PLA2G7

phospholipase A2 group VII, the group of Phospholipases

Basic information

Region (hg38): 6:46704201-46735693

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.

not_specified (82 variants)
Platelet-activating_factor_acetylhydrolase_deficiency (10 variants)
not_provided (6 variants)
PLA2G7-related_disorder (5 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. These statistics are base on transcript: NM_000005084.4. 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				7 clinvar		7
missense			65 clinvar	9 clinvar	2 clinvar	76
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)		3 clinvar	2 clinvar			5
Total	0	3	70	16	2

Highest pathogenic variant AF is 0.000058925027

Loading clinvar variants...

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
ghis

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