:18178167)
  • Analysis of the LCAT gene showed two novel point mutations in exon 2 and exon 3, leading to amino acid substitution. As far, these mutations have not been reported in FLD or FED patients. (PMID:18397721)
  • HbA1c provides an easy-to-assess, accurate measure of LCAT activity in type 2 diabetes. (PMID:18485513)
  • oxidation of a single Met in apoA-I results in impaired LCAT activation (PMID:18719109)
  • Plasma LCAT activity is elevated in metabolic syndrome and may be a marker of subclinical atherosclerosis (PMID:18782872)
  • Functional LCAT is not required for macrophage cholesterol efflux to human serum. (PMID:18922527)
  • Recent research findings from animal and human studies have revealed a potential beneficial role of LCAT in reducing atherosclerosis–REVIEW (PMID:19306528)
  • Suggest that a LCAT-/- genotype associated with an APOE epsilon2 allele could be a novel mechanism leading to dysbetalipoproteinemia in familial LCAT deficient patients. (PMID:19515369)
  • Low LCAT plasma levels are not associated with increased atherosclerosis in the general population. (PMID:19671930)
  • Genetically determined low LCAT activity in Italian families is not associated with enhanced preclinical atherosclerosis despite low high-density lipoprotein cholesterol levels. (PMID:19687369)
  • lecithin:cholesterol acyltransferase activity is not responsible for low incidence of cardiovascular events (PMID:19698944)
  • Plasma lecithin: cholesterol acyltransferase activity modifies the inverse relationship of C-reactive protein with HDL cholesterol in nondiabetic men. (PMID:19800416)
  • Novel N-terminal mutation of human apolipoprotein A-I reduces self-association and impairs LCAT activation (PMID:20884842)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriolcatENSDARG00000099424
mus_musculusLcatENSMUSG00000035237
rattus_norvegicusLcatENSRNOG00000019573

Paralogs (1): PLA2G15 (ENSG00000103066)

Protein

Protein identifiers

Phosphatidylcholine-sterol acyltransferaseP04180 (reviewed: P04180)

Alternative names: 1-alkyl-2-acetylglycerophosphocholine esterase, Lecithin-cholesterol acyltransferase, Phospholipid-cholesterol acyltransferase, Platelet-activating factor acetylhydrolase

All UniProt accessions (8): A0A140VK24, P04180, I3L0J6, I3L1Q6, I3L215, I3L3R0, J3QKT0, J3QSE5

UniProt curated annotations — full annotation on UniProt →

Function. Central enzyme in the extracellular metabolism of plasma lipoproteins. Synthesized mainly in the liver and secreted into plasma where it converts cholesterol and phosphatidylcholines (lecithins) to cholesteryl esters and lysophosphatidylcholines on the surface of high and low density lipoproteins (HDLs and LDLs). The cholesterol ester is then transported back to the liver. Has a preference for plasma 16:0-18:2 or 18:O-18:2 phosphatidylcholines. Also produced in the brain by primary astrocytes, and esterifies free cholesterol on nascent APOE-containing lipoproteins secreted from glia and influences cerebral spinal fluid (CSF) APOE- and APOA1 levels. Together with APOE and the cholesterol transporter ABCA1, plays a key role in the maturation of glial-derived, nascent lipoproteins. Required for remodeling high-density lipoprotein particles into their spherical forms. Catalyzes the hydrolysis of 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine (platelet-activating factor or PAF) to 1-O-alkyl-sn-glycero-3-phosphocholine (lyso-PAF). Also catalyzes the transfer of the acetate group from PAF to 1-hexadecanoyl-sn-glycero-3-phosphocholine forming lyso-PAF. Catalyzes the esterification of (24S)-hydroxycholesterol (24(S)OH-C), also known as cerebrosterol to produce 24(S)OH-C monoesters.

Subcellular location. Secreted.

Tissue specificity. Detected in blood plasma. Detected in cerebral spinal fluid (at protein level). Detected in liver. Expressed mainly in brain, liver and testes.

Post-translational modifications. O- and N-glycosylated. O-glycosylation on Thr-431 and Ser-433 consists of sialylated galactose beta 1–>3N-acetylgalactosamine structures. N-glycosylated sites contain sialylated triantennary and/or biantennary complex structures.

