Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	3931
Gene name	Lecithin-cholesterol acyltransferase
Gene symbol	LCAT
Synonyms (NCBI Gene)	-
Chromosome	16
Chromosome location	16q22.1
Summary	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

Show/Hide all (20)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28940886	C>T	Pathogenic	Missense variant, coding sequence variant
rs28940887	G>A	Pathogenic	Missense variant, coding sequence variant
rs28940888	G>A,T	Pathogenic	Missense variant, coding sequence variant
rs28942087	A>G	Pathogenic	Missense variant, coding sequence variant
rs121908048	C>T	Pathogenic	Coding sequence variant, missense variant
rs121908049	G>T	Pathogenic	Coding sequence variant, missense variant
rs121908050	G>A	Pathogenic	Coding sequence variant, missense variant
rs121908053	G>A	Pathogenic	Coding sequence variant, missense variant
rs121908054	A>G,T	Pathogenic	Coding sequence variant, missense variant
rs121908055	G>A,T	Pathogenic	Synonymous variant, coding sequence variant, stop gained
rs121908056	AGG>-	Pathogenic	Inframe deletion, coding sequence variant
rs121908057	T>C	Pathogenic	Coding sequence variant, missense variant
rs140068549	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs267607211	A>G	Pathogenic	Missense variant, coding sequence variant
rs387906300	G>A	Pathogenic	Missense variant, coding sequence variant
rs776035233	C>T	Pathogenic	Coding sequence variant, missense variant
rs779114194	T>C	Pathogenic	Coding sequence variant, missense variant
rs794726662	->CGC	Pathogenic	Coding sequence variant, inframe insertion
rs794726663	->T	Pathogenic	Coding sequence variant, frameshift variant
rs794726664	A>G	Pathogenic	Intron variant

Show/Hide all (31)

miRTarBase ID	miRNA	Experiments	Reference
MIRT029711	hsa-miR-26b-5p	Microarray	19088304
MIRT711551	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT711550	hsa-miR-1304-3p	HITS-CLIP	19536157
MIRT711549	hsa-miR-8064	HITS-CLIP	19536157
MIRT711548	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT711547	hsa-miR-3152-5p	HITS-CLIP	19536157
MIRT711551	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT711550	hsa-miR-1304-3p	HITS-CLIP	19536157
MIRT711549	hsa-miR-8064	HITS-CLIP	19536157
MIRT711548	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT711547	hsa-miR-3152-5p	HITS-CLIP	19536157
MIRT711551	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT711550	hsa-miR-1304-3p	HITS-CLIP	19536157
MIRT711549	hsa-miR-8064	HITS-CLIP	19536157
MIRT711548	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT711547	hsa-miR-3152-5p	HITS-CLIP	19536157
MIRT711551	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT711550	hsa-miR-1304-3p	HITS-CLIP	19536157
MIRT711549	hsa-miR-8064	HITS-CLIP	19536157
MIRT711548	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT711547	hsa-miR-3152-5p	HITS-CLIP	19536157
MIRT711551	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT711550	hsa-miR-1304-3p	HITS-CLIP	19536157
MIRT711549	hsa-miR-8064	HITS-CLIP	19536157
MIRT711548	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT711547	hsa-miR-3152-5p	HITS-CLIP	19536157
MIRT711551	hsa-miR-6890-3p	HITS-CLIP	19536157
MIRT711550	hsa-miR-1304-3p	HITS-CLIP	19536157
MIRT711549	hsa-miR-8064	HITS-CLIP	19536157
MIRT711548	hsa-miR-6836-3p	HITS-CLIP	19536157
MIRT711547	hsa-miR-3152-5p	HITS-CLIP	19536157

Show/Hide all (3)

Transcription factor	Regulation	Reference
SP1	Unknown	9610763
SP3	Unknown	9610763
STAT3	Unknown	12032172

