GPAT2

protein-coding

glycerol-3-phosphate acyltransferase 2, mitochondrial, the group of Glycerol-3-phosphate acyltransferases

Gene summary

Enables glycerol-3-phosphate O-acyltransferase activity. Predicted to be involved in glycerol-3-phosphate metabolic process; glycerolipid biosynthetic process; and piRNA processing. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001321527.2

Inheritance

—

ClinVar variants

P:3U:108B:10

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 0.8

Max pathogenic AF

—

Genomic locus

chr2:96,021,946-96,039,451

External References & Databases

Ensembl (ENSG00000186281)

Transcript & Mutation Effects

hg38 • Region Span ~17.5 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 GPAT2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 109

Male infertilityTotal: 6

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001321527.2. 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			1 clinvar	2 clinvar		3
missense		1 clinvar	105 clinvar	8 clinvar		114
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar	2 clinvar			3
Total	0	3	108	10	0	121

Highest pathogenic variant AF is 0.00003234845

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 124 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001321527.2	RefSeq	NP_001308456.1	21	MANE Select
ENST00000434632.6	Ensembl	ENSP00000389395.2	21	MANE Select
NM_001321525.2	RefSeq	NP_001308454.1	21	Standard
NM_001321526.2	RefSeq	NP_001308455.1	21	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)
Metabolism of lipids
Metabolism
CDP-diacylglycerol biosynthesis

Biological Process

glycerol-3-phosphate metabolic process
fatty acid metabolic process
phosphatidic acid biosynthetic process
phospholipid biosynthetic process
CDP-diacylglycerol biosynthetic process

Molecular Function

glycerol-3-phosphate O-acyltransferase activity
sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity

Cellular Component

mitochondrion
mitochondrial outer membrane
integral component of membrane
mitochondrial membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000434632
Coding exons: 21
Length: 17506
Individuals with no LoFs: 124742
Homozygous LoFs: 0
Heterozygous LoFs: 62
Defined: 124804
p: 0.000248

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.167	295	287	1.03	0.0000176	5024
Missense (PolyPhen)		13	16.168	0.80408		167
Synonymous	-0.856	140	128	1.10	0.00000766	1689
Loss of Function	1.02	24	30.0	0.799	0.00000154	454

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00027	0.00026	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00033	0.00033	rare
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.00022	0.00021	rare
South Asian	0.00023	0.00023	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Esterifies acyl-group from acyl-ACP to the sn-1 position of glycerol-3-phosphate, an essential step in glycerolipid biosynthesis. Required for primary processing step during piRNA biosynthesis. Molecular mechanisms by which it promotes piRNA biosynthesis are unclear and do not involve its acyltransferase activity. {ECO:0000250|UniProtKB:Q14DK4}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.123

Gene Damage Prediction

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