AGPAT3

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

Basic information

Region (hg38): 21:43865223-43987592

Links

ENSG00000160216

∙ NCBI:56894 ∙ OMIM:614794 ∙ HGNC:326 ∙ Uniprot:Q9NRZ7 ∙ 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 AGPAT3 gene.

not_specified (29 variants)
not_provided (4 variants)
Intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGPAT3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020132.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	1 clinvar	5
missense			27 clinvar			27
nonsense	1 clinvar					1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	27	4	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGPAT3	protein_coding	protein_coding	ENST00000398063	8	121351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000672	125734	0	7	125741	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.54	131	242	0.541	0.0000165	2434
Missense in Polyphen		12	62.055	0.19338		573
Synonymous	0.816	97	108	0.900	0.00000790	758
Loss of Function	4.25	0	21.1	0.00	0.00000109	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

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. Acts on LPA containing saturated or unsaturated fatty acids C16:0-C20:4 at the sn-1 position using C18:1, C20:4 or C18:2-CoA as the acyl donor. Also acts on lysophosphatidylcholine, lysophosphatidylinositol and lysophosphatidylserine using C18:1 or C20:4-CoA (PubMed:21173190). Has a preference for arachidonoyl-CoA as a donor. Has also a modest lysophosphatidylinositol acyltransferase (LPIAT) activity, converts lysophosphatidylinositol (LPI) into phosphatidylinositol (By similarity). {ECO:0000250|UniProtKB:Q9D517, ECO:0000269|PubMed:21173190}.;
Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Triacylglyceride Synthesis;Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;triacylglycerol biosynthesis;COPI-independent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool
rvis_EVS: -0.49
rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

pHI: 0.112
hipred: Y
hipred_score: 0.749
ghis: 0.538

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Agpat3
Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; skeleton phenotype;

Gene ontology

Biological process: phospholipid metabolic process;phosphatidic acid biosynthetic process;phospholipid biosynthetic process;CDP-diacylglycerol biosynthetic process
Cellular component: Golgi membrane;nuclear envelope;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;membrane;integral component of membrane
Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;transferase activity, transferring acyl groups