PLCD1

phospholipase C delta 1, the group of Phospholipases|C2 domain containing phospholipases|EF-hand domain containing

Basic information

Region (hg38): 3:38007495-38029642

Links

ENSG00000187091 ∙ NCBI:5333 ∙ OMIM:602142 ∙ HGNC:9060 ∙ Uniprot:P51178 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nonsyndromic congenital nail disorder 3 (Strong), mode of inheritance: AR
• nonsyndromic congenital nail disorder 3 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nail disorder, nonsyndromic congenital, 3	AD/AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dermatologic	21665001

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLCD1 gene.

• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCD1 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				14	7	21
missense		1	70	6	5	82
nonsense	2					2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	4		5
non coding			3	1	15	19
Total	2	2	73	21	27

Highest pathogenic variant AF is 0.000184

Variants in PLCD1

This is a list of pathogenic ClinVar variants found in the PLCD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-38007538-TG-T			Benign (Jun 20, 2021)
3-38008032-A-C		not specified	Uncertain significance (Apr 19, 2024)
3-38008065-T-G		not specified	Uncertain significance (Jun 21, 2023)
3-38008071-A-T		not specified	Uncertain significance (Oct 27, 2021)
3-38008094-A-G		not specified	Uncertain significance (Mar 18, 2024)
3-38008142-G-A		not specified	Uncertain significance (Oct 05, 2022)
3-38008155-G-A		not specified	Uncertain significance (Dec 30, 2023)
3-38008257-C-G		not specified	Uncertain significance (Apr 18, 2023)
3-38008261-C-T		not specified	Uncertain significance (Oct 21, 2021)
3-38008262-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-38008280-T-C		not specified	Likely benign (Sep 26, 2023)
3-38008283-C-T		not specified	Uncertain significance (Apr 17, 2024)
3-38008322-A-C		not specified	Uncertain significance (Jun 22, 2021)
3-38008330-T-C		not specified	Likely benign (Aug 14, 2023)
3-38008356-C-T			Likely benign (Aug 09, 2018)
3-38008464-G-C		not specified	Uncertain significance (Apr 12, 2024)
3-38008466-T-G		not specified	Uncertain significance (Feb 14, 2024)
3-38008471-C-T		not specified	Uncertain significance (Jan 19, 2024)
3-38008472-G-A		not specified	Uncertain significance (Mar 16, 2022)
3-38008481-C-A		not specified	Uncertain significance (Jan 04, 2024)
3-38008506-G-A			Benign (Dec 31, 2019)
3-38008511-G-A		not specified	Likely benign (Oct 26, 2022)
3-38008524-G-T		PLCD1-related disorder	Conflicting classifications of pathogenicity (Mar 30, 2021)
3-38008544-C-T		not specified	Uncertain significance (Mar 06, 2023)
3-38008571-C-T		not specified	Uncertain significance (Jun 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCD1	protein_coding	protein_coding	ENST00000463876	15	22267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.74e-19	0.0427	125576	0	172	125748	0.000684

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.241	445	460	0.968	0.0000314	5094
Missense in Polyphen		110	130.07	0.8457		1614
Synonymous	0.103	192	194	0.991	0.0000132	1522
Loss of Function	1.02	33	40.0	0.825	0.00000219	426

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000926	0.000924
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.000991	0.000925
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000926	0.000923
Middle Eastern	0.000991	0.000925
South Asian	0.000654	0.000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. Essential for trophoblast and placental development.
• Disease: DISEASE: Nail disorder, non-syndromic congenital, 3 (NDNC3) [MIM:151600]: A nail disorder characterized by a white appearance of the nail plate (true leukonychia), the nail bed (pseudoleukonychia), or neither (apparent leukonychia). Leukonychia may involve all of the nail (leukonychia totalis) or only part of the nail (leukonychia partialis), or can appear as one or more transverse bands (leukonychia striata) or white spots (leukonychia punctata). {ECO:0000269|PubMed:21665001}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;Myometrial Relaxation and Contraction Pathways;GPR40 Pathway;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;phospholipase c delta in phospholipid associated cell signaling;Inositol phosphate metabolism;Metabolism;phospholipases;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.151

Intolerance Scores

• loftool: 0.884
• rvis_EVS: -0.85
• rvis_percentile_EVS: 10.96

Haploinsufficiency Scores

• pHI: 0.985
• hipred: N
• hipred_score: 0.394
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.833

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plcd1
• Phenotype: hematopoietic system phenotype; neoplasm; immune system 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; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: angiogenesis;phospholipid metabolic process;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;regulation of cell population proliferation;inositol phosphate metabolic process;labyrinthine layer blood vessel development
• Cellular component: cytoplasm;cytosol;plasma membrane;extracellular exosome
• Molecular function: phosphatidylinositol phospholipase C activity;calcium ion binding;protein binding;phosphatidylinositol-4,5-bisphosphate binding;GTPase activating protein binding