Disease relevance. Lecithin-cholesterol acyltransferase deficiency (LCATD) [MIM:245900] A disorder of lipoprotein metabolism characterized by inadequate esterification of plasmatic cholesterol. Two clinical forms are recognized: complete LCAT deficiency and fish-eye disease. LCATD is generally referred to the complete form which is associated with absence of both alpha and beta LCAT activities resulting in esterification anomalies involving both HDL (alpha-LCAT activity) and LDL (beta-LCAT activity). It causes a typical triad of diffuse corneal opacities, target cell hemolytic anemia, and proteinuria with renal failure. The disease is caused by variants affecting the gene represented in this entry. Fish-eye disease (FED) [MIM:136120] A disorder of lipoprotein metabolism due to partial lecithin-cholesterol acyltransferase deficiency that affects only alpha-LCAT activity. FED is characterized by low plasma HDL and corneal opacities due to accumulation of cholesterol deposits in the cornea (‘fish-eye’). The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. APOA1 is the most potent activator in plasma. Also activated by APOE, APOC1 and APOA4. Inhibited by haptoglobin and 5,5’-dithiobis-(2-nitrobenzoic acid) (DTNB).

Miscellaneous. Levels of LCAT activity correlates inversely with leptin levels as well as with obesity for a wide range of BMI values.

Similarity. Belongs to the AB hydrolase superfamily. Lipase family.

RefSeq proteins (1): NP_000220* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003386LACT/PDAT_acylTrfaseFamily
IPR029058AB_hydrolase_foldHomologous_superfamily

Pfam: PF02450

Enzyme classification (BRENDA):

  • EC 2.3.1.43 — phosphatidylcholine-sterol O-acyltransferase (BRENDA: 17 organisms, 163 substrates, 53 inhibitors, 25 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

7 substrates with measured Km, best-characterized 7. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
1,2-BIS-(1-PYRENEBUTANOYL)-SN-GLYCERO-3-PHOSPHOC0.14–20.56
1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE0.0006–0.0273
CHOLESTEROL0.57–21.43
PHOSPHATIDYLCHOLINE2
1,2-BIS[4-(1-PYRENO)BUTANOYL]-SN-GLYCERO-3-PHOSP0.00061
APOLIPOPROTEIN-A-I0.00011
DEHYDROERGOSTEROL0.0031

Catalyzed reactions (Rhea), 12 shown:

  • a 1-O-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H2O = a 1-O-alkyl-sn-glycero-3-phosphocholine + acetate + H(+) (RHEA:17777)
  • a sterol + a 1,2-diacyl-sn-glycero-3-phosphocholine = a sterol ester + a 1-acyl-sn-glycero-3-phosphocholine (RHEA:21204)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + H2O = 1-hexadecanoyl-sn-glycero-3-phosphocholine + (5Z,8Z,11Z,14Z)-eicosatetraenoate + H(+) (RHEA:40427)
  • 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine + H2O = (9Z,12Z)-octadecadienoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine + H(+) (RHEA:40811)
  • a 1-hexadecanoyl-2-acyl-sn-glycero-3-phosphocholine + (24S)-hydroxycholesterol = (24S)-24-hydroxycholesterol ester + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:43216)
  • (24S)-hydroxycholesterol + 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine = (24S)-hydroxycholesterol 3-linoleoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:43224)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-sn-glycero-3-phosphocholine + cholesterol = cholesteryl (5Z,8Z,11Z,14Z)-eicosatetraenoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:53448)
  • 1-hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphocholine + cholesterol = cholesteryl (9Z-octadecenoate) + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:53456)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z-eicosatrienoyl)-sn-glycero-3-phosphocholine + cholesterol = cholesteryl (5Z,8Z,11Z)-eicosatrienoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:53460)
  • 1-hexadecanoyl-2-(8Z,11Z,14Z-eicosatrienoyl)-sn-glycero-3-phosphocholine + cholesterol = cholesteryl (8Z,11Z,14Z)-eicosatrienoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:53464)
  • 1-hexadecanoyl-2-(5Z,8Z,11Z,14Z,17Z-eicosapentaenoyl)-sn-glycero-3-phosphocholine + cholesterol = (5Z,8Z,11Z,14Z,17Z-eicosapentaenoyl)-cholesterol + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:53468)
  • 1-hexadecanoyl-2-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphocholine + cholesterol = cholesteryl (9Z,12Z)-octadecadienoate + 1-hexadecanoyl-sn-glycero-3-phosphocholine (RHEA:53472)

UniProt features (111 total): sequence variant 44, strand 19, helix 17, turn 11, glycosylation site 6, mutagenesis site 5, active site 3, disulfide bond 2, signal peptide 1, chain 1, site 1, sequence conflict 1

Structure

Experimental structures (PDB)

7 structures.

