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): 8:6708641-6761503

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.

• Inborn genetic diseases (14 variants)
• not provided (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.

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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	14	1	0

Variants in AGPAT5

This is a list of pathogenic ClinVar variants found in the AGPAT5 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-6708673-T-C		not specified	Uncertain significance (Oct 25, 2023)
8-6708723-G-C		not specified	Uncertain significance (Jul 16, 2021)
8-6708729-C-G		not specified	Uncertain significance (Oct 17, 2023)
8-6708754-T-A		not specified	Uncertain significance (Oct 20, 2023)
8-6708851-G-T		not specified	Uncertain significance (Jan 09, 2024)
8-6708867-G-A		not specified	Uncertain significance (Dec 20, 2023)
8-6730725-G-T		not specified	Uncertain significance (Feb 28, 2023)
8-6730729-A-G		not specified	Uncertain significance (Jul 14, 2021)
8-6730740-A-G		not specified	Uncertain significance (Aug 08, 2022)
8-6730763-T-A		not specified	Uncertain significance (Nov 06, 2023)
8-6730768-G-A		not specified	Uncertain significance (Nov 01, 2022)
8-6730788-T-A		not specified	Uncertain significance (Nov 07, 2022)
8-6732582-C-T		not specified	Uncertain significance (May 13, 2022)
8-6732646-C-G		not specified	Uncertain significance (Dec 16, 2023)
8-6732659-C-A			Likely benign (Aug 15, 2018)
8-6741710-C-T		not specified	Uncertain significance (Sep 15, 2021)
8-6741712-A-G		not specified	Uncertain significance (Oct 18, 2021)
8-6741714-A-T		not specified	Uncertain significance (Dec 20, 2023)
8-6747808-G-C		not specified	Uncertain significance (Apr 07, 2022)
8-6747816-C-G		not specified	Uncertain significance (Aug 16, 2021)
8-6747825-A-G		not specified	Likely benign (Dec 14, 2023)
8-6755078-T-C		not specified	Uncertain significance (Jul 27, 2022)
8-6755086-C-T		not specified	Uncertain significance (Dec 18, 2023)
8-6755155-C-T		not specified	Uncertain significance (Aug 12, 2021)
8-6757219-G-A		Keloid formation	Benign (Jun 22, 2017)

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

• 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