GPAT3

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

Basic information

Region (hg38): 4:83535913-83605875

Previous symbols: [ "AGPAT9" ]

Links

ENSG00000138678 ∙ NCBI:84803 ∙ OMIM:610958 ∙ HGNC:28157 ∙ Uniprot:Q53EU6 ∙ 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 GPAT3 gene.

• Inborn genetic diseases (16 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPAT3 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	1

Variants in GPAT3

This is a list of pathogenic ClinVar variants found in the GPAT3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
4-83536650-A-T		not specified	Uncertain significance (Jul 20, 2022)
4-83536720-G-A		not specified	Uncertain significance (Dec 26, 2023)
4-83544564-C-A		not specified	Uncertain significance (Nov 22, 2021)
4-83544578-A-G			Benign (Jul 16, 2018)
4-83544579-T-G		not specified	Uncertain significance (Sep 14, 2022)
4-83581580-A-G		not specified	Uncertain significance (Oct 13, 2023)
4-83581583-C-T		not specified	Uncertain significance (Oct 26, 2021)
4-83581760-A-T		not specified	Uncertain significance (Jul 14, 2021)
4-83581786-T-G		not specified	Uncertain significance (Aug 20, 2023)
4-83581796-G-A		not specified	Uncertain significance (May 18, 2023)
4-83581807-C-T		not specified	Uncertain significance (Dec 22, 2023)
4-83588253-C-T		not specified	Uncertain significance (Dec 18, 2023)
4-83590222-G-A		not specified	Uncertain significance (May 18, 2022)
4-83594875-A-T		not specified	Uncertain significance (Sep 17, 2021)
4-83596883-A-C		not specified	Uncertain significance (Apr 04, 2023)
4-83596887-A-G		not specified	Uncertain significance (Jul 14, 2022)
4-83596907-C-T		not specified	Uncertain significance (Dec 11, 2023)
4-83597508-C-T		not specified	Uncertain significance (Dec 13, 2023)
4-83598671-A-G		not specified	Uncertain significance (Jan 10, 2023)
4-83598677-G-T		not specified	Uncertain significance (Feb 28, 2023)
4-83598692-G-C		not specified	Uncertain significance (Jan 10, 2022)
4-83604676-G-A		not specified	Uncertain significance (Jan 05, 2022)
4-83604679-T-C		not specified	Uncertain significance (Jul 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPAT3	protein_coding	protein_coding	ENST00000395226	12	69962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.80e-12	0.340	125544	0	203	125747	0.000807

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.442	220	239	0.920	0.0000120	2820
Missense in Polyphen		72	75.444	0.95436		860
Synonymous	-1.32	103	87.3	1.18	0.00000443	854
Loss of Function	1.12	21	27.3	0.768	0.00000159	295

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00137
Ashkenazi Jewish	0.000694	0.000695
East Asian	0.00122	0.00120
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000900	0.000897
Middle Eastern	0.00122	0.00120
South Asian	0.000785	0.000784
Other	0.00130	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May transfer the acyl-group from acyl-coA to the sn-1 position of glycerol-3-phosphate, an essential step in glycerolipid biosynthesis. Also transfers the acyl-group from acyl-coA to the sn-2 position of 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid, or LPA), forming 1,2-diacyl-sn-glycerol-3- phosphate (phosphatidic acid, or PA). {ECO:0000269|PubMed:17002884, ECO:0000269|PubMed:17170135, ECO:0000269|PubMed:19318427}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);HIF1A and PPARG regulation of glycolysis;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: -0.09
• rvis_percentile_EVS: 46.99

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.316
• ghis: 0.431

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Gpat3
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: phosphatidic acid biosynthetic process;CDP-diacylglycerol biosynthetic process;triglyceride biosynthetic process;regulation of TOR signaling
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;glycerol-3-phosphate O-acyltransferase activity;sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity