PLCB4

gene
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Summary

PLCB4 (phospholipase C beta 4, HGNC:9059) is a protein-coding gene on chromosome 20p12.3-p12.2, encoding 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4 (Q15147). Activated phosphatidylinositol-specific phospholipase C enzymes catalyze the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) involved in G-protein coupled receptor signaling pathways.

The protein encoded by this gene catalyzes the formation of inositol 1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. This reaction uses calcium as a cofactor and plays an important role in the intracellular transduction of many extracellular signals in the retina. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 5332 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): auriculocondylar syndrome 2 (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 7
  • Clinical variants (ClinVar): 387 total — 16 pathogenic, 11 likely-pathogenic
  • Phenotypes (HPO): 66
  • MANE Select transcript: NM_001377142

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9059
Approved symbolPLCB4
Namephospholipase C beta 4
Location20p12.3-p12.2
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000101333
Ensembl biotypeprotein_coding
OMIM600810
Entrez5332

Gene structure

Transcript identifiers

Ensembl transcripts: 71 — 49 protein_coding, 9 retained_intron, 8 nonsense_mediated_decay, 5 protein_coding_CDS_not_defined

ENST00000278655, ENST00000378473, ENST00000378493, ENST00000378501, ENST00000407043, ENST00000414679, ENST00000416836, ENST00000437503, ENST00000441846, ENST00000464199, ENST00000473151, ENST00000482123, ENST00000492632, ENST00000684997, ENST00000685110, ENST00000685148, ENST00000685298, ENST00000685310, ENST00000685446, ENST00000685482, ENST00000685568, ENST00000685823, ENST00000685859, ENST00000686117, ENST00000686163, ENST00000686253, ENST00000686313, ENST00000686532, ENST00000686584, ENST00000686789, ENST00000686871, ENST00000686893, ENST00000686976, ENST00000687147, ENST00000687299, ENST00000687446, ENST00000687765, ENST00000688049, ENST00000688325, ENST00000688465, ENST00000688656, ENST00000688837, ENST00000689010, ENST00000689392, ENST00000689588, ENST00000689910, ENST00000689976, ENST00000690729, ENST00000690960, ENST00000691007, ENST00000691048, ENST00000691112, ENST00000692085, ENST00000692395, ENST00000693005, ENST00000693090, ENST00000693160, ENST00000693492, ENST00000693502, ENST00000693544, ENST00000693752, ENST00000920652, ENST00000920653, ENST00000920654, ENST00000946817, ENST00000946818, ENST00000946819, ENST00000946820, ENST00000946821, ENST00000946822, ENST00000946823

RefSeq mRNA: 8 — MANE Select: NM_001377142 NM_000933, NM_001172646, NM_001377134, NM_001377135, NM_001377136, NM_001377142, NM_001377143, NM_182797

CCDS: CCDS13104, CCDS13105, CCDS54447, CCDS93005

Canonical transcript exons

ENST00000378473 — 40 exons

ExonStartEnd
ENSE0000135778992173909217452
ENSE0000168290990690879069206
ENSE0000174178490962879096342
ENSE0000346160894533479453462
ENSE0000346332393935889393678
ENSE0000346876394110379411088
ENSE0000346897194079179408058
ENSE0000348124793380089338067
ENSE0000348705894732799473365
ENSE0000348896794441789444243
ENSE0000349421894574149457489
ENSE0000349755893078009307898
ENSE0000350383294237489423952
ENSE0000350707794355609435648
ENSE0000350793394212979421461
ENSE0000352264493730479373104
ENSE0000352338093654619365514
ENSE0000352569994767179476753
ENSE0000352626593712149371295
ENSE0000355344293371269337206
ENSE0000356168793905319390615
ENSE0000356554293955239395618
ENSE0000356865193800549380162
ENSE0000358094394685719468672
ENSE0000358294894090579409181
ENSE0000358837593723039372403
ENSE0000359895793388949339037
ENSE0000360965094053139405348
ENSE0000362130994370029437152
ENSE0000363030194596359459810
ENSE0000363162094014909401590
ENSE0000363979794439819444030
ENSE0000364055294727909472847
ENSE0000364219994086339408717
ENSE0000364975893874639387556
ENSE0000365478393628969362975
ENSE0000365528093898799389958
ENSE0000365599593842019384411
ENSE0000367008594198079419909
ENSE0000390629594789219480808

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 97.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.7461 / max 1049.4137, expressed in 1128 samples.

