PLA2G4D

protein-coding

phospholipase A2 group IVD, the group of Phospholipases|C2 domain containing phospholipases

Gene summary

The phospholipase A2 enzyme family, including PLA2G4D, catalyze the hydrolysis of glycerophospholipids at the sn-2 position and then liberate free fatty acids and lysophospholipids (Chiba et al., 2004 [PubMed 14709560]).[supplied by OMIM, Jun 2009]

MANE transcript

NM_178034.4

Inheritance

—

ClinVar variants

U:151B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr15:42,067,009-42,094,562

External References & Databases

Ensembl (ENSG00000159337)

Transcript & Mutation Effects

hg38 • Region Span ~27.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLA2G4D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 157

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178034.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	1 clinvar	4
missense			148 clinvar	11 clinvar		159
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar	1 clinvar		4
Total	0	0	151	15	1	167

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178034.4	RefSeq	NP_828848.3	20	MANE Select
ENST00000290472.4	Ensembl	ENSP00000290472.3	20	MANE Select
ENST00001137368.1	Ensembl	ENSP00000804779.1	20	Standard
XM_047432399.1	RefSeq	XP_047288355.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
Platelet activation - Homo sapiens (human)
Oxytocin signaling pathway - Homo sapiens (human)
Fc epsilon RI signaling pathway - Homo sapiens (human)
Fc gamma R-mediated phagocytosis - Homo sapiens (human)

Biological Process

phospholipid metabolic process
phosphatidic acid biosynthetic process
phosphatidylglycerol acyl-chain remodeling
phosphatidylinositol acyl-chain remodeling
phosphatidylserine acyl-chain remodeling

Molecular Function

lysophospholipase activity
phospholipase A2 activity
calcium ion binding
calcium-dependent phospholipid binding
phospholipase A1 activity

Cellular Component

cytoplasm
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000290472
Coding exons: 20
Length: 27546
Individuals with no LoFs: 119823
Homozygous LoFs: 174
Heterozygous LoFs: 5751
Defined: 125748
p: 0.0238

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.406	490	465	1.05	0.0000277	5232
Missense (PolyPhen)		118	109.41	1.0785		1345
Synonymous	0.376	200	207	0.967	0.0000127	1670
Loss of Function	1.98	28	41.8	0.669	0.00000197	476

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0030	0.0029	notable
Latino/Admixed American	0.062	0.062	notable
Ashkenazi Jewish	0.011	0.011	notable
East Asian	0.11	0.11	notable
Finnish	0.0086	0.0085	notable
European (Non-Finnish)	0.0073	0.0072	notable
South Asian	0.024	0.023	notable
Other	0.017	0.017	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position (PubMed:14709560). May have a substrate specificity for linoleic acid at the sn-2 position (PubMed:14709560). {ECO:0000269|PubMed:14709560}.;

Recessive Scores

pRec: 0.0982

Intolerance Scores

LoFtool: 0.952
RVIS EVS: 1.61
RVIS percentile EVS: 95.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.101

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High