PDBMethodResolution (Å)
5BV7X-RAY DIFFRACTION2.45
4XWGX-RAY DIFFRACTION2.65
5TXFX-RAY DIFFRACTION3.1
6MVDX-RAY DIFFRACTION3.1
4XX1X-RAY DIFFRACTION3.6
4X96X-RAY DIFFRACTION8.69
9MXZELECTRON MICROSCOPY9.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P04180-F187.330.73

Antibody-complex structures (SAbDab): 34XWG, 4XX1, 5BV7

Functional residue map

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

Catalytic / active sites (4): 205 (nucleophile); 369 (charge relay system); 401 (charge relay system); 173 (determinant for substrate specificity)

Disulfide bonds (2): 74–98, 337–380

Glycosylation sites (6): 431, 433, 44, 108, 296, 408

Mutagenesis-validated functional residues (5):

PositionPhenotype
173increased activity towards papc. increased papc/popc activity ratio.
173little change in enzyme specific activity nor in papc/popc activity ratio.
173decreased enzyme specific activity. increased papc/popc activity ratio.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-8964058HDL remodeling
R-HSA-174824Plasma lipoprotein assembly, remodeling, and clearance
R-HSA-382551Transport of small molecules
R-HSA-8963899Plasma lipoprotein remodeling

MSigDB gene sets: 239 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_METABOLIC_PROCESS, chr16q22, GOBP_STEROL_HOMEOSTASIS, GOBP_LIPOPROTEIN_METABOLIC_PROCESS, GOBP_PHOSPHATIDYLCHOLINE_BIOSYNTHETIC_PROCESS, GNF2_GSTM1, GOBP_RESPONSE_TO_CORTICOSTEROID, LFA1_Q6, GNF2_HPN, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_RESPONSE_TO_COPPER_ION, GOBP_PROTEIN_LIPID_COMPLEX_ASSEMBLY, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS

GO Biological Process (17): lipid metabolic process (GO:0006629), phospholipid metabolic process (GO:0006644), phosphatidylcholine biosynthetic process (GO:0006656), cholesterol metabolic process (GO:0008203), cholesterol transport (GO:0030301), very-low-density lipoprotein particle remodeling (GO:0034372), high-density lipoprotein particle remodeling (GO:0034375), lipoprotein biosynthetic process (GO:0042158), cholesterol homeostasis (GO:0042632), reverse cholesterol transport (GO:0043691), aflatoxin metabolic process (GO:0046222), phosphatidylcholine metabolic process (GO:0046470), response to copper ion (GO:0046688), response to glucocorticoid (GO:0051384), regulation of high-density lipoprotein particle assembly (GO:0090107), steroid metabolic process (GO:0008202), lipoprotein metabolic process (GO:0042157)

GO Molecular Function (11): 1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847), phosphatidylcholine-sterol O-acyltransferase activity (GO:0004607), A2-type glycerophospholipase activity (GO:0004623), sterol ester esterase activity (GO:0004771), apolipoprotein A-I binding (GO:0034186), platelet-activating factor acetyltransferase activity (GO:0047179), protein binding (GO:0005515), obsolete O-acyltransferase activity (GO:0008374), transferase activity (GO:0016740), acyltransferase activity (GO:0016746), hydrolase activity (GO:0016787)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), high-density lipoprotein particle (GO:0034364), extracellular exosome (GO:0070062), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Plasma lipoprotein remodeling1
Transport of small molecules1
Plasma lipoprotein assembly, remodeling, and clearance1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
carboxylic ester hydrolase activity3
lipid metabolic process2
catalytic activity2
cellular anatomical structure2
primary metabolic process1
organophosphate metabolic process1
phosphatidylcholine metabolic process1
glycerophospholipid biosynthetic process1
sterol metabolic process1
secondary alcohol metabolic process1
sterol transport1
triglyceride-rich lipoprotein particle remodeling1
plasma lipoprotein particle remodeling1
macromolecule biosynthetic process1
lipoprotein metabolic process1
sterol homeostasis1
cholesterol transport1
mycotoxin metabolic process1
glycerophospholipid metabolic process1
response to metal ion1
response to corticosteroid1
high-density lipoprotein particle assembly1
regulation of protein-containing complex assembly1
regulation of multicellular organismal process1
protein metabolic process1
acyltransferase activity, transferring groups other than amino-acyl groups1
glycerophospholipase activity1
lipase activity1
apolipoprotein binding1
acetyltransferase activity1
binding1
transferase activity1
plasma lipoprotein particle1
extracellular vesicle1