FANTOM5 promoters (20 alternative TSS)

Promoter IDTPM avgSamples expressed
1834425.2154996
1834444.0258434
1834432.8306407
1834451.7690311
1834471.3677398
1834391.3170582
1834410.8541389
1834460.3953184
1834400.3345218
1834750.2825111

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183197.37gold quality
lateral nuclear group of thalamusUBERON:000273696.18gold quality
sural nerveUBERON:001548895.30gold quality
bronchial epithelial cellCL:000232892.78gold quality
cerebellar cortexUBERON:000212992.10gold quality
cerebellar hemisphereUBERON:000224592.04gold quality
cerebellumUBERON:000203791.83gold quality
mucosa of sigmoid colonUBERON:000499391.78gold quality
mucosa of paranasal sinusUBERON:000503091.61gold quality
right hemisphere of cerebellumUBERON:001489091.10gold quality
epithelium of bronchusUBERON:000203190.80gold quality
colonic mucosaUBERON:000031790.79gold quality
bronchusUBERON:000218590.38gold quality
blood vessel layerUBERON:000479790.14gold quality
cerebellar vermisUBERON:000472089.65gold quality
colonic epitheliumUBERON:000039789.07gold quality
pigmented layer of retinaUBERON:000178288.68gold quality
retinaUBERON:000096688.65gold quality
ponsUBERON:000098888.41gold quality
cardiac muscle of right atriumUBERON:000337988.06gold quality
corpus epididymisUBERON:000435987.52gold quality
rectumUBERON:000105287.32gold quality
urethraUBERON:000005787.10gold quality
right uterine tubeUBERON:000130287.01gold quality
substantia nigra pars compactaUBERON:000196586.73gold quality
caput epididymisUBERON:000435886.60gold quality
choroid plexus epitheliumUBERON:000391186.57gold quality
nasal cavity mucosaUBERON:000182686.51gold quality
buccal mucosa cellCL:000233686.33gold quality
mucosa of stomachUBERON:000119985.91gold quality

Single-cell (SCXA)

Detected in 12 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-MTAB-7316yes702.22
E-MTAB-8410yes358.79
E-MTAB-10287yes66.73
E-MTAB-6701yes30.75
E-GEOD-137537yes16.30
E-ANND-3yes16.14
E-HCAD-25yes11.84
E-GEOD-81547yes11.74
E-ENAD-27yes10.26
E-HCAD-35yes9.72
E-GEOD-83139yes8.76
E-MTAB-10290no209.96

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF, PAX6, RORA

miRNA regulators (miRDB)

118 targeting PLCB4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-3924100.0072.092394
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-450099.9972.722367
HSA-MIR-548AW99.9972.573559
HSA-MIR-371A-3P99.9966.7791
HSA-MIR-428299.9975.366408
HSA-MIR-477599.9875.006394
HSA-MIR-548P99.9872.253784
HSA-MIR-4789-5P99.9870.762721
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-50799.9770.111915
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-548AN99.9770.912817
HSA-MIR-590-3P99.9674.346478
HSA-MIR-55799.9670.011640
HSA-MIR-1468-3P99.9672.743797
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-96-5P99.9572.802140
HSA-MIR-651-3P99.9473.485177

Literature-anchored findings (GeneRIF, showing 19)

