LPCAT2

lysophosphatidylcholine acyltransferase 2, the group of EF-hand domain containing|1-acylglycerol-3-phosphate O-acyltransferases

Basic information

Region (hg38): 16:55509071-55586666

Previous symbols: [ "AYTL1" ]

Links

ENSG00000087253 ∙ NCBI:54947 ∙ OMIM:612040 ∙ HGNC:26032 ∙ Uniprot:Q7L5N7 ∙ 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 LPCAT2 gene.

• Inborn genetic diseases (21 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPCAT2 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			10	3	3	16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			8			8
Total	0	0	18	4	3

Variants in LPCAT2

This is a list of pathogenic ClinVar variants found in the LPCAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-55509233-G-C		not specified	Uncertain significance (Apr 13, 2023)
16-55519320-G-A		Multicentric osteolysis nodulosis arthropathy spectrum	Pathogenic (-)
16-55525601-G-A			Benign (Dec 31, 2019)
16-55528412-G-A		not specified	Likely benign (Jan 19, 2022)
16-55528445-C-T		not specified	Uncertain significance (May 08, 2023)
16-55528447-G-A			Benign (Dec 31, 2019)
16-55528456-A-C		not specified	Uncertain significance (Feb 27, 2024)
16-55528565-A-G		not specified	Uncertain significance (Apr 18, 2023)
16-55529858-G-C		not specified	Uncertain significance (Feb 01, 2023)
16-55529906-G-A		not specified	Uncertain significance (Oct 18, 2021)
16-55537591-A-G		not specified	Likely benign (Jun 06, 2023)
16-55537626-A-C		not specified	Uncertain significance (Dec 03, 2021)
16-55545745-T-C		not specified	Uncertain significance (Jul 21, 2021)
16-55545802-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-55545807-T-G		not specified	Likely benign (Feb 14, 2023)
16-55550995-A-G		not specified	Uncertain significance (Oct 18, 2021)
16-55551060-T-C			Likely benign (Jul 01, 2022)
16-55566760-T-A		not specified	Uncertain significance (Jun 23, 2023)
16-55566784-G-A		not specified	Uncertain significance (Jan 23, 2024)
16-55566797-G-A		not specified	Uncertain significance (Dec 07, 2021)
16-55566809-C-T		not specified	Uncertain significance (Dec 12, 2023)
16-55566926-C-G		not specified	Uncertain significance (Feb 28, 2023)
16-55566926-C-T		not specified	Uncertain significance (Aug 20, 2023)
16-55566934-C-T		not specified	Uncertain significance (Dec 19, 2023)
16-55566985-G-C		not specified	Uncertain significance (Nov 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPCAT2	protein_coding	protein_coding	ENST00000262134	14	77673

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.12e-10	0.754	125683	0	62	125745	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	189	285	0.664	0.0000143	3490
Missense in Polyphen		51	84.448	0.60392		1051
Synonymous	-0.829	115	104	1.10	0.00000524	1086
Loss of Function	1.58	20	29.2	0.684	0.00000163	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00138	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000171	0.000167
Middle Eastern	0.000218	0.000217
South Asian	0.000263	0.000261
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses both acyltransferase and acetyltransferase activities. Activity is calcium-dependent. 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. Also catalyzes the conversion of 1-acyl-sn-glycero-3-phosphocholine to 1,2- diacyl-sn-glycero-3-phosphocholine. {ECO:0000269|PubMed:20363836, ECO:0000269|PubMed:21498505}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;Acyl chain remodelling of PC;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.475
• rvis_EVS: 0.42
• rvis_percentile_EVS: 77.06

Haploinsufficiency Scores

• pHI: 0.0714
• hipred: N
• hipred_score: 0.307
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.290

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpcat2

Gene ontology

• Biological process: platelet activating factor biosynthetic process;phosphatidylcholine acyl-chain remodeling;membrane organization
• Cellular component: Golgi membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi stack;lipid droplet;integral component of membrane
• Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;calcium ion binding;2-acylglycerol-3-phosphate O-acyltransferase activity;1-acylglycerophosphocholine O-acyltransferase activity;1-alkylglycerophosphocholine O-acetyltransferase activity