Protein interactions and networks

STRING

1590 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LCATAPOA1P02647997
LCATCETPP11597955
LCATAPOBP04114938
LCATAPOA2P02652912
LCATABCA1O95477911
LCATPON1P27169874
LCATAPODP05090856
LCATAPOC3P02656849
LCATPLTPP55058828
LCATPSKH1P11801810
LCATAPOEP02649800
LCATSCARB1Q8WTV0794
LCATLIPCP11150778
LCATAPOC2P02655777
LCATLPLP06858777

IntAct

6 interactions, top by confidence:

ABTypeScore
APOA1LCATpsi-mi:“MI:0407”(direct interaction)0.620
LCATWFS1psi-mi:“MI:0915”(physical association)0.560

BioGRID (13): APOA1 (Reconstituted Complex), PIKFYVE (Co-crystal Structure), LCAT (Affinity Capture-Western), LCAT (Reconstituted Complex), LCAT (Reconstituted Complex), LCAT (Reconstituted Complex), LCAT (Co-purification), LCAT (Co-purification), APOA1 (Biochemical Activity), APOA1 (Reconstituted Complex), APOA1 (Biochemical Activity), APOE (Biochemical Activity), LCAT (Two-hybrid)

ESM2 similar proteins: A0A3Q2HW92, A2AIG8, A4FV98, A5PK45, A6NDV4, A6QLK4, A6QQ24, D3YWP0, F1PZV2, O09009, O15303, O35790, O55240, P04180, P35349, Q08758, Q0P5C0, Q1JPJ0, Q3T0A0, Q3T9M1, Q3U481, Q501J2, Q5E9V4, Q5SX19, Q6AYG0, Q6NUT3, Q863I4, Q86VF5, Q86VU5, Q8BVM4, Q8K297, Q8NBJ5, Q8R2H9, Q8TCT0, Q8TCT1, Q8TCT7, Q8VCE6, Q92781, Q96AZ1, Q96FB5

Diamond homologs: O35502, O35573, O35724, O35840, P04180, P16301, P18424, P30930, P53760, P53761, Q08758, Q675A5, Q6XPZ3, Q8NCC3, Q8VEB4, Q8WMP9, Q9FZI8, P40345, Q10PI6, Q4VCM1, Q9FYC7, Q9FNA9

SIGNOR signaling

1 interactions.

AEffectBMechanism
APOA1“up-regulates activity”LCATbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic19
Likely pathogenic15
Uncertain significance143
Likely benign131
Benign8

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1969478NM_000229.2(LCAT):c.23G>A (p.Trp8Ter)Pathogenic
2736369NM_000229.2(LCAT):c.803G>A (p.Arg268His)Pathogenic
2879462NM_000229.2(LCAT):c.849G>A (p.Trp283Ter)Pathogenic
3581207NM_000229.2(LCAT):c.511C>T (p.Arg171Trp)Pathogenic
3656NM_000229.2(LCAT):c.508T>C (p.Trp170Arg)Pathogenic
3657NM_000229.2(LCAT):c.951G>A (p.Met317Ile)Pathogenic
3658NM_000229.2(LCAT):c.491_493dup (p.Arg164_Ala165insGly)Pathogenic
3659NM_000229.2(LCAT):c.756C>A (p.Asn252Lys)Pathogenic
3660NM_000229.2(LCAT):c.440C>T (p.Thr147Ile)Pathogenic
3661NM_000229.2(LCAT):c.101dup (p.His35fs)Pathogenic
3662NM_000229.2(LCAT):c.101C>T (p.Pro34Leu)Pathogenic
3665NM_000229.2(LCAT):c.827T>A (p.Met276Lys)Pathogenic
3666NM_000229.2(LCAT):c.698T>C (p.Leu233Pro)Pathogenic
3669NM_000229.2(LCAT):c.1197dup (p.Gln400fs)Pathogenic
3672NM_000229.2(LCAT):c.969CCT[1] (p.Leu325del)Pathogenic
3673NM_000229.2(LCAT):c.463A>G (p.Asn155Asp)Pathogenic
3674NM_000229.2(LCAT):c.524-22T>CPathogenic
626357NM_000229.2(LCAT):c.997G>A (p.Val333Met)Pathogenic
626358NM_000229.2(LCAT):c.1210A>G (p.Met404Val)Pathogenic
1338728NM_000229.2(LCAT):c.802C>T (p.Arg268Cys)Likely pathogenic
1764448NM_000229.2(LCAT):c.1267C>T (p.Arg423Cys)Likely pathogenic
2585273NM_000229.2(LCAT):c.428-2A>TLikely pathogenic
2631093NM_000229.2(LCAT):c.160G>A (p.Gly54Ser)Likely pathogenic
3067749NM_000229.2(LCAT):c.713del (p.Gly238fs)Likely pathogenic
3581201NM_000229.2(LCAT):c.799C>T (p.Gln267Ter)Likely pathogenic
3581202NM_000229.2(LCAT):c.794_795del (p.Glu265fs)Likely pathogenic
3581209NM_000229.2(LCAT):c.488_489del (p.Val163fs)Likely pathogenic
3581214NM_000229.2(LCAT):c.254G>A (p.Trp85Ter)Likely pathogenic
3581217NM_000229.2(LCAT):c.142_154+1dupLikely pathogenic
3581220NM_000229.2(LCAT):c.115A>T (p.Lys39Ter)Likely pathogenic

SpliceAI

1035 predictions. Top by Δscore:

VariantEffectΔscore
16:67940480:T:Gacceptor_loss1.0000
16:67942444:T:TAdonor_gain1.0000
16:67942588:C:CCacceptor_gain1.0000
16:67942666:CTCA:Cdonor_loss1.0000
16:67942667:TCA:Tdonor_loss1.0000
16:67942668:CACCG:Cdonor_loss1.0000
16:67942669:A:ACdonor_gain1.0000
16:67942669:A:Tdonor_loss1.0000
16:67942670:C:Adonor_loss1.0000
16:67942670:C:CCdonor_gain1.0000
16:67942670:CCGGG:Cdonor_gain1.0000
16:67942765:CC:Cacceptor_gain1.0000
16:67942766:CC:Cacceptor_gain1.0000
16:67942856:CAAA:Cdonor_loss1.0000
16:67942857:AAACC:Adonor_loss1.0000
16:67942858:AAC:Adonor_loss1.0000
16:67942859:A:Tdonor_loss1.0000
16:67942860:C:Adonor_loss1.0000
16:67942972:CAACC:Cacceptor_gain1.0000
16:67942975:CC:Cacceptor_gain1.0000
16:67942975:CCCT:Cacceptor_loss1.0000
16:67942976:CC:Cacceptor_gain1.0000
16:67942976:CCT:Cacceptor_loss1.0000
16:67942977:C:CCacceptor_gain1.0000
16:67942978:T:Aacceptor_loss1.0000
16:67943053:TA:Tdonor_loss1.0000
16:67943054:A:ATdonor_loss1.0000
16:67943055:CCT:Cdonor_loss1.0000
16:67943213:C:CCacceptor_gain1.0000
16:67940476:CAC:Cacceptor_gain0.9900

AlphaMissense

2864 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:67943074:C:GC98S0.998
16:67943075:A:TC98S0.998
16:67943146:C:GC74S0.998
16:67943147:A:TC74S0.998
16:67942497:C:AS205I0.997
16:67942739:A:GL152P0.996
16:67943074:C:TC98Y0.996
16:67943075:A:GC98R0.996
16:67943145:G:CC74W0.996
16:67943147:A:GC74R0.996
16:67943183:C:GA62P0.996
16:67940121:T:AD369V0.995
16:67942686:A:GW170R0.995
16:67942686:A:TW170R0.995
16:67943074:C:AC98F0.995
16:67943114:A:GW85R0.995
16:67943114:A:TW85R0.995
16:67943146:C:TC74Y0.995
16:67943193:A:CN58K0.995
16:67943193:A:TN58K0.995
16:67940122:C:GD369H0.994
16:67942419:A:TI231N0.994
16:67942431:A:TI227N0.994
16:67942442:C:AK223N0.994
16:67942442:C:GK223N0.994
16:67942703:C:GR164P0.994
16:67943073:G:CC98W0.994
16:67943146:C:AC74F0.994
16:67943188:A:GL60P0.994
16:67940099:G:CS376R0.993

