LPCAT3

lysophosphatidylcholine acyltransferase 3, the group of Membrane bound O-acyltransferase family

Basic information

Region (hg38): 12:6976184-7018477

Previous symbols: [ "OACT5", "MBOAT5" ]

Links

ENSG00000111684 ∙ NCBI:10162 ∙ OMIM:611950 ∙ HGNC:30244 ∙ Uniprot:Q6P1A2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LPCAT3 gene.

• Inborn genetic diseases (20 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPCAT3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	20	0	1

Variants in LPCAT3

This is a list of pathogenic ClinVar variants found in the LPCAT3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-6977155-C-G		not specified	Uncertain significance (Sep 16, 2021)
12-6977208-T-C		not specified	Uncertain significance (Feb 08, 2023)
12-6977229-A-T		not specified	Uncertain significance (Nov 08, 2022)
12-6977231-A-G		not specified	Uncertain significance (Sep 29, 2023)
12-6977497-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-6977725-T-C		not specified	Uncertain significance (Jun 08, 2022)
12-6978348-C-G		not specified	Uncertain significance (Nov 29, 2021)
12-6978357-T-G		not specified	Uncertain significance (Jan 23, 2023)
12-6978380-A-G		not specified	Uncertain significance (Jun 29, 2022)
12-6978389-G-A		not specified	Uncertain significance (Nov 18, 2022)
12-6978659-T-C		not specified	Uncertain significance (Jul 14, 2022)
12-6981145-C-G		not specified	Uncertain significance (Nov 04, 2022)
12-6981860-G-A			Benign (Dec 31, 2019)
12-6981910-A-G			Benign (Dec 31, 2019)
12-6982696-T-C		not specified	Uncertain significance (Apr 13, 2023)
12-6982702-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-6982716-C-T		not specified	Uncertain significance (Oct 05, 2023)
12-6982722-A-G		not specified	Uncertain significance (Oct 27, 2021)
12-6982732-G-C		not specified	Uncertain significance (Sep 16, 2021)
12-6983477-G-A		not specified	Uncertain significance (Aug 16, 2022)
12-7018351-T-C		not specified	Uncertain significance (Sep 01, 2021)
12-7018373-C-A		not specified	Uncertain significance (Oct 27, 2022)
12-7018381-A-G		not specified	Uncertain significance (Apr 07, 2023)
12-7018412-C-T		not specified	Uncertain significance (Jul 14, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPCAT3	protein_coding	protein_coding	ENST00000261407	12	40467

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00492	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	153	266	0.576	0.0000134	3164
Missense in Polyphen		46	105.89	0.4344		1246
Synonymous	-0.117	107	105	1.01	0.00000546	945
Loss of Function	4.47	3	29.0	0.104	0.00000150	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acyltransferase which mediates the conversion of lysophosphatidylcholine (1-acyl-sn-glycero-3-phosphocholine or LPC) into phosphatidylcholine (1,2-diacyl-sn-glycero-3- phosphocholine or PC) (LPCAT activity). Catalyzes also the conversion of lysophosphatidylserine (1-acyl-2-hydroxy-sn-glycero- 3-phospho-L-serine or LPS) into phosphatidylserine (1,2-diacyl-sn- glycero-3-phospho-L-serine or PS) (LPSAT activity). Has also weak lysophosphatidylethanolamine acyltransferase activity (LPEAT activity). Favors polyunsaturated fatty acyl-CoAs as acyl donors compared to saturated fatty acyl-CoAs. Seems to be the major enzyme contributing to LPCAT activity in the liver. Lysophospholipid acyltransferases (LPLATs) catalyze the reacylation step of the phospholipid remodeling pathway also known as the Lands cycle. {ECO:0000269|PubMed:18195019, ECO:0000269|PubMed:18772128}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Ferroptosis - Homo sapiens (human);Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Acyl chain remodelling of PC;triacylglycerol biosynthesis;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE (Consensus)

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.404
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.73

Haploinsufficiency Scores

• pHI: 0.295
• hipred: Y
• hipred_score: 0.658
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lpcat3
• Phenotype: liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: phospholipid biosynthetic process;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;regulation of plasma lipoprotein particle levels
• Cellular component: endoplasmic reticulum membrane;membrane;integral component of membrane
• Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;2-acylglycerol-3-phosphate O-acyltransferase activity;1-acylglycerophosphocholine O-acyltransferase activity