PLA2G7

phospholipase A2 group VII, the group of Phospholipases

Basic information

Region (hg38): 6:46704200-46735693

Links

ENSG00000146070 ∙ NCBI:7941 ∙ OMIM:601690 ∙ HGNC:9040 ∙ Uniprot:Q13093 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Platelet-activating factor acetylhydrolase deficiency	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Pulmonary	3198761; 8675689; 10194471; 10733466

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2G7 gene.

• Inborn genetic diseases (18 variants)
• not provided (8 variants)
• Platelet-activating factor acetylhydrolase deficiency (6 variants)
• not specified (4 variants)
• RECLASSIFIED - POLYMORPHISM (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G7 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				3		3
missense			20	1	3	24
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)		1	2			3
splice region						0
non coding					1	1
Total	0	1	24	4	4

Highest pathogenic variant AF is 0.00000659

Variants in PLA2G7

This is a list of pathogenic ClinVar variants found in the PLA2G7 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-46704602-G-A			Likely benign (Aug 28, 2018)
6-46704609-T-C		not specified	Uncertain significance (Sep 19, 2023)
6-46704657-T-C		not specified	Uncertain significance (Jan 26, 2022)
6-46704715-TAATC-T			Benign (Aug 19, 2020)
6-46705206-A-G		RECLASSIFIED - POLYMORPHISM • PLA2G7-related disorder	Benign (Sep 24, 2019)
6-46705275-T-C		not specified	Uncertain significance (Feb 13, 2024)
6-46705276-C-A		not specified	Uncertain significance (Jul 12, 2023)
6-46705318-C-T		not specified	Likely benign (Mar 07, 2024)
6-46708156-C-A		not specified	Uncertain significance (Aug 22, 2023)
6-46708163-T-C		Platelet-activating factor acetylhydrolase deficiency	Uncertain significance (Mar 18, 2016)
6-46709361-C-A		Platelet-activating factor acetylhydrolase deficiency • PLA2G7-related disorder	Benign (Feb 24, 2020)
6-46709399-T-C		not specified	Uncertain significance (Dec 02, 2022)
6-46709402-T-C		not specified	Uncertain significance (Aug 08, 2023)
6-46709409-C-T		not specified	Uncertain significance (Aug 30, 2021)
6-46710529-A-G		Platelet-activating factor acetylhydrolase deficiency	Uncertain significance (Apr 04, 2024)
6-46710548-C-T		not specified	Likely benign (Oct 17, 2023)
6-46710626-A-G			Likely benign (Feb 08, 2018)
6-46710636-C-T		not specified	Uncertain significance (Aug 02, 2021)
6-46710640-C-CTT		Platelet-activating factor acetylhydrolase deficiency	Uncertain significance (Mar 05, 2018)
6-46710645-G-C		not specified	Uncertain significance (Nov 06, 2023)
6-46710654-C-T		not specified	Likely benign (Mar 07, 2024)
6-46710655-G-A		not specified	Uncertain significance (Nov 17, 2023)
6-46711495-C-T		Platelet-activating factor acetylhydrolase deficiency • not specified	Uncertain significance (May 01, 2022)
6-46711525-C-T		not specified	Uncertain significance (Dec 28, 2023)
6-46711546-A-G		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G7	protein_coding	protein_coding	ENST00000274793	11	31493

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.33e-22	0.000104	125330	3	410	125743	0.00164

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.05	274	229	1.20	0.0000108	2919
Missense in Polyphen		108	87.815	1.2299		1148
Synonymous	-0.141	78	76.4	1.02	0.00000359	805
Loss of Function	-1.17	29	23.0	1.26	0.00000107	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00201	0.00201
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000829	0.000827
Middle Eastern	0.000381	0.000381
South Asian	0.00800	0.00794
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Modulates the action of platelet-activating factor (PAF) by hydrolyzing the sn-2 ester bond to yield the biologically inactive lyso-PAF. Has a specificity for substrates with a short residue at the sn-2 position. It is inactive against long-chain phospholipids.
• Disease: DISEASE: Asthma (ASTHMA) [MIM:600807]: The most common chronic disease affecting children and young adults. It is a complex genetic disorder with a heterogeneous phenotype, largely attributed to the interactions among many genes and between these genes and the environment. It is characterized by recurrent attacks of paroxysmal dyspnea, with wheezing due to spasmodic contraction of the bronchi. {ECO:0000269|PubMed:10733466}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Atopic hypersensitivity (ATOPY) [MIM:147050]: A condition characterized by predisposition to develop hypersensitivity reactions. Atopic individuals can develop eczema, allergic rhinitis and allergic asthma. {ECO:0000269|PubMed:10733466}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Ether lipid metabolism - Homo sapiens (human);IL1 and megakaryocytes in obesity;Peptide hormone metabolism;Synthesis, secretion, and deacylation of Ghrelin;Metabolism of proteins;Glycerophospholipid metabolism;Lissencephaly gene (LIS1) in neuronal migration and development (Consensus)

Recessive Scores

• pRec: 0.304

Intolerance Scores

• loftool: 1.00
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• pHI: 0.0609
• hipred: N
• hipred_score: 0.207

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0145

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g7
• Phenotype: immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: lipid catabolic process;low-density lipoprotein particle remodeling;lipid oxidation;plasma lipoprotein particle oxidation;platelet activating factor metabolic process;positive regulation of inflammatory response;positive regulation of monocyte chemotaxis
• Cellular component: extracellular region;cytoplasm;low-density lipoprotein particle
• Molecular function: 1-alkyl-2-acetylglycerophosphocholine esterase activity;phospholipid binding;hydrolase activity, acting on ester bonds;calcium-independent phospholipase A2 activity