LPCAT4

lysophosphatidylcholine acyltransferase 4, the group of 1-acylglycerol-3-phosphate O-acyltransferases

Basic information

Region (hg38): 15:34358633-34367196

Previous symbols: [ "AYTL3", "AGPAT7" ]

Links

ENSG00000176454 ∙ NCBI:254531 ∙ OMIM:612039 ∙ HGNC:30059 ∙ Uniprot:Q643R3 ∙ 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 LPCAT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LPCAT4 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						0
missense			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	0	0

Variants in LPCAT4

This is a list of pathogenic ClinVar variants found in the LPCAT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-34359248-G-C		not specified	Uncertain significance (Jun 29, 2022)
15-34359293-T-C		not specified	Uncertain significance (Dec 13, 2022)
15-34359302-C-G		not specified	Uncertain significance (Dec 01, 2022)
15-34359646-C-T		not specified	Uncertain significance (Jun 22, 2023)
15-34359655-G-A		not specified	Uncertain significance (Jun 17, 2024)
15-34359684-G-C		not specified	Uncertain significance (Aug 11, 2022)
15-34359684-G-T		not specified	Uncertain significance (Aug 12, 2021)
15-34359685-T-C		not specified	Uncertain significance (Jan 16, 2024)
15-34359694-C-T		not specified	Uncertain significance (Mar 13, 2023)
15-34360152-C-A		not specified	Uncertain significance (Jan 23, 2024)
15-34361504-C-A		not specified	Uncertain significance (Dec 27, 2023)
15-34361510-C-G		not specified	Uncertain significance (Apr 30, 2024)
15-34362205-C-G		not specified	Uncertain significance (Dec 09, 2023)
15-34362205-C-T		not specified	Uncertain significance (Dec 05, 2022)
15-34362206-G-A		not specified	Uncertain significance (Apr 22, 2022)
15-34362638-G-T		not specified	Likely benign (Mar 25, 2024)
15-34363678-G-T		not specified	Uncertain significance (Jan 26, 2023)
15-34363708-C-T		not specified	Uncertain significance (Jan 23, 2024)
15-34364233-C-G		not specified	Uncertain significance (Jul 19, 2023)
15-34364295-A-G		not specified	Uncertain significance (Jan 26, 2022)
15-34365050-C-T		not specified	Uncertain significance (Feb 12, 2024)
15-34365080-T-C		not specified	Uncertain significance (Jul 25, 2023)
15-34365080-T-G		not specified	Uncertain significance (Jan 02, 2024)
15-34365119-C-G		not specified	Uncertain significance (Dec 19, 2022)
15-34365133-C-A		not specified	Uncertain significance (Nov 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LPCAT4	protein_coding	protein_coding	ENST00000314891	14	8374

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.482	0.518	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.55	224	299	0.749	0.0000171	3300
Missense in Polyphen		60	113.72	0.52762		1209
Synonymous	0.709	110	120	0.918	0.00000638	1147
Loss of Function	4.12	7	32.2	0.217	0.00000206	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. {ECO:0000269|PubMed:18458083}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Acyl chain remodelling of PC;Glycerophospholipid metabolism;triacylglycerol biosynthesis;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.121
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.169
• hipred: Y
• hipred_score: 0.523
• ghis: 0.614

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lpcat4

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidic acid biosynthetic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling
• Cellular component: endoplasmic reticulum;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-alkenylglycerophosphoethanolamine O-acyltransferase activity;1-acylglycerophosphocholine O-acyltransferase activity;1-alkylglycerophosphocholine O-acetyltransferase activity;lysophospholipid acyltransferase activity