PLD4

phospholipase D family member 4, the group of Phospholipases

Basic information

Region (hg38): 14:104924712-104937761

Previous symbols: [ "C14orf175" ]

Links

ENSG00000166428 ∙ NCBI:122618 ∙ OMIM:618488 ∙ HGNC:23792 ∙ Uniprot:Q96BZ4 ∙ 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 PLD4 gene.

• Inborn genetic diseases (30 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLD4 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						0
missense			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	30	0	0

Variants in PLD4

This is a list of pathogenic ClinVar variants found in the PLD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-104927689-C-T		not specified	Likely benign (Dec 08, 2023)
14-104927715-G-A		not specified	Likely benign (Aug 10, 2021)
14-104927748-C-G		not specified	Uncertain significance (Oct 02, 2023)
14-104927835-G-A		not specified	Uncertain significance (Feb 16, 2023)
14-104928882-T-C		not specified	Uncertain significance (May 24, 2023)
14-104928909-G-A		not specified	Uncertain significance (Dec 07, 2021)
14-104928919-C-G		not specified	Uncertain significance (Aug 12, 2021)
14-104928936-C-T			Likely benign (Jul 14, 2017)
14-104929312-G-C		not specified	Uncertain significance (Jun 29, 2023)
14-104929316-C-G		not specified	Uncertain significance (Oct 12, 2021)
14-104929328-C-A		not specified	Uncertain significance (Jan 18, 2023)
14-104929334-C-A		not specified	Uncertain significance (Mar 01, 2024)
14-104929338-T-C		not specified	Uncertain significance (Mar 29, 2023)
14-104929367-G-A		not specified	Uncertain significance (May 18, 2023)
14-104929380-C-T		not specified	Uncertain significance (Jan 09, 2023)
14-104929392-G-A		not specified	Uncertain significance (Jan 31, 2022)
14-104929403-G-A		not specified	Uncertain significance (Oct 16, 2023)
14-104929421-G-A		not specified	Uncertain significance (Oct 30, 2023)
14-104930007-C-T		not specified	Uncertain significance (Aug 12, 2021)
14-104930008-G-T		not specified	Uncertain significance (Jan 31, 2024)
14-104930031-T-G		not specified	Uncertain significance (Feb 15, 2023)
14-104930075-T-G		not specified	Uncertain significance (Sep 20, 2023)
14-104930092-G-A		not specified	Uncertain significance (Aug 09, 2021)
14-104930887-G-A		not specified	Uncertain significance (Aug 14, 2023)
14-104931770-C-T		not specified	Uncertain significance (Aug 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLD4	protein_coding	protein_coding	ENST00000392593	10	8422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.73e-13	0.0693	124467	4	257	124728	0.00105

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.167	295	287	1.03	0.0000165	3180
Missense in Polyphen		117	102.49	1.1416		1164
Synonymous	2.23	95	127	0.748	0.00000776	1054
Loss of Function	0.453	20	22.3	0.897	0.00000113	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00117
Ashkenazi Jewish	0.000907	0.000597
East Asian	0.0000557	0.0000556
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000564	0.000371
Middle Eastern	0.0000557	0.0000556
South Asian	0.00653	0.00554
Other	0.00144	0.00132

dbNSFP

Source: dbNSFP

• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Metabolism of lipids;Role of phospholipids in phagocytosis;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;Metabolism;phospholipases;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PG (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.853
• rvis_EVS: 0.11
• rvis_percentile_EVS: 61.91

Haploinsufficiency Scores

• pHI: 0.0921
• hipred: N
• hipred_score: 0.144
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pld4
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: hematopoietic progenitor cell differentiation;phagocytosis;lipid catabolic process;inositol phosphate metabolic process
• Cellular component: nucleus;endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;trans-Golgi network membrane;phagocytic vesicle
• Molecular function: phosphatidylinositol phospholipase C activity;phospholipase D activity;N-acylphosphatidylethanolamine-specific phospholipase D activity