PLD2

phospholipase D2, the group of Phospholipases

Basic information

Region (hg38): 17:4807151-4823434

Links

ENSG00000129219 ∙ NCBI:5338 ∙ OMIM:602384 ∙ HGNC:9068 ∙ Uniprot:O14939 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (50 variants)
• not provided (12 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.

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				1		1
missense			49	4	3	56
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding					1	1
Total	0	0	50	5	4

Variants in PLD2

This is a list of pathogenic ClinVar variants found in the PLD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4807793-C-G		not specified	Uncertain significance (Nov 17, 2022)
17-4807795-T-C		not specified	Uncertain significance (May 08, 2023)
17-4807821-T-G		not specified	Uncertain significance (Apr 25, 2022)
17-4807843-C-T		not specified	Uncertain significance (Jan 04, 2024)
17-4808013-T-A		not specified	Uncertain significance (Jan 03, 2022)
17-4808284-G-A		not specified	Uncertain significance (Oct 05, 2022)
17-4808301-C-T		not specified	Uncertain significance (Sep 27, 2022)
17-4809134-G-T		not specified	Uncertain significance (Nov 04, 2023)
17-4809138-A-G		not specified	Uncertain significance (Dec 27, 2023)
17-4809140-A-G		not specified	Uncertain significance (Apr 22, 2022)
17-4809161-C-T		not specified	Uncertain significance (Apr 25, 2023)
17-4809346-C-T		not specified	Uncertain significance (Jun 18, 2021)
17-4809499-T-C		not specified	Uncertain significance (Aug 28, 2023)
17-4809542-G-T		not specified	Uncertain significance (Jun 12, 2023)
17-4809753-G-A		not specified	Uncertain significance (Oct 06, 2021)
17-4809990-C-T		not specified	Uncertain significance (Jul 21, 2021)
17-4810001-C-T			Benign (Jul 11, 2018)
17-4810016-G-A		not specified	Uncertain significance (May 27, 2022)
17-4810019-A-G		not specified	Uncertain significance (May 03, 2023)
17-4810839-C-T		not specified	Uncertain significance (Mar 11, 2022)
17-4810875-G-T		not specified	Uncertain significance (Oct 13, 2021)
17-4810929-C-T		not specified	Uncertain significance (Oct 19, 2021)
17-4810930-G-A			Benign (Dec 31, 2019)
17-4810949-G-A			Likely benign (Dec 31, 2019)
17-4814646-G-A		not specified	Likely benign (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLD2	protein_coding	protein_coding	ENST00000263088	24	16339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.14e-27	0.00703	125413	0	335	125748	0.00133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.119	577	585	0.986	0.0000373	6031
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00350	0.00350
Ashkenazi Jewish	0.00	0.00
East Asian	0.00131	0.00125
Finnish	0.000739	0.000739
European (Non-Finnish)	0.00139	0.00139
Middle Eastern	0.00131	0.00125
South Asian	0.000923	0.000915
Other	0.00180	0.00179

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

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

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