  • Presence of PLCbeta(4) in the heart and in HL-1 cardiomyocytes showing a different species-dependent pattern of expression of the PLCbeta((1-4)) transcripts. (PMID:19856080)
  • The significant contribution of PSMD3-CSF3 and PLCB4 loci to the regulation of neutrophil count, is demonstrated. (PMID:20172861)
  • The phenotypic variability of auriculocondylar syndrome suggests that mutations in this pathway, especially those affecting core signaling molecules such as PLCB4 and GNAI3, should be considered as potential candidates for other ear and jaw malformations. (PMID:22560091)
  • PLCbeta4 is enriched at the plasma membrane. (PMID:23006664)
  • Auriculocondylar syndrome is caused by PLCB4 mutations inherited not only in an autosomal dominant manner (catalytic domain missense mutations) but also inherited as autosomal recessive (complete loss of function). (PMID:23913798)
  • This study demonistrated by Gene expression profile that PLCB4 upregulaion in fibroblasts of Huntington’s disease patients. (PMID:24296361)
  • Phospholipase C-beta1 and beta4 contribute to non-genetic cell-to-cell variability in histamine-induced calcium signals in HeLa cells. (PMID:24475116)
  • Polymorphism of the PLCB4/B1 genes might be involved in the coronary artery aneurysm pathogenesis of Kawasaki disease. (PMID:26434682)
  • Dysregulation of primary PLC signaling is linked to several brain disorders including epilepsy, schizophrenia, bipolar disorder, Huntington’s disease, depression and Alzheimer’s disease. (Review) (PMID:26639088)
  • recurrent mutation in PLCB4 is associated with uveal melanoma. (PMID:26683228)
  • Our observations of this case further delineate the phenotype of ACS associated with autosomal recessive PLCB4 loss-of-function mutations, underscoring gastrointestinal dysfunction and severe sleep-related breathing abnormalities as additional features when compared to patients with heterozygous mutations with a presumed dominant negative effect. (PMID:27007857)
  • PLCB4 copy gain and PLCB4 overexpression is associated with gastrointestinal stromal tumors. (PMID:28212550)
  • Novel pathogenic variants in PLCB4 have been found in two of three index patients with typical Auriculocondylar syndrome. (PMID:28328130)
  • Mutations of GNAQ, GNA11, SF3B1, EIF1AX, PLCB4 and CYSLTR in Uveal Melanoma in Chinese Patients. (PMID:31614358)
  • A familial PLCB4 mutation causing auriculocondylar syndrome 2 with variable severity. (PMID:32201334)
  • The Polymorphism at PLCB4 Promoter (rs6086746) Changes the Binding Affinity of RUNX2 and Affects Osteoporosis Susceptibility: An Analysis of Bioinformatics-Based Case-Control Study and Functional Validation. (PMID:34899595)
  • Uveal melanoma-associated mutations in PLCbeta4 are constitutively activating and promote melanocyte proliferation and tumorigenesis. (PMID:34905385)
  • Auriculocondylar syndrome 2 results from the dominant-negative action of PLCB4 variants. (PMID:35284927)
  • Interaction between MARK3 (rs11623869), PLCB4 (rs6086746) and GEMIN2 (rs2277458) variants with bone mineral density and serum 25-hidroxivitamin D levels in Mexican Mestizo women. (PMID:38715801)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioPLCB4ENSDARG00000100786
mus_musculusPlcb4ENSMUSG00000039943
rattus_norvegicusPlcb4ENSRNOG00000033119
drosophila_melanogasternorpAFBGN0262738
caenorhabditis_elegansWBGENE00001177

Paralogs (14): PLCH1 (ENSG00000114805), PLCD4 (ENSG00000115556), PLCL1 (ENSG00000115896), PLCG1 (ENSG00000124181), PLCB2 (ENSG00000137841), PLCE1 (ENSG00000138193), PLCZ1 (ENSG00000139151), PLCH2 (ENSG00000149527), PLCB3 (ENSG00000149782), PLCL2 (ENSG00000154822), PLCD3 (ENSG00000161714), PLCB1 (ENSG00000182621), PLCD1 (ENSG00000187091), PLCG2 (ENSG00000197943)

Protein

Protein identifiers

1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4Q15147 (reviewed: Q15147)

Alternative names: Phosphoinositide phospholipase C-beta-4, Phospholipase C-beta-4

