PLCD4
Basic information
Region (hg38): 2:218607855-218637184
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 44 | 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) | ||
2-218615965-G-T | not specified | Uncertain significance (Oct 17, 2023) | ||
2-218615966-T-C | not specified | Uncertain significance (Feb 07, 2023) | ||
2-218616010-C-T | Likely benign (Nov 01, 2022) | |||
2-218616032-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
2-218618611-G-T | not specified | Uncertain significance (Jul 19, 2022) | ||
2-218618689-C-T | not specified | Uncertain significance (Jun 28, 2022) | ||
2-218618695-T-G | not specified | Uncertain significance (Jun 02, 2023) | ||
2-218618759-T-C | not specified | Uncertain significance (Aug 30, 2022) | ||
2-218618774-T-C | not specified | Uncertain significance (Jun 12, 2023) | ||
2-218618783-T-C | not specified | Uncertain significance (Oct 05, 2022) | ||
2-218618798-G-A | not specified | Uncertain significance (Dec 27, 2022) | ||
2-218618803-G-C | not specified | Uncertain significance (Jun 24, 2022) | ||
2-218618813-G-A | Likely benign (Nov 01, 2022) | |||
2-218621480-G-A | not specified | Uncertain significance (Oct 27, 2023) | ||
2-218621540-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
2-218621541-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
2-218622719-C-T | not specified | Uncertain significance (Nov 07, 2022) | ||
2-218622722-G-A | not specified | Uncertain significance (Apr 16, 2024) | ||
2-218622737-C-A | not specified | Uncertain significance (Nov 09, 2021) | ||
2-218622824-T-C | not specified | Likely benign (Mar 06, 2023) | ||
2-218622858-G-A | not specified | Uncertain significance (May 15, 2024) | ||
2-218628127-G-T | not specified | Uncertain significance (Mar 20, 2023) | ||
2-218628139-C-A | not specified | Uncertain significance (Feb 21, 2024) | ||
2-218628173-A-G | not specified | Uncertain significance (Feb 05, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PLCD4 | protein_coding | protein_coding | ENST00000450993 | 15 | 29420 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.29e-13 | 0.910 | 124334 | 0 | 323 | 124657 | 0.00130 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.42 | 361 | 445 | 0.810 | 0.0000259 | 5033 |
Missense in Polyphen | 148 | 184.68 | 0.80137 | 2038 | ||
Synonymous | 1.78 | 138 | 167 | 0.825 | 0.00000887 | 1435 |
Loss of Function | 2.09 | 27 | 41.5 | 0.651 | 0.00000212 | 453 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0130 | 0.0129 |
Ashkenazi Jewish | 0.000202 | 0.000199 |
East Asian | 0.00139 | 0.00139 |
Finnish | 0.000140 | 0.000139 |
European (Non-Finnish) | 0.000466 | 0.000460 |
Middle Eastern | 0.00139 | 0.00139 |
South Asian | 0.000793 | 0.000785 |
Other | 0.000504 | 0.000495 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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