dbSNP variants (sampled 300 via entrez): RS1001326689 (16:67939513 T>C), RS1001452642 (16:67942544 C>T), RS1001580962 (16:67945274 TC>T), RS1002920761 (16:67939502 C>T), RS1002935033 (16:67939686 G>A,T), RS1003101800 (16:67944195 G>A,T), RS1003139704 (16:67942571 G>A), RS1003444341 (16:67942772 G>A,C), RS1003769357 (16:67944193 A>G), RS1003800705 (16:67943911 T>C,G), RS1004727769 (16:67941827 T>C), RS1004923760 (16:67941342 C>T), RS1005551039 (16:67941574 G>A,T), RS1005597574 (16:67944230 G>A,T), RS1005931116 (16:67942791 G>A,C)

Disease associations

OMIM: gene MIM:606967 | disease phenotypes: MIM:245900, MIM:136120

GenCC curated gene-disease

DiseaseClassificationInheritance
LCAT deficiencyDefinitiveAutosomal recessive
fish eye diseaseDefinitiveAutosomal recessive
Norum diseaseStrongAutosomal recessive

Mondo (3): Norum disease (MONDO:0009515), fish eye disease (MONDO:0007620), LCAT deficiency (MONDO:0018999)

Orphanet (3): Familial LCAT deficiency (Orphanet:79293), LCAT deficiency (Orphanet:650), Fish-eye disease (Orphanet:79292)

HPO phenotypes

21 total (21 of 21 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000083Renal insufficiency
HP:0000093Proteinuria
HP:0000505Visual impairment
HP:0001084Corneal arcus
HP:0001681Angina pectoris
HP:0001744Splenomegaly
HP:0001878Hemolytic anemia
HP:0001895Normochromic anemia
HP:0002155Hypertriglyceridemia
HP:0002240Hepatomegaly
HP:0002621Atherosclerosis
HP:0002716Lymphadenopathy
HP:0003141Increased LDL cholesterol concentration
HP:0003233Decreased HDL cholesterol concentration
HP:0003362Increased VLDL cholesterol concentration
HP:0003581Adult onset
HP:0003651Foam cells
HP:0007759Opacification of the corneal stroma
HP:0007957Corneal opacity
HP:0025433Decreased lecithin cholesterol acyl transferase level

GWAS associations

21 associations (top):

StudyTraitp-value
GCST000135_8HDL cholesterol1.000000e-07
GCST000284_3HDL cholesterol3.000000e-08
GCST000290_13HDL cholesterol9.000000e-13
GCST000755_31HDL cholesterol8.000000e-33
GCST000805_12HDL cholesterol2.000000e-07
GCST000974_7HDL cholesterol2.000000e-11
GCST002223_11HDL cholesterol8.000000e-54
GCST002539_84Schizophrenia2.000000e-08
GCST002899_33HDL cholesterol9.000000e-26
GCST004232_35HDL cholesterol levels3.000000e-09
GCST004232_4HDL cholesterol levels3.000000e-57
GCST004234_11HDL cholesterol levels4.000000e-10
GCST005446_33Total cholesterol levels in HDL6.000000e-10
GCST006614_16Total cholesterol levels1.000000e-14
GCST006803_42Schizophrenia4.000000e-08
GCST007850_6HDL cholesterol2.000000e-10
GCST008035_65High density lipoprotein cholesterol levels2.000000e-16
GCST008035_66High density lipoprotein cholesterol levels1.000000e-06
GCST010002_113Refractive error2.000000e-14
GCST90002397_246Mean spheric corpuscular volume2.000000e-32
GCST90002403_680Red blood cell count1.000000e-15

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004574total cholesterol measurement
EFO:0004305erythrocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5942 (SINGLE PROTEIN)

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

Binding affinities (BindingDB)

5 measured of 6 human assays (6 total across all organisms); most potent 5 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
(+)-4,5-Dihydroxy-4-(trifluoromethyl)-3-{1-[5-(trifluoromethyl)pyrazin-2-yl]piperidin-4-yl}-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-oneEC504 nMUS-10138240: Crystal of 5-hydroxy-4-(trifluoromethyl)pyrazolopyridine derivative
(+)-cis-5-Hydroxy-4-(trifluoromethyl)-3-{1-[2-(trifluoromethyl)pyrimidin-5-yl]piperidin-4-yl}-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-oneEC5018 nMUS-10138240: Crystal of 5-hydroxy-4-(trifluoromethyl)pyrazolopyridine derivative
Difluoroketone phospholipid analogue, 3IC5028 nM
Difluoroketone phospholipid analogue, 2IC5060 nM
Difluoroketone phospholipid analogue, 4IC5060 nM

