AGPAT4

protein-coding

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

Gene summary

This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. This integral membrane protein converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020133.3

Inheritance

—

ClinVar variants

U:36B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr6:161,129,967-161,274,061

External References & Databases

Ensembl (ENSG00000026652)

Transcript & Mutation Effects

hg38 • Region Span ~144.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AGPAT4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 33

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020133.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar			2
missense			33 clinvar	2 clinvar		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	36	2	0	38

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020133.3	RefSeq	NP_064518.1	8	MANE Select
ENST00000320285.9	Ensembl	ENSP00000314036.4	8	MANE Select
ENST00000366905.3	Ensembl	ENSP00000355872.3	2	Standard
ENST00000366905.4	Ensembl	ENSP00000355872.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerolipid metabolism - Homo sapiens (human)
Glycerophospholipid metabolism - Homo sapiens (human)
Phospholipase D signaling pathway - Homo sapiens (human)
Triacylglyceride Synthesis
Metabolism of lipids

Biological Process

phospholipid metabolic process
phosphatidic acid biosynthetic process
phospholipid biosynthetic process
CDP-diacylglycerol biosynthetic process
macromolecule metabolic process

Molecular Function

1-acylglycerol-3-phosphate O-acyltransferase activity
protein binding
transferase activity, transferring acyl groups

Cellular Component

mitochondrial outer membrane
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000320285
Coding exons: 8
Length: 144083
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.23	136	231	0.588	0.0000146	2464
Missense (PolyPhen)		40	82.009	0.48775		839
Synonymous	0.958	88	100	0.878	0.00000691	725
Loss of Function	3.19	6	22.2	0.270	0.00000130	219

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Converts lysophosphatidic acid (LPA) into phosphatidic acid by incorporating an acyl moiety at the sn-2 position of the glycerol backbone. {ECO:0000250}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.212
RVIS EVS: -0.51
RVIS percentile EVS: 21.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.972

Gene Damage Prediction

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