All UniProt accessions (28): Q15147, A0A7P0MRI8, A0A8I5KPD4, A0A8I5KPQ9, A0A8I5KQ87, A0A8I5KQF5, A0A8I5KQI1, A0A8I5KQZ0, A0A8I5KR92, A0A8I5KRA0, A0A8I5KRK2, A0A8I5KRP3, A0A8I5KS50, A0A8I5KVM8, A0A8I5KW09, A0A8I5KWR8, A0A8I5KX58, A0A8I5KX82, A0A8I5KXD7, A0A8I5KXT9, A0A8I5KXW3, A0A8I5KYY7, A0A8I5QJ53, A0A8I5QJE7, A0A8I5QL35, A0A8J8Z831, B1AJW1, B1AJW3

UniProt curated annotations — full annotation on UniProt →

Function. Activated phosphatidylinositol-specific phospholipase C enzymes catalyze the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) involved in G-protein coupled receptor signaling pathways. PLCB4 is a direct effector of the endothelin receptor signaling pathway that plays an essential role in lower jaw and middle ear structures development.

Subcellular location. Cell membrane.

Tissue specificity. Preferentially expressed in the retina.

Disease relevance. Auriculocondylar syndrome 2A (ARCND2A) [MIM:614669] An autosomal dominant form of auriculocondylar syndrome, a craniofacial malformation syndrome characterized by variable mandibular anomalies, including mild to severe micrognathia, temporomandibular joint ankylosis, cleft palate, and a characteristic ear malformation that consists of separation of the lobule from the external ear, giving the appearance of a question mark (question-mark ear). Other frequently described features include prominent cheeks, cupped and posteriorly rotated ears, preauricular tags, and microstomia. Glossoptosis, masticatory abnormalities, orthodontic problems, and malocclusion occur in a majority of affected subjects. The disease is caused by variants affecting the gene represented in this entry. Auriculocondylar syndrome 2B (ARCND2B) [MIM:620458] An autosomal recessive form of auriculocondylar syndrome, a craniofacial malformation syndrome characterized by variable mandibular anomalies, including mild to severe micrognathia, temporomandibular joint ankylosis, cleft palate, and a characteristic ear malformation that consists of separation of the lobule from the external ear, giving the appearance of a question mark (question-mark ear). Other frequently described features include prominent cheeks, cupped and posteriorly rotated ears, preauricular tags, and microstomia. Glossoptosis, masticatory abnormalities, orthodontic problems, and malocclusion occur in a majority of affected subjects. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (4)

UniProt IDNamesCanonical?
Q15147-12yes
Q15147-21
Q15147-43
Q15147-54

RefSeq proteins (8): NP_000924, NP_001166117, NP_001364063, NP_001364064, NP_001364065, NP_001364071, NP_001364072, NP_877949 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000008C2_domDomain
IPR000909PLipase_C_PInositol-sp_X_domDomain
IPR001192PI-PLC_famFamily
IPR001711PLipase_C_Pinositol-sp_YDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR014815PLC-beta_CDomain
IPR016280PLC-betaFamily
IPR017946PLC-like_Pdiesterase_TIM-brlHomologous_superfamily
IPR035892C2_domain_sfHomologous_superfamily
IPR037862PLC-beta_PHDomain
IPR042531PLC-beta_C_sfHomologous_superfamily
IPR053945PLCB1-4-like_EFhDomain

Pfam: PF00168, PF00387, PF00388, PF08703, PF17787, PF22631

Enzyme classification (BRENDA):

  • EC 3.1.4.11 — phosphoinositide phospholipase C (BRENDA: 69 organisms, 175 substrates, 159 inhibitors, 27 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
1-PHOSPHATIDYL-1D-MYO-INOSITOL 4,5-BISPHOSPHATE0.006–0.458
PHOSPHATIDYLINOSITOL0.012–1007
1-PHOSPHATIDYL-1D-MYO-INOSITOL0.058–18.76
PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE0.031–0.1823
PHOSPHATIDYLINOSITOL 4-PHOSPHATE0.0311

Catalyzed reactions (Rhea), 2 shown:

