GPAT2

glycerol-3-phosphate acyltransferase 2, mitochondrial, the group of Glycerol-3-phosphate acyltransferases

Basic information

Region (hg38): 2:96021946-96039451

Links

ENSG00000186281 ∙ NCBI:150763 ∙ OMIM:616431 ∙ HGNC:27168 ∙ Uniprot:Q6NUI2 ∙ 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 GPAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPAT2 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				2	1	3
missense		1	61	5		67
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	3	61	7	1

Variants in GPAT2

This is a list of pathogenic ClinVar variants found in the GPAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-96022175-T-C		not specified	Uncertain significance (Aug 28, 2023)
2-96022175-T-G		not specified	Uncertain significance (Feb 15, 2023)
2-96022178-C-G		not specified	Uncertain significance (Dec 28, 2023)
2-96022178-C-T		not specified	Uncertain significance (May 28, 2024)
2-96022179-G-A		not specified	Uncertain significance (Apr 09, 2024)
2-96022197-T-G		not specified	Uncertain significance (May 23, 2023)
2-96022229-G-C		not specified	Uncertain significance (Jul 30, 2024)
2-96022262-G-A		not specified	Likely benign (Dec 02, 2022)
2-96022274-A-C		not specified	Uncertain significance (Dec 13, 2023)
2-96022678-C-G		not specified	Uncertain significance (Feb 21, 2024)
2-96022684-G-A		not specified	Uncertain significance (Nov 07, 2024)
2-96022703-C-T		not specified	Uncertain significance (Jun 18, 2024)
2-96022717-G-A		not specified	Uncertain significance (Apr 23, 2024)
2-96022723-T-G		not specified	Uncertain significance (Nov 13, 2024)
2-96022979-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-96022985-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-96022993-A-C		not specified	Uncertain significance (Jan 08, 2024)
2-96023015-A-G		not specified	Uncertain significance (Feb 27, 2024)
2-96023119-C-A		not specified	Uncertain significance (Jan 24, 2023)
2-96023130-G-A		not specified	Uncertain significance (Dec 17, 2023)
2-96023139-C-T		not specified	Likely benign (Feb 20, 2025)
2-96023160-T-C		not specified	Uncertain significance (Jun 22, 2024)
2-96023187-G-A		not specified	Uncertain significance (Jan 17, 2023)
2-96023190-A-G		not specified	Uncertain significance (Nov 10, 2022)
2-96023210-T-C		not specified	Likely benign (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPAT2	protein_coding	protein_coding	ENST00000434632	21	17506

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.84e-14	0.177	124742	0	62	124804	0.000248

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.167	295	287	1.03	0.0000176	5024
Missense in Polyphen		13	16.168	0.80408		167
Synonymous	-0.856	140	128	1.10	0.00000766	1689
Loss of Function	1.02	24	30.0	0.799	0.00000154	454

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000404
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000335	0.000334
Finnish	0.000605	0.000603
European (Non-Finnish)	0.000221	0.000212
Middle Eastern	0.000335	0.000334
South Asian	0.000231	0.000229
Other	0.000331	0.000330

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. Required for primary processing step during piRNA biosynthesis. Molecular mechanisms by which it promotes piRNA biosynthesis are unclear and do not involve its acyltransferase activity. {ECO:0000250|UniProtKB:Q14DK4}.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Metabolism;CDP-diacylglycerol biosynthesis;Triglyceride biosynthesis;Triglyceride metabolism;triacylglycerol biosynthesis;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.123

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpat2

Gene ontology

• Biological process: glycerol-3-phosphate metabolic process;fatty acid metabolic process;phosphatidic acid biosynthetic process;phospholipid biosynthetic process;CDP-diacylglycerol biosynthetic process;triglyceride biosynthetic process;piRNA biosynthetic process
• Cellular component: mitochondrion;mitochondrial outer membrane;integral component of membrane;mitochondrial membrane
• Molecular function: glycerol-3-phosphate O-acyltransferase activity;sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity