AGPAT5

protein-coding

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

Gene summary

This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. This integral membrane protein converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. A pseudogene of this gene is present on the Y chromosome. [provided by RefSeq, Aug 2014]

MANE transcript

NM_018361.5

Inheritance

—

ClinVar variants

P:1U:71B:3

Top phenotype

Keloid formation

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr8:6,708,642-6,761,503

External References & Databases

Ensembl (ENSG00000155189)

Transcript & Mutation Effects

hg38 • Region Span ~52.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to AGPAT5 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 71

not providedTotal: 2

Keloid formationTotal: 1

Hypercholesterolemia, familial, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018361.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			70 clinvar	1 clinvar	1 clinvar	72
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	71	2	1	75

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018361.5	RefSeq	NP_060831.2	8	MANE Select
ENST00000285518.11	Ensembl	ENSP00000285518.6	8	MANE Select
ENST00000518327.1	Ensembl	ENSP00000430751.1	3	Standard
ENST00000523234.5	Ensembl	ENSP00000430016.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glycerolipid metabolism - Homo sapiens (human)
Glycerophospholipid metabolism - Homo sapiens (human)
Phospholipase D signaling pathway - Homo sapiens (human)
Triacylglyceride Synthesis
Metabolism of lipids

Biological Process

hematopoietic progenitor cell differentiation
acylglycerol metabolic process
phospholipid metabolic process
phosphatidic acid biosynthetic process
phospholipid biosynthetic process

Molecular Function

1-acylglycerol-3-phosphate O-acyltransferase activity
protein binding
transferase activity, transferring acyl groups

Cellular Component

nuclear envelope
mitochondrion
mitochondrial outer membrane
endoplasmic reticulum membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000285518
Coding exons: 8
Length: 51307
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 31
Defined: 125748
p: 0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.66	262	196	1.33	0.0000105	2351
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.123

Intolerance Scores

RVIS EVS: -0.51
RVIS percentile EVS: 21.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.779

Gene Damage Prediction

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