  • a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol-4,5-bisphosphate) + H2O = 1D-myo-inositol 1,4,5-trisphosphate + a 1,2-diacyl-sn-glycerol + H(+) (RHEA:33179)
  • a 1,2-diacyl-sn-glycero-3-phospho-(1D-myo-inositol) + H2O = 1D-myo-inositol 1-phosphate + a 1,2-diacyl-sn-glycerol + H(+) (RHEA:43484)

UniProt features (40 total): sequence variant 15, sequence conflict 5, compositionally biased region 4, splice variant 4, domain 3, region of interest 3, active site 2, modified residue 2, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q15147-F186.030.65

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (2): 328; 375

Post-translational modifications (2): 2, 886

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-112043PLC beta mediated events
R-HSA-1855204Synthesis of IP3 and IP4 in the cytosol
R-HSA-416476G alpha (q) signalling events

MSigDB gene sets: 407 (showing top): GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, BROWNE_HCMV_INFECTION_6HR_DN, GOBP_PHOSPHATIDYLINOSITOL_METABOLIC_PROCESS, DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN, SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GGGCATT_MIR365, DAWSON_METHYLATED_IN_LYMPHOMA_TCL1, GOBP_MAINTENANCE_OF_LOCATION, ROZANOV_MMP14_TARGETS_UP, KEGG_HUNTINGTONS_DISEASE, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS

GO Biological Process (10): G protein-coupled receptor signaling pathway (GO:0007186), lipid catabolic process (GO:0016042), phosphatidylinositol metabolic process (GO:0046488), phosphatidylinositol-mediated signaling (GO:0048015), release of sequestered calcium ion into cytosol (GO:0051209), phospholipase C-activating endothelin receptor signaling pathway (GO:0160135), lipid metabolic process (GO:0006629), signal transduction (GO:0007165), intracellular signal transduction (GO:0035556), modulation of chemical synaptic transmission (GO:0050804)

GO Molecular Function (8): phosphatidylinositol-4,5-bisphosphate phospholipase C activity (GO:0004435), C-type glycerophospholipase activity (GO:0004629), calcium ion binding (GO:0005509), phosphatidylinositol phospholipase C activity (GO:0120548), protein binding (GO:0005515), phosphoric diester hydrolase activity (GO:0008081), hydrolase activity (GO:0016787), metal ion binding (GO:0046872)

GO Cellular Component (11): cytosol (GO:0005829), plasma membrane (GO:0005886), nucleus (GO:0005634), smooth endoplasmic reticulum (GO:0005790), endomembrane system (GO:0012505), postsynaptic density (GO:0014069), membrane (GO:0016020), dendrite (GO:0030425), parallel fiber to Purkinje cell synapse (GO:0098688), postsynapse (GO:0098794), glutamatergic synapse (GO:0098978)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
G-protein mediated events1
Inositol phosphate metabolism1
GPCR downstream signalling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
signal transduction2
C-type glycerophospholipase activity2
synapse2
G protein-coupled receptor activity1
lipid metabolic process1
catabolic process1
phosphorus metabolic process1
intracellular signal transduction1
intercellular transport1
calcium ion transmembrane import into cytosol1
phospholipase C-activating G protein-coupled receptor signaling pathway1
endothelin receptor signaling pathway1
primary metabolic process1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
intracellular anatomical structure1
chemical synaptic transmission1
regulation of trans-synaptic signaling1
glycerophospholipase activity1
phosphoric diester hydrolase activity1
metal ion binding1
binding1
phosphoric ester hydrolase activity1
catalytic activity1
cation binding1
cytoplasm1
membrane1
cell periphery1
intracellular membrane-bounded organelle1
endoplasmic reticulum1
vacuole1
plasma membrane1
asymmetric synapse1
postsynaptic specialization1
neuron projection1
dendritic tree1

