PLA2G10

phospholipase A2 group X, the group of Phospholipases

Basic information

Region (hg38): 16:14672547-14694308

Links

ENSG00000069764 ∙ NCBI:8399 ∙ OMIM:603603 ∙ HGNC:9029 ∙ Uniprot:O15496 ∙ 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 PLA2G10 gene.

• Inborn genetic diseases (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G10 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				1		1
missense			2	1		3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	2	0

Variants in PLA2G10

This is a list of pathogenic ClinVar variants found in the PLA2G10 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-14672718-C-G		not specified	Uncertain significance (Sep 16, 2021)
16-14672745-C-T			Likely benign (Jun 13, 2018)
16-14672746-G-A		not specified	Uncertain significance (Jul 17, 2023)
16-14688174-C-T		not specified	Likely benign (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G10	protein_coding	protein_coding	ENST00000438167	4	22122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0695	0.538	125602	0	1	125603	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0287	25	24.6	1.02	0.00000123	1039
Missense in Polyphen		8	7.7625	1.0306		337
Synonymous	0.661	9	11.9	0.756	7.40e-7	338
Loss of Function	-0.679	1	0.488	2.05	2.06e-8	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. Has a powerful potency for releasing arachidonic acid from cell membrane phospholipids. Prefers phosphatidylethanolamine and phosphatidylcholine liposomes to those of phosphatidylserine. {ECO:0000269|PubMed:12161451, ECO:0000269|PubMed:9188469}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Synthesis of PA;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.123

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.123
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.269

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Pla2g10
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; muscle phenotype

Gene ontology

• Biological process: phospholipid metabolic process;phosphatidic acid biosynthetic process;axon guidance;positive regulation of macrophage derived foam cell differentiation;positive regulation of lipid storage;lipid catabolic process;arachidonic acid metabolic process;positive regulation of cellular protein metabolic process;positive regulation of prostaglandin secretion;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;cholesterol homeostasis;regulation of macrophage activation;negative regulation of DNA-binding transcription factor activity;arachidonic acid secretion;lysophospholipid transport;positive regulation of arachidonic acid secretion;negative regulation of cholesterol efflux;cellular response to leukemia inhibitory factor
• Cellular component: extracellular region;extracellular space
• Molecular function: phospholipase activity;phospholipase A2 activity;calcium ion binding;phospholipid binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)