PLD2
protein-codingphospholipase D2, the group of Phospholipases
Gene summary
The protein encoded by this gene catalyzes the hydrolysis of phosphatidylcholine to phosphatidic acid and choline. The activity of the encoded enzyme is enhanced by phosphatidylinositol 4,5-bisphosphate and ADP-ribosylation factor-1. This protein localizes to the peripheral membrane and may be involved in cytoskeletal organization, cell cycle control, transcriptional regulation, and/or regulated secretion. Two transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jul 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.3 kbGenCC 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 PLD2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002663.5. 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 | 6 | 2 | 1 | 9 | ||
| missense | 163 | 5 | 3 | 171 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 179 | 7 | 4 | 190 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002654.3 | 24 | MANE Select | |
| Ensembl | ENSP00000263088.5 | 24 | MANE Select | |
| RefSeq | NP_001230037.1 | 24 | Standard | |
| Ensembl | ENSP00000459571.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- phosphatidic acid biosynthetic process
- cytoskeleton organization
- small GTPase mediated signal transduction
- lipid catabolic process
- synaptic vesicle recycling
Molecular Function
- phospholipase D activity
- protein binding
- phosphatidylinositol binding
- N-acylphosphatidylethanolamine-specific phospholipase D activity
Cellular Component
- endoplasmic reticulum membrane
- Golgi apparatus
- plasma membrane
- presynapse
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263088
- Coding exons
- 24
- Length
- 16339
- Individuals with no LoFs
- 125413
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 335
- Defined
- 125748
- p
- 0.00133
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.119 | 577 | 585 | 0.986 | 0.0000373 | 6031 |
| Missense (PolyPhen) | 179 | 180.95 | 0.98922 | 1873 | ||
| Synonymous | -0.154 | 237 | 234 | 1.01 | 0.0000143 | 1916 |
| Loss of Function | 1.15 | 46 | 55.2 | 0.833 | 0.00000299 | 575 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0023 | 0.0023 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.00074 | 0.00074 | rare |
| European (Non-Finnish) | 0.0014 | 0.0014 | notable |
| South Asian | 0.00092 | 0.00091 | rare |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May have a role in signal-induced cytoskeletal regulation and/or endocytosis. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.253
Intolerance Scores
- LoFtool
- 0.929
- RVIS EVS
- 0.41
- RVIS percentile EVS
- 76.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.997
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |