GPAT4

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

Basic information

Region (hg38): 8:41577187-41625001

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.

• not_specified (30 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. These statistics are base on transcript: NM_000178819.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1		1	2
missense			31	1		32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5			5
Total	0	0	37	1	1

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
		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

Essentials

• essential_gene_gene_trap: N

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