PLD2

phospholipase D2, the group of Phospholipases

Basic information

Region (hg38): 17:4807152-4823434

Links

ENSG00000129219NCBI:5338OMIM:602384HGNC:9068Uniprot:O14939AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLD2 gene.

  • not_specified (147 variants)
  • not_provided (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002663.5. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
146
clinvar
5
clinvar
3
clinvar
154
nonsense
0
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 0 0 147 7 4
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PLD2protein_codingprotein_codingENST00000263088 2416339
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.14e-270.0070312541303351257480.00133
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1195775850.9860.00003736031
Missense in Polyphen179180.950.989221873
Synonymous-0.1542372341.010.00001431916
Loss of Function1.154655.20.8330.00000299575

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003500.00350
Ashkenazi Jewish0.000.00
East Asian0.001310.00125
Finnish0.0007390.000739
European (Non-Finnish)0.001390.00139
Middle Eastern0.001310.00125
South Asian0.0009230.000915
Other0.001800.00179

dbNSFP

Source: dbNSFP

Function
FUNCTION: May have a role in signal-induced cytoskeletal regulation and/or endocytosis. {ECO:0000250}.;
Pathway
Fc gamma R-mediated phagocytosis - Homo sapiens (human);Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Endocytosis - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);cAMP signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Phospholipid Biosynthesis;Ras Signaling;EGF-EGFR Signaling Pathway;metabolism of anandamide an endogenous cannabinoid;Metabolism of lipids;Role of phospholipids in phagocytosis;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;Metabolism;phospholipases;Phosphatidylinositol phosphate metabolism;Glycerophospholipid metabolism;EGFR1;ErbB1 downstream signaling;Arf1 pathway;Arf6 trafficking events;Angiopoietin receptor Tie2-mediated signaling;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG;Synthesis of PA;mTOR signaling pathway;LPA receptor mediated events;Fc-epsilon receptor I signaling in mast cells;Arf6 downstream pathway;Alpha-synuclein signaling;IL8- and CXCR2-mediated signaling events;RhoA signaling pathway (Consensus)

Recessive Scores

pRec
0.253

Intolerance Scores

loftool
0.929
rvis_EVS
0.41
rvis_percentile_EVS
76.56

Haploinsufficiency Scores

pHI
0.336
hipred
Y
hipred_score
0.621
ghis
0.536

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.997

Gene Damage Prediction

AllRecessiveDominant
MendelianHighMediumHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Pld2
Phenotype
homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal phenotype; hematopoietic system phenotype;

Gene ontology

Biological process
phosphatidic acid biosynthetic process;cytoskeleton organization;small GTPase mediated signal transduction;lipid catabolic process;synaptic vesicle recycling;Fc-gamma receptor signaling pathway involved in phagocytosis;inositol lipid-mediated signaling;cell motility
Cellular component
endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;presynapse
Molecular function
phospholipase D activity;protein binding;phosphatidylinositol binding;N-acylphosphatidylethanolamine-specific phospholipase D activity