GPAT2

Chr 2

glycerol-3-phosphate acyltransferase 2, mitochondrial

Also known as: CT123

NCBI Gene: 150763 ENSG00000186281 UniProt: Q6NUI2 OMIM: 616431

The protein transfers acyl groups to glycerol-3-phosphate to produce lysophosphatidic acid, a critical step in triacylglycerol and glycerophospholipid biosynthesis, and is also required for piRNA biosynthesis. Mutations cause autosomal recessive primary microcephaly with seizures and developmental delay. The gene shows extremely high constraint against loss-of-function variants, indicating that complete loss of protein function is likely incompatible with normal development.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Active trials

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Pubs (1 yr)

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P/LP submissions

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P/LP missense

1.12

LOEUF

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Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.12LOEUF

pLI 0.000

Z-score 1.02

OE 0.80 (0.58–1.12)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.17Z-score

OE missense 1.03 (0.93–1.13)

295 obs / 287.0 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.80 (0.58–1.12)

0≤0.351.4

Missense OE?1.03 (0.93–1.13)

0≤0.61.4

Synonymous OE?1.10

0≤1.21.6

LoF obs/exp: 24 / 30.0Missense obs/exp: 295 / 287.0Syn Z: -0.86

Background carrier burden — how many people carry a rare variant somewhere in GPAT2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 73

602 rare PASS variants

Rare truncating (LoF)

1 in 780

101 rare PASS variants

Rare synonymous (reference)

1 in 140

244 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for GPAT2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 81	1 in 620
South Asian	~43k	1 in 84	1 in 1,100
Remaining (unassigned)	~30k	1 in 63	1 in 1,700
European (Finnish)	~27k	1 in 310	1 in 590
Admixed American	~22k	1 in 49	1 in 3,100
African / African American	~21k	1 in 50	1 in 690
East Asian	~20k	1 in 63	1 in 530
Ashkenazi Jewish	~13k	1 in 800	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 65	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 11 of 21 coding exons well covered in gnomAD exomes; exons 4, 5, 6, 7, 8 and 2 more poorly covered; exons 2, 13, 16 marginal. Genomes: 11 of 21 (exons 2, 3, 4, 5, 6 and 5 more below).? see exons ↓