AGPAT5

1-acylglycerol-3-phosphate O-acyltransferase 5, the group of 1-acylglycerol-3-phosphate O-acyltransferases|MicroRNA protein coding host genes

Basic information

Region (hg38): 8:6708642-6761503

Links

ENSG00000155189

∙ NCBI:55326 ∙ OMIM:614796 ∙ HGNC:20886 ∙ Uniprot:Q9NUQ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the AGPAT5 gene.

not_specified (56 variants)
not_provided (1 variants)
Keloid_formation (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AGPAT5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000018361.5. 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						0
missense			55 clinvar	1 clinvar	1 clinvar	57
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	55	1	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AGPAT5	protein_coding	protein_coding	ENST00000285518	8	51307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000708	0.912	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.66	262	196	1.33	0.0000105	2351
Missense in Polyphen		23	30.061	0.76512		345
Synonymous	-3.52	116	76.7	1.51	0.00000440	678
Loss of Function	1.63	11	18.6	0.592	0.00000105	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000422	0.000421
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

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 C15:0-C20:4 at the sn-1 position using C18:1-CoA as the acyl donor. Also acts on lysophosphatidylethanolamine using oleoyl-CoA, but not arachidonoyl-CoA, and lysophosphatidylinositol using arachidonoyl-CoA, but not oleoyl-CoA. Activity toward lysophosphatidylglycerol not detectable. {ECO:0000269|PubMed:21173190}.;
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;Glycerophospholipid metabolism;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Recessive Scores

pRec: 0.123

Intolerance Scores

loftool
rvis_EVS: -0.51
rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

pHI: 0.558
hipred: Y
hipred_score: 0.507
ghis: 0.641

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.779

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Agpat5
Phenotype: liver/biliary system phenotype;

Gene ontology

Biological process: hematopoietic progenitor cell differentiation;acylglycerol metabolic process;phospholipid metabolic process;phosphatidic acid biosynthetic process;phospholipid biosynthetic process;CDP-diacylglycerol biosynthetic process
Cellular component: nuclear envelope;mitochondrion;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