PLA2G4D

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

Basic information

Region (hg38): 15:42067009-42094562

Links

ENSG00000159337NCBI:283748OMIM:612864HGNC:30038Uniprot:Q86XP0AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLA2G4D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G4D 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
clinvar
1
clinvar
4
missense
67
clinvar
3
clinvar
1
clinvar
71
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 67 6 3

Variants in PLA2G4D

This is a list of pathogenic ClinVar variants found in the PLA2G4D region.

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

Position Type Phenotype Significance ClinVar
15-42068728-C-G not specified Uncertain significance (Mar 18, 2024)3307185
15-42068779-T-A not specified Uncertain significance (Mar 29, 2023)2531378
15-42068807-C-T not specified Uncertain significance (Mar 29, 2022)3214136
15-42068819-T-C not specified Uncertain significance (Jul 25, 2024)3419726
15-42068825-G-C not specified Uncertain significance (May 18, 2023)2548805
15-42068893-G-A not specified Uncertain significance (Mar 18, 2024)3307189
15-42068932-C-T not specified Uncertain significance (Jan 03, 2022)2399331
15-42068933-G-T not specified Uncertain significance (Sep 03, 2024)3419730
15-42069965-G-A not specified Uncertain significance (Aug 27, 2024)2215437
15-42069972-C-T not specified Uncertain significance (Oct 25, 2023)3214135
15-42069975-G-A not specified Uncertain significance (Feb 02, 2024)3214134
15-42069982-G-A Likely benign (Oct 01, 2022)2645232
15-42069999-G-A not specified Uncertain significance (Mar 11, 2022)2278189
15-42070025-T-C not specified Uncertain significance (Nov 17, 2022)2326274
15-42070031-C-T not specified Uncertain significance (Mar 11, 2022)2222514
15-42070038-C-G not specified Uncertain significance (Oct 12, 2022)2409828
15-42070052-G-A not specified Uncertain significance (Sep 08, 2024)2360906
15-42070062-G-C not specified Uncertain significance (Sep 10, 2024)3419717
15-42070067-C-T not specified Uncertain significance (Oct 06, 2021)2381575
15-42070082-G-A not specified Uncertain significance (Sep 30, 2024)3419723
15-42070727-G-A not specified Uncertain significance (Oct 05, 2023)3214132
15-42070761-C-G not specified Uncertain significance (Dec 19, 2023)3214131
15-42070769-C-T not specified Uncertain significance (Nov 17, 2023)3214130
15-42070770-G-A not specified Uncertain significance (Dec 17, 2023)3214129
15-42070778-C-T not specified Uncertain significance (Aug 27, 2024)2293566

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PLA2G4Dprotein_codingprotein_codingENST00000290472 2027546
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.63e-140.84911982317457511257480.0238
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4064904651.050.00002775232
Missense in Polyphen118109.411.07851345
Synonymous0.3762002070.9670.00001271670
Loss of Function1.982841.80.6690.00000197476

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.06550.0654
Ashkenazi Jewish0.01080.0109
East Asian0.1070.108
Finnish0.008630.00849
European (Non-Finnish)0.007260.00723
Middle Eastern0.1070.108
South Asian0.02380.0231
Other0.01670.0168

dbNSFP

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}.;
Pathway
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);Ether lipid metabolism - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Long-term depression - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Necroptosis - 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);MAPK signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);MAPK Signaling Pathway;Ras Signaling;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Acyl chain remodelling of PE;Synthesis of PA (Consensus)

Recessive Scores

pRec
0.0982

Intolerance Scores

loftool
0.952
rvis_EVS
1.61
rvis_percentile_EVS
95.93

Haploinsufficiency Scores

pHI
0.114
hipred
N
hipred_score
0.246
ghis
0.386

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.101

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Pla2g4d
Phenotype

Gene ontology

Biological process
phospholipid metabolic process;phosphatidic acid biosynthetic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;glycerophospholipid catabolic process
Cellular component
cytoplasm;cytosol;membrane
Molecular function
lysophospholipase activity;phospholipase A2 activity;calcium ion binding;calcium-dependent phospholipid binding;phospholipase A1 activity;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)