PLCB3
phospholipase C beta 3, the group of C2 domain containing phospholipases|Phospholipases
Basic information
Region (hg38): 11:64251530-64269150
Links
Phenotypes
GenCC
Source:
- spondylometaphyseal dysplasia (Limited), mode of inheritance: AR
- spondylometaphyseal dysplasia with corneal dystrophy (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Spondylometaphyseal dysplasia with corneal dystrophy | AR | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 29122926 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (115 variants)
- not_provided (14 variants)
- Spondylometaphyseal_dysplasia_with_corneal_dystrophy (2 variants)
- PLCB3-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCB3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000932.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | |||||
| missense | 111 | 122 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 111 | 11 | 5 |
Highest pathogenic variant AF is 0.000017458213
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PLCB3 | protein_coding | protein_coding | ENST00000540288 | 31 | 17628 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.940 | 0.0600 | 125723 | 0 | 24 | 125747 | 0.0000954 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.27 | 512 | 766 | 0.668 | 0.0000533 | 7922 |
| Missense in Polyphen | 150 | 313.86 | 0.47791 | 3377 | ||
| Synonymous | -0.285 | 330 | 323 | 1.02 | 0.0000224 | 2468 |
| Loss of Function | 6.06 | 13 | 66.2 | 0.196 | 0.00000356 | 734 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000289 | 0.000275 |
| Ashkenazi Jewish | 0.000108 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000980 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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.;
- Pathway
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Platelet activation - Homo sapiens (human);Cortisol synthesis and secretion - Homo sapiens (human);Relaxin signaling pathway - Homo sapiens (human);Aldosterone synthesis and secretion - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Inositol phosphate metabolism - Homo sapiens (human);Long-term potentiation - Homo sapiens (human);Retrograde endocannabinoid signaling - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Long-term depression - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Gap junction - Homo sapiens (human);African trypanosomiasis - Homo sapiens (human);Gastric acid secretion - Homo sapiens (human);Chemokine signaling pathway - Homo sapiens (human);Circadian entrainment - Homo sapiens (human);Amoebiasis - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);Endocrine and other factor-regulated calcium reabsorption - Homo sapiens (human);Renin secretion - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Salivary secretion - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cholinergic synapse - Homo sapiens (human);Insulin secretion - Homo sapiens (human);Melanogenesis - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;Selective Serotonin Reuptake Inhibitor Pathway, Pharmacodynamics;Beta-agonist/Beta-blocker Pathway, Pharmacodynamics;Alzheimers Disease;Signal Transduction of S1P Receptor;Myometrial Relaxation and Contraction Pathways;G Protein Signaling Pathways;GPR40 Pathway;VEGFA-VEGFR2 Signaling Pathway;Chemokine signaling pathway;MAPK Cascade;Wnt Signaling Pathway;Calcium Regulation in the Cardiac Cell;Signaling by GPCR;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Signaling by WNT;Signal Transduction;GPCR GroupI metabotropic glutamate receptor;GPCR signaling-G alpha q;Inositol phosphate metabolism;Metabolism;phospholipases;Fatty Acids bound to GPR40 (FFAR1) regulate insulin secretion;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds;Presynaptic function of Kainate receptors;Activation of kainate receptors upon glutamate binding;Acetylcholine regulates insulin secretion;Free fatty acids regulate insulin secretion;Regulation of insulin secretion;Neuronal System;CRH;Phosphatidylinositol phosphate metabolism;Synthesis of IP3 and IP4 in the cytosol;Ca2+ pathway;Beta-catenin independent WNT signaling;CXCR4-mediated signaling events;Inositol phosphate metabolism;PLC beta mediated events;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;G beta:gamma signalling through PLC beta;Integration of energy metabolism;G alpha (q) signalling events;G-protein beta:gamma signalling;GPCR downstream signalling;PAR1-mediated thrombin signaling events;LPA receptor mediated events;IL8- and CXCR1-mediated signaling events;Plasma membrane estrogen receptor signaling;Nongenotropic Androgen signaling;Endothelins;IL8- and CXCR2-mediated signaling events
(Consensus)
Recessive Scores
- pRec
- 0.173
Intolerance Scores
- loftool
- 0.488
- rvis_EVS
- -0.64
- rvis_percentile_EVS
- 16.74
Haploinsufficiency Scores
- pHI
- 0.572
- hipred
- Y
- hipred_score
- 0.655
- ghis
- 0.507
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.818
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Plcb3
- 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); homeostasis/metabolism phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype;
Zebrafish Information Network
- Gene name
- plcb3
- Affected structure
- osteoblast
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- regulation of systemic arterial blood pressure;G protein-coupled receptor signaling pathway;Wnt signaling pathway, calcium modulating pathway;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;inositol phosphate metabolic process;phosphatidylinositol-mediated signaling;release of sequestered calcium ion into cytosol
- Cellular component
- nucleoplasm;cytosol;membrane;protein-containing complex;postsynaptic cytosol
- Molecular function
- phosphatidylinositol phospholipase C activity;phospholipase C activity;calcium ion binding;protein binding;calmodulin binding;cadherin binding