Protein interactions and networks

STRING

1440 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PLCB4GNA11P29992736
PLCB4GNAQP50148736
PLCB4CYSLTR2Q9NS75721
PLCB4EIF1AXP47813671
PLCB4OPN4Q9UHM6540
PLCB4GNAI3P08754514
PLCB4GRM1Q13255511
PLCB4TRPC6Q9Y210492
PLCB4PLCB3Q01970475
PLCB4ITPR1Q14643460
PLCB4ADCY5O95622454
PLCB4GNA14O95837452
PLCB4BAP1Q92560445
PLCB4PRKCGP05129440
PLCB4ZNF37AP17032429

IntAct

116 interactions, top by confidence:

ABTypeScore
PLCB4RELpsi-mi:“MI:0915”(physical association)0.560
RELPLCB4psi-mi:“MI:0915”(physical association)0.560
PLCB4MEOX2psi-mi:“MI:0915”(physical association)0.560
PLCB4PDZD7psi-mi:“MI:0407”(direct interaction)0.440
LNX2PLCB4psi-mi:“MI:0407”(direct interaction)0.440
PLCB4SNTB1psi-mi:“MI:0407”(direct interaction)0.440
PLCB4MAGI3psi-mi:“MI:0407”(direct interaction)0.440
PLCB4ARHGEF11psi-mi:“MI:0407”(direct interaction)0.440
PLCB4ARHGEF12psi-mi:“MI:0407”(direct interaction)0.440
PLCB4MAST1psi-mi:“MI:0407”(direct interaction)0.440
MAGI2PLCB4psi-mi:“MI:0407”(direct interaction)0.440
PLCB4PATJpsi-mi:“MI:0407”(direct interaction)0.440
PLCB4DLG1psi-mi:“MI:0407”(direct interaction)0.440
PLCB4DLG4psi-mi:“MI:0407”(direct interaction)0.440
PLCB4DLG3psi-mi:“MI:0407”(direct interaction)0.440
PLCB4DLG2psi-mi:“MI:0407”(direct interaction)0.440
PLCB4HTRA1psi-mi:“MI:0407”(direct interaction)0.440
PLCB4GORASP2psi-mi:“MI:0407”(direct interaction)0.440
PLCB4NOS1psi-mi:“MI:0407”(direct interaction)0.440
PLCB4SCRIBpsi-mi:“MI:0407”(direct interaction)0.440
PLCB4SNTA1psi-mi:“MI:0407”(direct interaction)0.440
PLCB4PDZRN3psi-mi:“MI:0407”(direct interaction)0.440
PLCB4GORASP1psi-mi:“MI:0407”(direct interaction)0.440
GOPCPLCB4psi-mi:“MI:0407”(direct interaction)0.440
FRMPD2PLCB4psi-mi:“MI:0407”(direct interaction)0.440
PLCB4LNX1psi-mi:“MI:0407”(direct interaction)0.440
TAMALINPLCB4psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (39): REL (Two-hybrid), PLCB4 (Two-hybrid), PLCB4 (Affinity Capture-RNA), PLCB4 (Synthetic Lethality), MEOX2 (Two-hybrid), PLCB4 (Affinity Capture-MS), PLCB4 (Proximity Label-MS), PLCB4 (Proximity Label-MS), PLCB4 (Affinity Capture-MS), PLCB4 (Affinity Capture-MS), PLCB4 (Affinity Capture-MS), PLCB4 (Affinity Capture-MS), PLCB4 (Affinity Capture-MS), PLCB4 (Affinity Capture-MS), PLCB4 (Affinity Capture-MS)

ESM2 similar proteins: A0A075QQ08, A0A1D8EJF9, A0A1U8F5V2, A0A1U8GR65, A0A2J6L8Y7, A0A3Q7FGP1, A0A3Q7I7R4, A0A445AGS0, A0A7U2QYM2, A7KWF8, C6ZJZ3, C7SG33, D3UW26, K0P2S0, M1J8U6, M1JJT8, O23252, O60573, O77210, O81481, O81482, P0DXI0, P0DXI5, P10687, P10894, P29557, P48599, P48600, P48722, P97789, Q03389, Q0GRC4, Q15147, Q28GH3, Q3UTA9, Q4QXS7, Q4VQY1, Q4VQY3, Q5GFD8, Q642Q1

