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PLD1

phospholipase D1, the group of Phospholipases|Pleckstrin homology domain containing

Basic information

Region (hg38): 3:171600404-171810950

Links

ENSG00000075651 ∙ NCBI:5337 ∙ OMIM:602382 ∙ HGNC:9067 ∙ Uniprot:Q13393 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • cardiac valvular defect, developmental (Moderate), mode of inheritance: AR
  • PLD1-related congenital heart disease (Definitive), mode of inheritance: AR
  • cardiac valvular defect, developmental (Strong), mode of inheritance: AR
  • cardiac valvular defect, developmental (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cardiac valvular dysplasia 1ARCardiovascularIndividuals may manifest with cardiac valvular disease, and awareness may allow early diagnosis and medical or surgical managementCardiovascular27799408

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLD1 gene.

  • not_provided (186 variants)
  • Inborn_genetic_diseases (138 variants)
  • Cardiac_valvular_defect,_developmental (31 variants)
  • PLD1-related_disorder (21 variants)
  • not_specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002662.5. 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
28
clinvar
7
clinvar
 35
missense
1
clinvar
6
clinvar
185
clinvar
17
clinvar
9
clinvar
 218
nonsense
4
clinvar
3
clinvar
1
clinvar
 8
start loss
0
frameshift
5
clinvar
4
clinvar
 9
splice donor/acceptor (+/-2bp)
2
clinvar
6
clinvar
6
clinvar
 14
Total 12 19 192 45 16

Highest pathogenic variant AF is 0.00027938478

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PLD1protein_codingprotein_codingENST00000351298 26210546
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
12557801701257480.000676
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1846026150.9790.00003417120
Missense in Polyphen224237.250.944172763
Synonymous0.9572002180.9180.00001281956
Loss of Function2.364262.00.6770.00000327737

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001210.00121
Ashkenazi Jewish0.000.00
East Asian0.0009260.000925
Finnish0.00004680.0000462
European (Non-Finnish)0.0009050.000897
Middle Eastern0.0009260.000925
South Asian0.0004780.000359
Other0.0005010.000489

dbNSFP

Source: dbNSFP

Function
FUNCTION: Implicated as a critical step in numerous cellular pathways, including signal transduction, membrane trafficking, and the regulation of mitosis. May be involved in the regulation of perinuclear intravesicular membrane traffic (By similarity). {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);Pathways in cancer - Homo sapiens (human);Pancreatic cancer - Homo sapiens (human);Human Thyroid Stimulating Hormone (TSH) signaling pathway;Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;One carbon metabolism and related pathways;Ras Signaling;EGF-EGFR Signaling Pathway;Neutrophil degranulation;ras signaling pathway;metabolism of anandamide an endogenous cannabinoid;rac1 cell motility signaling pathway;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;Arf6 trafficking events;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG;Synthesis of PA;mTOR signaling pathway;CDC42 signaling events;IL8- and CXCR1-mediated signaling events;Arf6 downstream pathway;Alpha-synuclein signaling;RhoA signaling pathway (Consensus)

Recessive Scores

pRec
0.226

Intolerance Scores

loftool
0.977
rvis_EVS
-0.01
rvis_percentile_EVS
52.36

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Zebrafish Information Network

Gene name
pld1b
Affected structure
whole organism
Phenotype tag
abnormal
Phenotype quality
curved

Gene ontology

Biological process
phosphatidic acid biosynthetic process;chemotaxis;small GTPase mediated signal transduction;Ras protein signal transduction;lipid catabolic process;regulation of microvillus assembly;neutrophil degranulation;inositol lipid-mediated signaling;cell motility;regulation of synaptic vesicle cycle
Cellular component
Golgi membrane;lysosomal membrane;endosome;endoplasmic reticulum membrane;Golgi apparatus;plasma membrane;membrane;apical plasma membrane;endocytic vesicle;late endosome membrane;specific granule membrane;perinuclear region of cytoplasm;tertiary granule membrane;cholinergic synapse
Molecular function
phospholipase D activity;protein binding;phosphatidylinositol binding;N-acylphosphatidylethanolamine-specific phospholipase D activity
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