ChEMBL bioactivities

152 potent at pChembl≥5 of 152 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.40EC504nMCHEMBL4571766
8.40EC504nMCHEMBL4444702
8.15EC507nMCHEMBL4543681
8.15EC507nMCHEMBL4444091
8.15EC507nMCHEMBL4567833
8.10EC508nMCHEMBL4449961
8.05EC509nMCHEMBL4438875
7.96EC5011nMCHEMBL4565710
7.92EC5012nMCHEMBL4565889
7.89EC5013nMCHEMBL4475628
7.89EC5013nMCHEMBL4449770
7.89EC5013nMCHEMBL4444770
7.82EC5015nMCHEMBL4462753
7.75EC5018nMCHEMBL4438084
7.75EC5018nMCHEMBL4435610
7.75EC5018nMCHEMBL4592989
7.75EC5018nMCHEMBL4463860
7.70EC5020nMCHEMBL4453452
7.68EC5021nMCHEMBL4438084
7.68EC5021nMCHEMBL4455643
7.68EC5021nMCHEMBL4445217
7.66EC5022nMCHEMBL4567833
7.64EC5023nMCHEMBL4443799
7.64EC5023nMCHEMBL4445235
7.62EC5024nMCHEMBL4456783
7.58EC5026nMCHEMBL4442211
7.57EC5027nMCHEMBL4445217
7.57EC5027nMCHEMBL4541184
7.57EC5027nMCHEMBL4435684
7.54EC5029nMCHEMBL4514555
7.52EC5030nMCHEMBL4536836
7.51EC5031nMCHEMBL4483570
7.51EC5031nMCHEMBL4563848
7.50EC5032nMCHEMBL4575561
7.50EC5032nMCHEMBL4461575
7.47EC5034nMCHEMBL4450717
7.46EC5035nMCHEMBL4515289
7.46EC5035nMCHEMBL4577479
7.46EC5035nMCHEMBL4466792
7.46EC5035nMCHEMBL4567145
7.43EC5037nMCHEMBL4461964
7.43EC5037nMCHEMBL4440456
7.43EC5037nMCHEMBL4448781
7.40EC5040nMCHEMBL4526869
7.39EC5041nMCHEMBL4436647
7.37EC5043nMCHEMBL4440507
7.35EC5045nMCHEMBL4435430
7.34EC5046nMCHEMBL4453731
7.32EC5048nMCHEMBL4567290
7.30EC5050nMCHEMBL4454322

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporinedecreases expression3
bisphenol Aaffects expression, affects cotreatment, decreases methylation2
Hydrogen Peroxidedecreases expression, affects cotreatment, decreases activity, increases oxidation2
Tobacco Smoke Pollutiondecreases activity, decreases expression2
Valproic Aciddecreases expression, increases methylation2
Particulate Matterdecreases expression, increases abundance, increases expression2
aristolochic acid Iincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
tris(2-butoxyethyl) phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
1,2-oleoylphosphatidylcholineaffects binding1
4-hydroxy-2-nonenaldecreases expression1
polyserinedecreases reaction, increases chemical synthesis, increases metabolic processing1
27-hydroxycholesterolincreases metabolic processing1
K 7174decreases expression1
obeticholic aciddecreases expression1
abrineincreases expression1
Decitabineaffects expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyrenedecreases expression1
Cadmiumdecreases expression, increases abundance1
Chlorineaffects binding, decreases activity, increases reaction1
Cholesterolincreases acylation1
Cholesterol Estersincreases chemical synthesis, increases metabolic processing, decreases reaction1
Cisplatinaffects expression1
Copperdecreases activity1

