PLCB2

phospholipase C beta 2, the group of Phospholipases|C2 domain containing phospholipases

Basic information

Region (hg38): 15:40278175-40307935

Links

ENSG00000137841 ∙ NCBI:5330 ∙ OMIM:604114 ∙ HGNC:9055 ∙ Uniprot:Q00722 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLCB2 gene.

• Inborn genetic diseases (42 variants)
• not provided (6 variants)
• Thrombocytopenia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCB2 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					2	2
missense			40	3	1	44
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding				1		1
Total	0	0	40	4	4

Variants in PLCB2

This is a list of pathogenic ClinVar variants found in the PLCB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-40281518-G-T		not specified	Uncertain significance (Jan 13, 2023)
15-40281520-G-A		not specified	Uncertain significance (Mar 11, 2024)
15-40281605-G-C		not specified	Uncertain significance (Mar 29, 2022)
15-40281637-T-C		not specified	Uncertain significance (Feb 28, 2023)
15-40281640-G-A		not specified	Uncertain significance (Nov 08, 2022)
15-40281640-G-C		not specified	Uncertain significance (Jan 06, 2023)
15-40281727-G-A		not specified	Uncertain significance (Jul 20, 2022)
15-40281824-G-A		not specified	Uncertain significance (Jun 13, 2023)
15-40281953-G-A		not specified	Uncertain significance (Jul 09, 2021)
15-40281976-G-C		not specified	Uncertain significance (Aug 29, 2022)
15-40282007-G-T		not specified	Uncertain significance (Jul 20, 2022)
15-40282100-C-T		not specified	Uncertain significance (Apr 13, 2023)
15-40282132-C-A		not specified	Uncertain significance (Oct 14, 2021)
15-40282291-G-A		not specified	Uncertain significance (Jun 21, 2022)
15-40282388-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-40288759-C-T		not specified	Uncertain significance (Nov 18, 2022)
15-40288873-G-C		not specified	Uncertain significance (Sep 01, 2021)
15-40288905-G-A		not specified	Uncertain significance (Jan 08, 2024)
15-40289322-C-T		not specified	Uncertain significance (Apr 27, 2023)
15-40289336-T-G		not specified	Uncertain significance (Mar 29, 2022)
15-40290618-C-A		not specified	Uncertain significance (Dec 08, 2023)
15-40290625-C-T		not specified	Uncertain significance (Dec 05, 2022)
15-40290751-G-A			Likely benign (May 24, 2018)
15-40290782-G-A		not specified	Uncertain significance (Jun 11, 2021)
15-40290834-T-C		not specified	Uncertain significance (Feb 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCB2	protein_coding	protein_coding	ENST00000260402	32	29760

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.07e-20	0.939	125095	6	478	125579	0.00193

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.51	583	695	0.838	0.0000401	7753
Missense in Polyphen		212	292.57	0.7246		3236
Synonymous	0.754	262	278	0.942	0.0000168	2220
Loss of Function	2.51	41	62.4	0.657	0.00000301	746

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00153	0.00150
Ashkenazi Jewish	0.00	0.00
East Asian	0.000445	0.000435
Finnish	0.0142	0.0138
European (Non-Finnish)	0.000765	0.000739
Middle Eastern	0.000445	0.000435
South Asian	0.00119	0.00118
Other	0.00363	0.00360

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. {ECO:0000269|PubMed:1644792}.
• 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);Carbohydrate digestion and absorption - 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);Taste transduction - 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;MicroRNAs in cardiomyocyte hypertrophy;Alzheimers Disease;Signal Transduction of S1P Receptor;GPR40 Pathway;Chemokine signaling pathway;Wnt Signaling Pathway;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;Phosphatidylinositol phosphate metabolism;Synthesis of IP3 and IP4 in the cytosol;Ca2+ pathway;Beta-catenin independent WNT signaling;CXCR4-mediated signaling events;Thromboxane A2 receptor signaling;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;PAR4-mediated thrombin signaling events;PAR1-mediated thrombin signaling events;RAC1 signaling pathway;IL8- and CXCR1-mediated signaling events;S1P1 pathway;Plasma membrane estrogen receptor signaling;Nongenotropic Androgen signaling;Alpha-synuclein signaling;Endothelins;IL8- and CXCR2-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.185

Intolerance Scores

• loftool: 0.855
• rvis_EVS: -0.7
• rvis_percentile_EVS: 14.81

Haploinsufficiency Scores

• pHI: 0.268
• hipred: Y
• hipred_score: 0.744
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.695

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plcb2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system phenotype; hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; immune system phenotype; taste/olfaction 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)

Gene ontology

• Biological process: phospholipid metabolic process;G protein-coupled receptor signaling pathway;activation of phospholipase C activity;Wnt signaling pathway, calcium modulating pathway;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;inositol phosphate metabolic process;phosphatidylinositol-mediated signaling;sensory perception of bitter taste;release of sequestered calcium ion into cytosol
• Cellular component: cytosol
• Molecular function: phosphatidylinositol phospholipase C activity;phospholipase C activity;calcium ion binding