Diamond homologs: A2AP18, A3KGF7, A5D6R3, G5EBH0, G5EFI8, O75038, O89040, P10687, P10688, P10894, P10895, P21671, P25455, P51178, P51432, Q00722, Q01970, Q07722, Q15111, Q15147, Q1RML2, Q2VRL0, Q32NH8, Q3USB7, Q4KWH5, Q4KWH8, Q4R6L3, Q5FX52, Q5RET0, Q62688, Q62711, Q6NMA7, Q7YRU3, Q86YW0, Q8K2J0, Q8K394, Q8K3R3, Q8K4D7, Q8K4S1, Q8L706

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 77 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ras activation upon Ca2+ influx through NMDA receptor664.6×2e-08
Unblocking of NMDA receptors, glutamate binding and activation661.6×2e-08
Negative regulation of NMDA receptor-mediated neuronal transmission661.6×2e-08
Long-term potentiation653.9×3e-08
Assembly and cell surface presentation of NMDA receptors1152.7×8e-15
Dopamine Neurotransmitter Release Cycle546.8×2e-06
Neurexins and neuroligins1244.6×5e-15
Protein-protein interactions at synapses735.1×3e-08

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity1076.5×2e-14
receptor clustering757.5×7e-09
protein localization to synapse550.4×3e-06
regulation of postsynaptic membrane neurotransmitter receptor levels745.6×3e-08
protein-containing complex assembly913.5×2e-06
cell-cell adhesion1013.4×4e-07
chemical synaptic transmission88.1×3e-04
nervous system development84.8×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

387 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic16
Likely pathogenic11
Uncertain significance182
Likely benign36
Benign90

Top pathogenic / likely-pathogenic (27)

Variant IDHGVSClassification
1706453NM_001377142.1(PLCB4):c.2814+1G>CPathogenic
209128NM_001377142.1(PLCB4):c.986A>C (p.Asn329Thr)Pathogenic
2875083NM_001377142.1(PLCB4):c.3031_3032del (p.Glu1011fs)Pathogenic
31637NM_001377142.1(PLCB4):c.1904A>G (p.Tyr635Cys)Pathogenic
31638NM_001377142.1(PLCB4):c.986A>G (p.Asn329Ser)Pathogenic
31639NM_001377142.1(PLCB4):c.1898G>A (p.Arg633His)Pathogenic
31640NM_001377142.1(PLCB4):c.1897C>T (p.Arg633Cys)Pathogenic
31641NM_001377142.1(PLCB4):c.1984A>C (p.Asn662His)Pathogenic
3248283NC_000020.10:g.(?7812350)(10654278_?)delPathogenic
4082118NM_001377142.1(PLCB4):c.1918del (p.Arg640fs)Pathogenic
633597NM_001377142.1(PLCB4):c.1924G>T (p.Asp642Tyr)Pathogenic
64692NM_001377142.1(PLCB4):c.1898G>T (p.Arg633Leu)Pathogenic
64693NM_001377142.1(PLCB4):c.1073A>T (p.Glu358Val)Pathogenic
64694NM_001377142.1(PLCB4):c.1078G>A (p.Asp360Asn)Pathogenic
64695NM_001377142.1(PLCB4):c.1079A>T (p.Asp360Val)Pathogenic
64696NM_001377142.1(PLCB4):c.1648-279_2051+1546delPathogenic
1030923NM_001377142.1(PLCB4):c.1124A>G (p.His375Arg)Likely pathogenic
1067926NM_001377142.1(PLCB4):c.3409-1G>TLikely pathogenic
2432743NM_001377142.1(PLCB4):c.815_821del (p.Ile272fs)Likely pathogenic
3342734NM_001377142.1(PLCB4):c.21del (p.Phe7fs)Likely pathogenic
3382174NM_001377142.1(PLCB4):c.1057G>A (p.Gly353Ser)Likely pathogenic
3767226NM_001377142.1(PLCB4):c.1656dup (p.Thr553fs)Likely pathogenic
3769206NC_000020.10:g.(9319685_9343542)_(9346162_9351860)dupLikely pathogenic
3777145NM_001377142.1(PLCB4):c.1732T>C (p.Ser578Pro)Likely pathogenic
382944NM_001377142.1(PLCB4):c.453G>T (p.Trp151Cys)Likely pathogenic
4294389NM_001377142.1(PLCB4):c.1080C>G (p.Asp360Glu)Likely pathogenic
451364NM_001377142.1(PLCB4):c.1925A>T (p.Asp642Val)Likely pathogenic

