PLCD1 phospholipase C delta 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PLCD1provided by HGNC
Official Full Name: phospholipase C delta 1provided by HGNC
Primary source: HGNC:HGNC:9060
See related: Ensembl:ENSG00000187091 MIM:602142; AllianceGenome:HGNC:9060
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NDNC3; PLC-III
Summary: This gene encodes a member of the phospholipase C family. Phospholipase C isozymes play critical roles in intracellular signal transduction by catalyzing the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into the second messengers diacylglycerol (DAG) and inositol triphosphate (IP3). The encoded protein functions as a tumor suppressor in several types of cancer, and mutations in this gene are a cause of hereditary leukonychia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression: Broad expression in testis (RPKM 17.3), esophagus (RPKM 7.7) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p22.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (38007496..38029642, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (38011677..38033823, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (38048987..38071133, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

One recurrent heterozygous mutation of the PLCD1 gene in a Chinese family with hereditary leukonychia: A case report and genotype-phenotype correlation analysis.
Title: One recurrent heterozygous mutation of the PLCD1 gene in a Chinese family with hereditary leukonychia: A case report and genotype-phenotype correlation analysis.
MicroRNA-191 regulates oral squamous cell carcinoma cells growth by targeting PLCD1 via the Wnt/beta-catenin signaling pathway.
Title: MicroRNA-191 regulates oral squamous cell carcinoma cells growth by targeting PLCD1 via the Wnt/β-catenin signaling pathway.
lncRNA MIR503HG Targets miR-191-5p/PLCD1 Axis and Negatively Modulates Apoptosis, Extracellular Matrix Disruption, and Inflammation in Abdominal Aortic Aneurysm.
Title: lncRNA MIR503HG Targets miR-191-5p/PLCD1 Axis and Negatively Modulates Apoptosis, Extracellular Matrix Disruption, and Inflammation in Abdominal Aortic Aneurysm.
Identification of a Novel PLCD1 Variant in a Danish Family with Hereditary Leukonychia.
Title: Identification of a Novel PLCD1 Variant in a Danish Family with Hereditary Leukonychia.
Phospholipase C delta 1 inhibits WNT/beta-catenin and EGFR-FAK-ERK signaling and is disrupted by promoter CpG methylation in renal cell carcinoma.
Title: Phospholipase C delta 1 inhibits WNT/β-catenin and EGFR-FAK-ERK signaling and is disrupted by promoter CpG methylation in renal cell carcinoma.
The tumor suppressor activity of DLC1 requires the interaction of its START domain with Phosphatidylserine, PLCD1, and Caveolin-1.
Title: The tumor suppressor activity of DLC1 requires the interaction of its START domain with Phosphatidylserine, PLCD1, and Caveolin-1.
Germline Mutation of PLCD1 Contributes to Human Multiple Pilomatricomas through Protein Kinase D/Extracellular Signal-Regulated Kinase1/2 Cascade and TRPV6.
Title: Germline Mutation of PLCD1 Contributes to Human Multiple Pilomatricomas through Protein Kinase D/Extracellular Signal-Regulated Kinase1/2 Cascade and TRPV6.
Identification of two novel mutations in the PLCD1 gene in Chinese patients with hereditary leukonychia.
Title: Identification of two novel mutations in the PLCD1 gene in Chinese patients with hereditary leukonychia.
PLCD1 Suppressed Cellular Proliferation, Invasion, and Migration via Inhibition of Wnt/beta-Catenin Signaling Pathway in Esophageal Squamous Cell Carcinoma.
Title: PLCD1 Suppressed Cellular Proliferation, Invasion, and Migration via Inhibition of Wnt/β-Catenin Signaling Pathway in Esophageal Squamous Cell Carcinoma.
Phospholipase C controls chloride-dependent short-circuit current in human bronchial epithelial cells.
Title: Phospholipase C controls chloride-dependent short-circuit current in human bronchial epithelial cells.

Submit: New GeneRIF Correction See all GeneRIFs (53)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Nonsyndromic congenital nail disorder 3 MedGen: C0544855 OMIM: 151600 GeneReviews: Not available	not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 envelope glycoproteins gp120 and gp160 directly and specifically impair the CD3/TcR-mediated activation of phospholipase C (PLC) via the CD4 molecule in uninfected T cells	PubMed
Pr55(Gag)	gag	HIV-1 Gag co-localizes with the PH domain of PLC-delta at the long and thin connections termed tunnelling nanotube tips	PubMed
	gag	Replacement of the myristoylation signal of MA in HIV-1 with a plasma membrane targeting motif (N-terminal 120 amino acids) of the phospholipase C-delta1 pleckstrin homology (PH) domain results in infectious virus particle production	PubMed
Tat	tat	Phospholipase C/protein kinase C pathway-dependent phosphorylation of p44/42 and JNK MAP kinases is partially involved in IL-1beta induction by HIV-1 Tat	PubMed
	tat	HIV-1 Tat induces release of calcium and TNF-alpha production, an effect mediated at least in part by activation of phospholipase C	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S1298 (e-PCR)
- UniSTS:150016

D3S1298 (e-PCR)
- UniSTS:13884

SHGC-76834 (e-PCR)
- UniSTS:53375

D3S1298 (e-PCR)
- UniSTS:77505

SHGC-76845 (e-PCR)
- UniSTS:33226

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase activating protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables phosphatidylinositol phospholipase C activity	IBA Inferred from Biological aspect of Ancestor more info
enables phosphatidylinositol phospholipase C activity	IDA Inferred from Direct Assay more info	PubMed
enables phosphatidylinositol-4,5-bisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in lipid catabolic process	IEA Inferred from Electronic Annotation more info
involved_in phosphatidylinositol metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in phosphatidylinositol metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphatidylinositol-mediated signaling	IBA Inferred from Biological aspect of Ancestor more info
involved_in phospholipid metabolic process	TAS Traceable Author Statement more info	PubMed
involved_in release of sequestered calcium ion into cytosol	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1

Names: PLC-delta-1; Phospholipase C I 1; epididymis secretory sperm binding protein; phosphoinositide phospholipase C-delta-1; phospholipase C-III

NP_001124436.1

EC 3.1.4.11

NP_006216.2

EC 3.1.4.11

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_031922.1 RefSeqGene

Range

5022..27168

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001130964.2 → NP_001124436.1 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 isoform 1

See identical proteins and their annotated locations for NP_001124436.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AK090774, BC050382, DA083758

Consensus CDS

CCDS46793.1

UniProtKB/TrEMBL

Q5HYD7

Related

ENSP00000430344.1, ENST00000463876.5

Conserved Domains (7) summary

cd00275
Location:650 → 776

C2_PLC_like; C2 domain present in Phosphoinositide-specific phospholipases C (PLC)

cd08593
Location:316 → 617

PI-PLCc_delta; Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta

PLN02228
Location:233 → 776

PLN02228; Phosphoinositide phospholipase C

cd13363
Location:43 → 160

PH_PLC_delta; Phospholipase C-delta (PLC-delta) pleckstrin homology (PH) domain

pfam00169
Location:51 → 151

PH; PH domain

pfam09279
Location:234 → 316

EF-hand_like; Phosphoinositide-specific phospholipase C, efhand-like

pfam14788
Location:180 → 229

EF-hand_10; EF hand
NM_006225.4 → NP_006216.2 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 isoform 2

See identical proteins and their annotated locations for NP_006216.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon compared to transcript variant 1, and initiates translation from an in-frame upstream AUG, resulting in a shorter isoform (2) with a different N-terminus compared to isoform 1.

Source sequence(s)

AK292324, BC050382

Consensus CDS

CCDS2671.1

UniProtKB/Swiss-Prot

B3KR14, P51178, Q86VN8

UniProtKB/TrEMBL

A0A384MR47, A8K8F9

Related

ENSP00000335600.4, ENST00000334661.5

Conserved Domains (4) summary

cd00275
Location:629 → 755

C2_PLC_like; C2 domain present in Phosphoinositide-specific phospholipases C (PLC)

cd08593
Location:295 → 596

PI-PLCc_delta; Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta

cd13363
Location:22 → 139

PH_PLC_delta; Phospholipase C-delta (PLC-delta) pleckstrin homology (PH) domain

cd16217
Location:144 → 283

EFh_PI-PLCdelta1; EF-hand motif found in phosphoinositide phospholipase C delta 1 (PI-PLC-delta1)

RNA

NR_024071.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) skips splicing at 2 adjacent internal coding exons, thus retaining the intervening sequence, compared to transcript variant 1. This results in a frame-shift and premature translation termination, rendering this transcript susceptible to NMD. This variant has transcript support, but is not expected to encode a viable protein product.

Source sequence(s)

AK090774, BC050382, CX164303, DA083758