Show/Hide all (47)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003847	Function	1-alkyl-2-acetylglycerophosphocholine esterase activity	IDA	8016111
GO:0003847	Function	1-alkyl-2-acetylglycerophosphocholine esterase activity	IEA
GO:0004607	Function	Phosphatidylcholine-sterol O-acyltransferase activity	IBA
GO:0004607	Function	Phosphatidylcholine-sterol O-acyltransferase activity	IDA	3458198, 4335615, 10559507, 15654758, 26195816
GO:0004607	Function	Phosphatidylcholine-sterol O-acyltransferase activity	IEA
GO:0004607	Function	Phosphatidylcholine-sterol O-acyltransferase activity	NAS	11966470
GO:0004607	Function	Phosphatidylcholine-sterol O-acyltransferase activity	TAS
GO:0004623	Function	Phospholipase A2 activity	IEA
GO:0004771	Function	Sterol ester esterase activity	IDA	8016111
GO:0005515	Function	Protein binding	IPI	1587806, 11435418, 14967812, 15654758, 17676061, 32814053
GO:0005576	Component	Extracellular region	IEA
GO:0005576	Component	Extracellular region	TAS
GO:0005615	Component	Extracellular space	IBA
GO:0005615	Component	Extracellular space	IDA	3458198, 4335615, 8016111, 10559507
GO:0005615	Component	Extracellular space	IEA
GO:0006629	Process	Lipid metabolic process	IBA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006644	Process	Phospholipid metabolic process	IDA	4335615
GO:0006656	Process	Phosphatidylcholine biosynthetic process	IDA	11966470
GO:0006656	Process	Phosphatidylcholine biosynthetic process	IMP	12354767
GO:0008202	Process	Steroid metabolic process	IEA
GO:0008203	Process	Cholesterol metabolic process	IDA	10559507
GO:0008203	Process	Cholesterol metabolic process	IDA	3458198, 4335615, 15654758, 26195816
GO:0008203	Process	Cholesterol metabolic process	IEA
GO:0008203	Process	Cholesterol metabolic process	IEA
GO:0008374	Function	O-acyltransferase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0030301	Process	Cholesterol transport	IDA	10559507
GO:0034186	Function	Apolipoprotein A-I binding	IPI	1587806
GO:0034364	Component	High-density lipoprotein particle	IDA	3104518
GO:0034372	Process	Very-low-density lipoprotein particle remodeling	IDA	15654758
GO:0034375	Process	High-density lipoprotein particle remodeling	IDA	4335615, 10722751, 12167653, 15210842
GO:0034375	Process	High-density lipoprotein particle remodeling	TAS
GO:0042157	Process	Lipoprotein metabolic process	IEA
GO:0042158	Process	Lipoprotein biosynthetic process	IEA
GO:0042632	Process	Cholesterol homeostasis	IDA	4335615
GO:0043691	Process	Reverse cholesterol transport	IDA	4335615
GO:0046222	Process	Aflatoxin metabolic process	IEA
GO:0046470	Process	Phosphatidylcholine metabolic process	IDA	15654758, 26195816
GO:0046688	Process	Response to copper ion	IEA
GO:0047179	Function	Platelet-activating factor acetyltransferase activity	IDA	8016111
GO:0047179	Function	Platelet-activating factor acetyltransferase activity	IEA
GO:0051384	Process	Response to glucocorticoid	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0090107	Process	Regulation of high-density lipoprotein particle assembly	IEA

MIM	HGNC	e!Ensembl
606967	6522	ENSG00000213398

P04180

Protein name

Phosphatidylcholine-sterol acyltransferase (EC 2.3.1.43) (1-alkyl-2-acetylglycerophosphocholine esterase) (EC 3.1.1.47) (Lecithin-cholesterol acyltransferase) (Phospholipid-cholesterol acyltransferase) (Platelet-activating factor acetylhydrolase) (PAF ace

Protein 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

PDB

4X96 , 4XWG , 4XX1 , 5BV7 , 5TXF , 6MVD

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02450	LCAT	81 → 408	Lecithin:cholesterol acyltransferase	Family

Tissue specificity

TISSUE SPECIFICITY: Detected in blood plasma (PubMed:10222237, PubMed:3458198, PubMed:8820107). Detected in cerebral spinal fluid (at protein level) (PubMed:10222237). Detected in liver (PubMed:3458198, PubMed:3797244). Expressed mainly in brain, liver an

Sequence

MGPPGSPWQWVTLLLGLLLPPAAPFWLLNVLFPPHTTPKAELSNHTRPVILVPGCLGNQL
EAKLDKPDVVNWMCYRKTEDFFTIWLDLNMFLPLGVDCWIDNTRVVYNRSSGLVSNAPGV
QIRVPGFGKTYSVEYLDSSKLAGYLHTLVQNLVNNGYVRDETVRAAPYDWRLEPGQQEEY
YRKLAGLVEEMHAAYGKPVFLIGHSLGCLHLLYFLLRQPQAWKDRFIDGFISLGAPWGGS
IKPMLVLASGDNQGIPIMSSIKLKEEQRITTTSPWMFPSRMAWPEDHVFISTPSFNYTGR
DFQRFFADLHFEEGWYMWLQSRDLLAGLPAPGVEVYCLYGVGLPTPRTYIYDHGFPYTDP
VGVLYEDGDDTVATRSTELCGLWQGRQPQPVHLLPLHGIQHLNMVFSNLTLEHINAILLG
AYRQGPPASPTASPEPPPPE

Sequence length

440

Interactions

View interactions

	KEGG		Reactome
	Glycerophospholipid metabolism Cholesterol metabolism		HDL remodeling

285

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cardiovascular phenotype	Likely pathogenic; Pathogenic	rs370803551, rs967875404, rs28940888	RCV002373478 RCV002362554 RCV006342070
Fish-eye disease	Likely pathogenic; Pathogenic	rs2151319998, rs121908050, rs121908051, rs28940888, rs121908055, rs121908056, rs121908057, rs794726664, rs140068549	RCV005006315 RCV000003845 RCV000003847 RCV005016233 RCV002496248 RCV000003857 RCV000003858 RCV000003859 RCV002501012
LCAT deficiency	Pathogenic; Likely pathogenic	rs267607211, rs121908048, rs794726662, rs121908049, rs967875404, rs121908054, rs28942087, rs28940887, rs794726663, rs28940888, rs121908055, rs776035233, rs779114194, rs140068549	RCV000003841 RCV000003842 RCV000003843 RCV000003844 RCV000003846 RCV000003850 RCV000003851 RCV000003853 RCV000003854 RCV000003855 RCV000003856 RCV000782355 RCV000782356 RCV000779196
LCAT-related disorder	Pathogenic; Likely pathogenic	rs121908050, rs1461145750	RCV004754238 RCV003405840
Norum disease	Likely pathogenic; Pathogenic	rs745320775, rs2151319998, rs121908050, rs121908051, rs28940888, rs121908055, rs2544406643, rs140068549	RCV001818098 RCV005006315 RCV002504739 RCV002504740 RCV005016233 RCV002496248 RCV003337889 RCV002501012

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
-	no classification for the single variant	rs28940886	-
Cervical cancer	Benign	rs13306496	RCV005914867
Gastric cancer	Benign	rs13306496	RCV005914868
Malignant tumor of esophagus	Benign	rs13306496	RCV005914866
Ovarian serous cystadenocarcinoma	Benign	rs13306496	RCV005914869
Uterine carcinosarcoma	Benign	rs13306496	RCV005914870

Show/Hide Text Mining Associations (49)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Anemia	Associate	31164121
Anemia Sickle Cell	Associate	28436274
Atherosclerosis	Associate	22133847, 29748187, 30333156
Bone Diseases	Inhibit	35235770
Carcinoma Hepatocellular	Associate	31695766, 32813933, 34034705, 34147074, 35196258, 36894886, 37215201, 39380994, 40389832, 40500772
Cardiovascular Diseases	Associate	23078883, 27112635
Corneal Dystrophies Hereditary	Associate	10869098
Corneal Opacity	Associate	31164121
Coronary Artery Disease	Associate	8675648
Coronary Disease	Associate	30479275
De Barsy syndrome	Associate	8445342
Diabetes Mellitus	Inhibit	10412780
Diabetes Mellitus	Associate	30055622, 8820100
Dyslipidemias	Associate	28315561, 29084231, 29758034
Genetic Diseases Inborn	Associate	8755645, 8820100
Glomerulonephritis Membranous	Associate	37511514
Hemolytic Uremic Syndrome	Inhibit	10412780
Hemolytic Uremic Syndrome	Associate	6482172
HIV Infections	Associate	33173066
Hydrocephalus Normal Pressure	Associate	34360799
Hyperlipoproteinemia Type II	Associate	27112635
Hypertriglyceridemia	Associate	26687706
Hypoalphalipoproteinemias	Associate	1737840, 22658148, 30333156, 31164121
Hypobetalipoproteinemias	Associate	22658148
Hypogonadism	Associate	25565309
Hypoxia	Associate	37481543
Kidney Diseases	Associate	28576974
Lecithin Cholesterol Acyltransferase Deficiency	Associate	10450185, 10849435, 1516702, 1737840, 19687369, 2052566, 21597230, 25589508, 28576974, 29748187, 30479275, 31164121, 39537502, 7721870, 7989589 View all (5 more)
Lecithin Cholesterol Acyltransferase Deficiency	Inhibit	17183024, 21597230, 22658148, 30529744, 35598637, 7294021, 8445342
Liver Cirrhosis	Associate	35235770
Liver Diseases	Associate	35235770
Liver Failure	Inhibit	35235770
Lupus Erythematosus Systemic	Associate	32678854
Lysosomal acid lipase deficiency	Associate	32058863
Macular Degeneration	Associate	37447314
Metabolic Diseases	Associate	29084231, 35598637
Metabolic Syndrome	Associate	30055622
Neoplasms	Inhibit	37215201
Nephritis Interstitial	Associate	25565309
Nephrotic Syndrome	Stimulate	37511514
Obesity	Associate	29758034
Optic Nerve Hypoplasia	Associate	32602905
Osteoporosis	Associate	37447314
Proteinuria	Associate	8445342
Pseudohypoparathyroidism	Associate	35235770
Rhinitis Allergic	Associate	31185305
Stiff Skin Syndrome	Associate	23078883
Tangier Disease	Associate	26687706
Weight Loss	Associate	28545455

LCAT (lecithin-cholesterol acyltransferase)