AtlasGene
AGPAT2
1-acylglycerol-3-phosphate O-acyltransferase 2
- HGNC 325↗(opens in a new tab)
- Ensembl gene ENSG00000169692↗(opens in a new tab)
- NCBI Gene 10555↗(opens in a new tab)
Summary
- Cytogenetic location
- 9q34.3
- Coordinates
- Chromosome 9: 136,673,143–136,687,457 (GRCh38)
- Exons
- 6 exons across 14.3 kb
- Protein
- 278 amino acids
- Also known as
- LPAAT-beta, LPLAT2
- Previous symbols
- BSCL
- MANE Select transcript
- ENST00000371696.7NM_006412.4
- Locus type
- Protein-coding
- Very high
- Confident
- Low
- Very low
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Get my Genome TestCurated report relevant to this gene
Lipodystrophy
- Berardinelli-Seip Congenital LipodystrophyAutosomal recessive
A lipodystrophy characterized by the association of lipoatrophy, hypertriglyceridemia, hepatomegaly and acromegaloid features. BSCL belongs to the group of extreme insulin resistance syndromes, which also includes leprechaunism, Rabson-Mendenhall syndrome, acquired generalized lipodystrophy, and types A and B insulin resistance.
- 4 GenCC submitters rate it definitive or strong
- Congenital Generalized LipodystrophyAutosomal recessive
An extremely rare autosomal recessive condition, characterized by an extreme scarcity of fat in the subcutaneous tissues.
- 4 GenCC submitters rate it definitive or strong
How AGPAT2 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 1.5 kb of the gene's 14.3 kb; 837 of those bases code for the protein.
Sequencing AGPAT2
10Moderate
How hard AGPAT2 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Some of AGPAT2's exons sit where short reads can miss or misplace a change.
What adds to it: the share of AGPAT2's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. Weight 35%.0%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. Weight 30%.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. Weight 15%.5.7%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. Weight 10%.96%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. Weight 10%.0%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of AGPAT2's exon bases in that kind of difficult region. The score weighs them by how much each costs a short-read call: 0 when no base is in any, 100 when every base is in all of them.
24
positions in AGPAT2 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 14.3 kb of AGPAT2, introns included, not only the 1.5 kb of exons.
ClinVar pathogenic variants (24)
The AGPAT2 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Pathogenic 9
- Pathogenic/likely pathogenic 4
- Likely pathogenic 11
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_006412.4(AGPAT2):c.589-2A>G (opens in a new tab) | congenital generalized lipodystrophy and 1 other | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.492+1G>A (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.377dup (p.Pro128fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.202C>T (p.Arg68Ter) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.662-2A>C (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.646A>T (p.Lys216Ter) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.514G>A (p.Glu172Lys) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.493-1G>C (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic/likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.493-2A>G (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| NM_006412.4(AGPAT2):c.530_537dup (p.Asp180fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.406G>A (p.Gly136Arg) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.369_372del (p.Leu124fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.176_178delinsC (p.Asn59fs) (opens in a new tab) | congenital generalized lipodystrophy | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.38T>A (p.Leu13Ter) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.790C>T (p.Gln264Ter) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.769del (p.Leu257fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.731T>C (p.Leu244Pro) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.685G>T (p.Glu229Ter) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.683T>C (p.Leu228Pro) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.335del (p.Pro112fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.254_258dup (p.Gln87fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.242_245del (p.Arg81fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.158del (p.Gly53fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_006412.4(AGPAT2):c.34del (p.Leu12fs) (opens in a new tab) | congenital generalized lipodystrophy type 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Genes linked to the same conditions
Traits linked to AGPAT2
The Human Phenotype Ontology lists these as features of the rare conditions AGPAT2 can cause. Each trait's page lists the other genes linked to it.
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-17: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.18-e609d43e.
Cite this page
Dante Labs. (n.d.). AGPAT2 gene: 1-acylglycerol-3-phosphate O-acyltransferase 2. Retrieved 18 October 2026, from https://dantelabs.com/genes/agpat2
Dante Labs. AGPAT2 gene: 1-acylglycerol-3-phosphate O-acyltransferase 2 [Internet]. [cited 18 October 2026]. Available from: https://dantelabs.com/genes/agpat2
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