PLA2G2D

phospholipase A2 group IID, the group of Phospholipases

Basic information

Region (hg38): 1:20111939-20119566

Links

ENSG00000117215 ∙ NCBI:26279 ∙ OMIM:605630 ∙ HGNC:9033 ∙ Uniprot:Q9UNK4 ∙ 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 PLA2G2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G2D 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in PLA2G2D

This is a list of pathogenic ClinVar variants found in the PLA2G2D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20114127-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-20114154-T-A		not specified	Uncertain significance (Apr 22, 2022)
1-20115584-T-C		not specified	Uncertain significance (Jun 21, 2022)
1-20116338-C-T			Benign (Jul 01, 2024)
1-20116358-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-20116373-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-20116385-C-T			Likely benign (Jul 01, 2024)
1-20116434-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-20116435-A-C		not specified	Uncertain significance (Apr 14, 2022)
1-20116435-A-G		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G2D	protein_coding	protein_coding	ENST00000375105	4	7619

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000181	0.273	125628	1	119	125748	0.000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.406	94	83.6	1.13	0.00000457	943
Missense in Polyphen		41	35.636	1.1505		399
Synonymous	-0.964	40	33.0	1.21	0.00000170	264
Loss of Function	-0.113	7	6.68	1.05	2.84e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000423
Ashkenazi Jewish	0.00	0.00
East Asian	0.00370	0.00370
Finnish	0.00	0.00
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.00370	0.00370
South Asian	0.000849	0.000817
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. L-alpha-1-palmitoyl-2- linoleoyl phosphatidylethanolamine is more efficiently hydrolyzed than the other phospholipids examined.
• 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);Phospholipid Biosynthesis;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: 0.0833

Intolerance Scores

• loftool: 0.682
• rvis_EVS: 1.1
• rvis_percentile_EVS: 91.96

Haploinsufficiency Scores

• pHI: 0.0578
• hipred: N
• hipred_score: 0.123

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	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pla2g2d
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation;phospholipid metabolic process;phosphatidic acid biosynthetic process;inflammatory response;lipid catabolic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;negative regulation of T cell proliferation;arachidonic acid secretion
• Cellular component: extracellular region
• Molecular function: phospholipase A2 activity;calcium ion binding;phospholipid binding;heparin binding;heparan sulfate proteoglycan binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)