GPAT4

glycerol-3-phosphate acyltransferase 4, the group of Glycerol-3-phosphate acyltransferases|1-acylglycerol-3-phosphate O-acyltransferases

Basic information

Region (hg38): 8:41577186-41625001

Previous symbols: [ "AGPAT6" ]

Links

ENSG00000158669 ∙ NCBI:137964 ∙ OMIM:608143 ∙ HGNC:20880 ∙ Uniprot:Q86UL3 ∙ 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 GPAT4 gene.

• Inborn genetic diseases (8 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPAT4 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					1	1
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	8	0	1

Variants in GPAT4

This is a list of pathogenic ClinVar variants found in the GPAT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-41599266-C-G		not specified	Uncertain significance (Sep 13, 2023)
8-41609432-T-C		not specified	Uncertain significance (Apr 26, 2023)
8-41609438-G-A		not specified	Uncertain significance (Nov 08, 2022)
8-41609457-C-A		not specified	Uncertain significance (Aug 17, 2021)
8-41609665-A-G			Benign (Aug 01, 2018)
8-41609697-A-G		not specified	Uncertain significance (Dec 17, 2023)
8-41611928-G-A		not specified	Uncertain significance (Sep 26, 2022)
8-41611979-A-G		not specified	Uncertain significance (Nov 22, 2023)
8-41612000-C-T			Benign (Nov 15, 2017)
8-41612888-C-T		not specified	Uncertain significance (Jan 03, 2024)
8-41612911-G-A		not specified	Uncertain significance (Jul 25, 2023)
8-41612927-C-T		not specified	Uncertain significance (Nov 09, 2023)
8-41618751-G-A		not specified	Uncertain significance (Dec 14, 2021)
8-41618802-T-A		not specified	Uncertain significance (Jan 26, 2022)
8-41620897-G-T		not specified	Uncertain significance (Dec 18, 2023)
8-41620928-C-T		not specified	Uncertain significance (Dec 01, 2022)
8-41620981-A-G		not specified	Likely benign (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPAT4	protein_coding	protein_coding	ENST00000396987	12	47815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0881	0.912	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.70	140	263	0.531	0.0000144	2996
Missense in Polyphen		35	77.196	0.45339		838
Synonymous	0.0446	100	101	0.994	0.00000583	872
Loss of Function	3.47	7	26.2	0.268	0.00000135	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

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. Active against both saturated and unsaturated long- chain fatty acyl-CoAs. {ECO:0000269|PubMed:18238778}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Glycerophospholipid metabolism;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.178
• hipred: Y
• hipred_score: 0.707
• ghis: 0.598

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Gpat4
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: glandular epithelial cell maturation;fatty acid metabolic process;acyl-CoA metabolic process;phosphatidic acid biosynthetic process;phosphatidylcholine biosynthetic process;lactation;lipid biosynthetic process;CDP-diacylglycerol biosynthetic process;triglyceride biosynthetic process;regulation of multicellular organism growth;diacylglycerol metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;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