PLCD4

phospholipase C delta 4, the group of Phospholipases|C2 domain containing phospholipases|EF-hand domain containing

Basic information

Region (hg38): 2:218607855-218637184

Links

ENSG00000115556NCBI:84812OMIM:605939HGNC:9062Uniprot:Q9BRC7AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLCD4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCD4 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
3
clinvar
3
missense
44
clinvar
3
clinvar
47
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 44 6 0

Variants in PLCD4

This is a list of pathogenic ClinVar variants found in the PLCD4 region.

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

Position Type Phenotype Significance ClinVar
2-218615744-C-T not specified Uncertain significance (Jan 16, 2024)3214463
2-218615965-G-T not specified Uncertain significance (Oct 17, 2023)3214464
2-218615966-T-C not specified Uncertain significance (Feb 07, 2023)2482118
2-218616010-C-T Likely benign (Nov 01, 2022)2651881
2-218616032-C-T not specified Uncertain significance (Nov 09, 2023)3214457
2-218618611-G-T not specified Uncertain significance (Jul 19, 2022)2302462
2-218618689-C-T not specified Uncertain significance (Jun 28, 2022)2365594
2-218618695-T-G not specified Uncertain significance (Jun 02, 2023)2556186
2-218618759-T-C not specified Uncertain significance (Aug 30, 2022)2309809
2-218618774-T-C not specified Uncertain significance (Jun 12, 2023)2569936
2-218618783-T-C not specified Uncertain significance (Oct 05, 2022)2210132
2-218618798-G-A not specified Uncertain significance (Dec 27, 2022)2366720
2-218618803-G-C not specified Uncertain significance (Jun 24, 2022)2314562
2-218618813-G-A Likely benign (Nov 01, 2022)2651882
2-218621480-G-A not specified Uncertain significance (Oct 27, 2023)3214461
2-218621540-C-T not specified Uncertain significance (Jan 03, 2024)3214462
2-218621541-G-A not specified Uncertain significance (Mar 06, 2023)2456576
2-218622719-C-T not specified Uncertain significance (Nov 07, 2022)2368030
2-218622722-G-A not specified Uncertain significance (Apr 16, 2024)3307343
2-218622737-C-A not specified Uncertain significance (Nov 09, 2021)2394714
2-218622824-T-C not specified Likely benign (Mar 06, 2023)2494675
2-218622858-G-A not specified Uncertain significance (May 15, 2024)3307338
2-218628127-G-T not specified Uncertain significance (Mar 20, 2023)2527305
2-218628139-C-A not specified Uncertain significance (Feb 21, 2024)3214466
2-218628173-A-G not specified Uncertain significance (Feb 05, 2024)3214467

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PLCD4protein_codingprotein_codingENST00000450993 1529420
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.29e-130.91012433403231246570.00130
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.423614450.8100.00002595033
Missense in Polyphen148184.680.801372038
Synonymous1.781381670.8250.000008871435
Loss of Function2.092741.50.6510.00000212453

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01300.0129
Ashkenazi Jewish0.0002020.000199
East Asian0.001390.00139
Finnish0.0001400.000139
European (Non-Finnish)0.0004660.000460
Middle Eastern0.001390.00139
South Asian0.0007930.000785
Other0.0005040.000495

dbNSFP

Source: dbNSFP

Function
FUNCTION: Hydrolyzes the phosphatidylinositol 4,5-bisphosphate (PIP2) to generate 2 second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). DAG mediates the activation of protein kinase C (PKC), while IP3 releases Ca(2+) from intracellular stores. Required for acrosome reaction in sperm during fertilization, probably by acting as an important enzyme for intracellular Ca(2+) mobilization in the zona pellucida- induced acrosome reaction. May play a role in cell growth. Modulates the liver regeneration in cooperation with nuclear PKC. Overexpression up-regulates the Erk signaling pathway and proliferation. {ECO:0000269|PubMed:15140260}.;
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;Serotonin and anxiety;Serotonin and anxiety-related events;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;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
0.116

Intolerance Scores

loftool
0.801
rvis_EVS
-0.93
rvis_percentile_EVS
9.68

Haploinsufficiency Scores

pHI
0.361
hipred
N
hipred_score
0.475
ghis
0.547

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.757

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Plcd4
Phenotype
reproductive system phenotype; cellular phenotype;

Gene ontology

Biological process
acrosome reaction;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;inositol phosphate metabolic process;phosphatidylinositol metabolic process
Cellular component
endoplasmic reticulum membrane;cytosol;plasma membrane;nuclear membrane
Molecular function
phosphatidylinositol phospholipase C activity;calcium ion binding