ChEMBL screening assays

5 unique, capped per target: 5 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1015040BindingInhibition of LCAT activity in human plasma assessed as change in cholesteryl ester/free cholesterol ratio by cell based assayDesign, synthesis, and biological evaluation of (2R,alphaS)-3,4-dihydro-2-[3-(1,1,2,2-tetrafluoroethoxy)phenyl]-5-[3-(trifluoromethoxy)-phenyl]-alpha-(trifluoromethyl)-1(2H)-quinolineethanol as potent and orally active cholesteryl ester transfer protein inhibitor. — J Med Chem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03368066PHASE3COMPLETEDIs Adrenal Insufficiency Under-diagnosed in Hospitalized Cirrhosis Patients?
NCT01283867PHASE1COMPLETEDBioequivalence Study of Mycophenolate Mofetil 500 mg Tablets of Dr.Reddy’s Laboratories Limited Under Non-Fasting Conditions
NCT01283932PHASE1COMPLETEDBioequivalence Study of Pantoprazole Sodium DR Tablets 40 mg of Dr. Reddy’s Laboratories Limited Under Fed Condition
NCT01314352PHASE1COMPLETEDBioavailability Study of Desloratadine 5 mg Tablet of Dr. Reddy’s Under Fed Conditions
NCT01372306PHASE1COMPLETEDGalantamine Bioequivalence Study of Dr. Reddy’s Under Fed Condition
NCT01372358PHASE1COMPLETEDBioavailability Study of Ciprofloxacin 1000 mg ER Tablets of Dr. Reddy’s Under Non-Fasting Conditions
NCT01503424PHASE1COMPLETEDBioequivalence Study of Olanzapine Tablets, 5 mg Under Fed Study
NCT01503450PHASE1COMPLETEDBioequivalence Study of Olanzapine Orally Disintegrating Tablets, 5 mg Under Fed Condition
NCT01505998PHASE1COMPLETEDBioequivalence Study of Amlodipine Besylate/Benazepril HCl 10 mg/40 mg Capsules of Dr. Reddy’s Under Fed Conditions
NCT01567501PHASE1COMPLETEDBioequivalence Study of Levocetirizine Dihydrochloride Tablets 5 mg Under Fed Condition
NCT01578265PHASE1COMPLETEDBioequivalence Study of Ondansetron Tablets USP 8 mg Under Fed Condition
NCT01603186PHASE1COMPLETEDBioequivalence Study of Quetiapine Fumarate Tablets 25 mg Under Fed Condition
NCT01618760PHASE1COMPLETEDBioequivalence Study of Risperidone Tablet 1 mg Under Fed Condition
NCT01618825PHASE1COMPLETEDBioequivalence Study of Lamotrigine Tablets 25 mg (2 x 25 mg Tablets) Under Fed Condition
NCT01722110PHASE1COMPLETEDBioequivalence Study of Indomethacin Extended-Release Capsules 75 mg Under Fed Condition
NCT01735344PHASE1COMPLETEDBioequivalence Study of Lisinopril Tablets 40 mg Under Fed Condition
NCT01735383PHASE1COMPLETEDBioequivalence Study of Etodolac Tablet USP 500 mg Under Fed Condition
NCT01744873PHASE1COMPLETEDBioequivalence Study of Bisoprolol Fumarate Tablet 10 mg Under Fed Condition
NCT01827878PHASE1COMPLETEDBioequivalence Study of Lisinopril and Hydrochlorothiazide Tablets (20+25) mg Under Fed Conditions
NCT01884909PHASE1COMPLETEDBioequivalence Study of Metoprolol Succinate Extended Release Tablets 200 mg Under Fed Conditions
NCT07396844PHASE1NOT_YET_RECRUITINGThe Food Effect on Pharmacokinetics of Fixed Dose Combination of Gemigliptin/Dapagliflozin/Metformin in Healthy Volunteers
NCT01782027Not specifiedTERMINATEDMendelian Reverse Cholesterol Transport Study
NCT04737720Not specifiedCOMPLETEDIntravenous ACP-501 for Familial LCAT Deficiency (rhLCAT)
NCT06217588Not specifiedRECRUITINGLCAT (Lecithin Cholesterol Acyl Transferase) Natural History Study
NCT05995119EARLY_PHASE1COMPLETEDComparative Bioavailability Study of TAH3311 5 mg Oral Dissolving Film vs ELIQUIS® 5 mg Tablet in Healthy Volunteers
NCT01721187Not specifiedCOMPLETEDSatiety Effects on the Neural Valuation of Food
NCT03390881Not specifiedCOMPLETEDUse of Breath Acetone aa a Marker of Energy Balance
NCT05837572Not specifiedUNKNOWNDevelopment of the Leeds Food Preference Questionnaire in Spanish