PLCB4
Basic information
Region (hg38): 20:9067825-9504593
Links
Phenotypes
GenCC
Source:
- auriculocondylar syndrome 1 (Strong), mode of inheritance: AD
- auriculocondylar syndrome 2 (Moderate), mode of inheritance: Semidominant
- auriculocondylar syndrome 2 (Definitive), mode of inheritance: AD
- auriculocondylar syndrome (Supportive), mode of inheritance: AD
- auriculocondylar syndrome 2 (Strong), mode of inheritance: AR
- auriculocondylar syndrome 2 (Strong), mode of inheritance: AD
- auriculocondylar syndrome 2 (Definitive), mode of inheritance: AD
- auriculocondylar syndrome 2 (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Auriculocondylar syndrome 2A; Auriculocondylar syndrome 2B | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Genitourinary; Gastrointestinal; Pulmonary | 16114046; 22560091; 23913798; 27007857; 28328130; 32201334; 35170830 |
ClinVar
This is a list of variants' phenotypes submitted to
- Auriculocondylar syndrome 2 (5 variants)
- Auriculocondylar syndrome 1 (5 variants)
- not provided (2 variants)
- Auriculocondylar syndrome (1 variants)
- Inborn genetic diseases (1 variants)
- Ocular melanocytosis;Uveal melanoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCB4 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 | 16 | 28 | ||||
missense | 56 | 81 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 3 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 8 | 3 | 12 | 23 | ||
non coding | 29 | 60 | 98 | |||
Total | 8 | 6 | 92 | 34 | 74 |
Highest pathogenic variant AF is 0.0000132
Variants in PLCB4
This is a list of pathogenic ClinVar variants found in the PLCB4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-9307832-AT-A | Likely pathogenic (Mar 23, 2024) | |||
20-9307875-G-A | Auriculocondylar syndrome 2 | Benign (Jan 29, 2024) | ||
20-9307876-C-A | Inborn genetic diseases | Uncertain significance (Sep 17, 2021) | ||
20-9307904-G-T | Auriculocondylar syndrome 2 | Uncertain significance (Jan 13, 2018) | ||
20-9337160-A-C | Inborn genetic diseases | Uncertain significance (Sep 01, 2021) | ||
20-9338200-G-A | Benign (May 14, 2021) | |||
20-9338886-C-T | Auriculocondylar syndrome 2 | Benign (Jan 12, 2018) | ||
20-9338978-A-G | Inborn genetic diseases | Uncertain significance (Aug 02, 2022) | ||
20-9338996-A-C | Inborn genetic diseases | Uncertain significance (Jan 07, 2022) | ||
20-9362753-A-G | Benign (May 15, 2021) | |||
20-9362934-C-A | Malignant tumor of prostate | Uncertain significance (-) | ||
20-9362947-G-A | Auriculocondylar syndrome 2 | Benign (Jan 12, 2018) | ||
20-9362969-A-G | Inborn genetic diseases | Uncertain significance (Feb 27, 2023) | ||
20-9362974-C-G | not specified | Uncertain significance (Dec 02, 2016) | ||
20-9362974-C-T | Long QT syndrome | Likely benign (-) | ||
20-9365464-G-T | Likely pathogenic (Aug 03, 2016) | |||
20-9365473-G-A | Auriculocondylar syndrome 2 | Benign/Likely benign (Jul 10, 2023) | ||
20-9365521-A-AATC | Likely benign (Aug 16, 2022) | |||
20-9365555-A-G | Benign (May 18, 2021) | |||
20-9371208-C-T | Auriculocondylar syndrome 2 | Benign (Jan 13, 2018) | ||
20-9371235-G-A | Uncertain significance (Jan 08, 2022) | |||
20-9371245-G-A | Auriculocondylar syndrome 2 | Uncertain significance (Jan 13, 2018) | ||
20-9371268-C-T | PLCB4-related disorder | Likely benign (Sep 04, 2019) | ||
20-9371285-C-G | Inborn genetic diseases | Uncertain significance (Apr 26, 2023) | ||
20-9372069-C-T | Benign (May 14, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PLCB4 | protein_coding | protein_coding | ENST00000378501 | 36 | 412480 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000304 | 1.00 | 125674 | 0 | 74 | 125748 | 0.000294 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.57 | 382 | 635 | 0.601 | 0.0000331 | 7945 |
Missense in Polyphen | 120 | 265.56 | 0.45188 | 3253 | ||
Synonymous | 0.134 | 224 | 227 | 0.989 | 0.0000128 | 2081 |
Loss of Function | 5.55 | 25 | 77.8 | 0.321 | 0.00000419 | 942 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000415 | 0.000415 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.000220 | 0.000109 |
Finnish | 0.000186 | 0.000185 |
European (Non-Finnish) | 0.000115 | 0.000114 |
Middle Eastern | 0.000220 | 0.000109 |
South Asian | 0.00131 | 0.00131 |
Other | 0.000327 | 0.000326 |
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. This form has a role in retina signal transduction.;
- 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;Chemokine signaling pathway;Splicing factor NOVA regulated synaptic proteins;Wnt Signaling Pathway;Signaling by GPCR;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Signal Transduction;GPCR GroupI metabotropic glutamate receptor;GPCR signaling-G alpha q;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;PLC beta mediated events;G-protein mediated events;Opioid Signalling;G alpha (i) signalling events;G alpha (q) signalling events;GPCR downstream signalling
(Consensus)
Recessive Scores
- pRec
- 0.146
Intolerance Scores
- loftool
- 0.679
- rvis_EVS
- -0.91
- rvis_percentile_EVS
- 10.07
Haploinsufficiency Scores
- pHI
- 0.123
- hipred
- Y
- hipred_score
- 0.682
- ghis
- 0.584
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.109
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | Medium | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Plcb4
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye 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); growth/size/body region phenotype;
Gene ontology
- Biological process
- G protein-coupled receptor signaling pathway;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;inositol phosphate metabolic process;modulation of chemical synaptic transmission
- Cellular component
- nucleus;smooth endoplasmic reticulum;cytosol;postsynaptic density;dendrite;parallel fiber to Purkinje cell synapse;glutamatergic synapse
- Molecular function
- phosphatidylinositol phospholipase C activity;phospholipase C activity;calcium ion binding;protein binding