AGPAT4

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

Basic information

Region (hg38): 6:161129967-161274061

Links

ENSG00000026652

∙ NCBI:56895 ∙ OMIM:614795 ∙ HGNC:20885 ∙ Uniprot:Q9NRZ5 ∙ 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 AGPAT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGPAT4 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			9 clinvar	1 clinvar		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in AGPAT4

This is a list of pathogenic ClinVar variants found in the AGPAT4 region.

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

Position	Phenotype	Significance	ClinVar
6-161136601-G-A	not specified	Uncertain significance (Jun 19, 2024)	3276287
6-161139560-G-A	not specified	Uncertain significance (May 31, 2023)	2554532
6-161139569-T-C	not specified	Uncertain significance (May 10, 2023)	2569848
6-161139592-G-A	not specified	Uncertain significance (Apr 18, 2023)	2518535
6-161146562-C-T	not specified	Likely benign (Oct 29, 2021)	2354751
6-161146595-T-A	not specified	Uncertain significance (Jan 10, 2023)	2469947
6-161149206-G-C	not specified	Uncertain significance (Apr 19, 2023)	2539079
6-161153414-C-T	not specified	Uncertain significance (Jun 22, 2024)	3276279
6-161154202-T-G	not specified	Uncertain significance (Jan 31, 2022)	2411094
6-161154241-C-T	not specified	Uncertain significance (May 25, 2022)	2290927
6-161232086-T-G	not specified	Uncertain significance (Mar 04, 2024)	3096448
6-161232156-C-G	not specified	Uncertain significance (Aug 13, 2021)	2244954

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGPAT4	protein_coding	protein_coding	ENST00000320285	8	144083

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.102	0.898	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.23	136	231	0.588	0.0000146	2464
Missense in Polyphen		40	82.009	0.48775		839
Synonymous	0.958	88	100	0.878	0.00000691	725
Loss of Function	3.19	6	22.2	0.270	0.00000130	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000909
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
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. {ECO:0000250}.;
Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Triacylglyceride Synthesis;Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

pRec: 0.106

Intolerance Scores

loftool: 0.212
rvis_EVS: -0.51
rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

pHI: 0.323
hipred: Y
hipred_score: 0.783
ghis: 0.517

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.972

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Agpat4
Phenotype: adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; normal phenotype; skeleton phenotype;

Gene ontology

Biological process: phospholipid metabolic process;phosphatidic acid biosynthetic process;phospholipid biosynthetic process;CDP-diacylglycerol biosynthetic process;macromolecule metabolic process
Cellular component: mitochondrial outer membrane;endoplasmic reticulum membrane;integral component of membrane
Molecular function: 1-acylglycerol-3-phosphate O-acyltransferase activity;protein binding;transferase activity, transferring acyl groups