SpliceAI

5729 predictions. Top by Δscore:

VariantEffectΔscore
20:9307895:GGAG:Gdonor_gain1.0000
20:9307896:GAGG:Gdonor_gain1.0000
20:9307897:AGGT:Adonor_loss1.0000
20:9307898:GGT:Gdonor_loss1.0000
20:9307899:G:Tdonor_loss1.0000
20:9307900:T:Gdonor_loss1.0000
20:9338063:CAAAG:Cdonor_loss1.0000
20:9338064:AAAGG:Adonor_loss1.0000
20:9338066:AG:Adonor_loss1.0000
20:9338067:GG:Gdonor_loss1.0000
20:9338068:G:Adonor_loss1.0000
20:9338069:T:Gdonor_loss1.0000
20:9338877:T:TAacceptor_gain1.0000
20:9338879:T:TAacceptor_gain1.0000
20:9338882:A:AGacceptor_gain1.0000
20:9338883:C:Gacceptor_gain1.0000
20:9338890:ACAG:Aacceptor_gain1.0000
20:9338891:C:Gacceptor_gain1.0000
20:9338892:A:AGacceptor_gain1.0000
20:9338892:AG:Aacceptor_gain1.0000
20:9338892:AGG:Aacceptor_loss1.0000
20:9338893:G:GTacceptor_gain1.0000
20:9338893:GG:Gacceptor_gain1.0000
20:9338893:GGAT:Gacceptor_gain1.0000
20:9338893:GGATC:Gacceptor_gain1.0000
20:9339026:G:GTdonor_gain1.0000
20:9339033:CTAAG:Cdonor_loss1.0000
20:9339035:AAG:Adonor_loss1.0000
20:9339036:AG:Adonor_loss1.0000
20:9339038:GTA:Gdonor_loss1.0000

AlphaMissense

8070 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:9365508:T:AV166D1.000
20:9371267:T:CL186P1.000
20:9372352:T:CL212P1.000
20:9380061:G:CR251P1.000
20:9384234:T:CL296P1.000
20:9384239:T:CS298P1.000
20:9384324:C:TS326F1.000
20:9384327:C:TS327F1.000
20:9384329:C:GH328D1.000
20:9384329:C:TH328Y1.000
20:9384330:A:GH328R1.000
20:9384330:A:TH328L1.000
20:9384331:T:AH328Q1.000
20:9384331:T:GH328Q1.000
20:9384334:C:AN329K1.000
20:9384334:C:GN329K1.000
20:9384338:T:CY331H1.000
20:9384338:T:GY331D1.000
20:9384342:T:AL332H1.000
20:9384342:T:CL332P1.000
20:9384355:G:CQ336H1.000
20:9384355:G:TQ336H1.000
20:9384357:T:CF337S1.000
20:9384369:C:TS341F1.000
20:9387464:T:CC356R1.000
20:9387466:T:GC356W1.000
20:9387468:T:AV357D1.000
20:9387470:G:AE358K1.000
20:9387471:A:TE358V1.000
20:9387472:A:CE358D1.000

dbSNP variants (sampled 300 via entrez): RS1000004620 (20:9342218 C>G), RS1000025087 (20:9156682 A>G), RS1000033742 (20:9470765 G>A,T), RS1000045426 (20:9258335 C>A), RS1000048714 (20:9429418 A>G), RS1000051425 (20:9478452 C>T), RS1000058443 (20:9432402 A>G), RS1000061228 (20:9334004 G>A), RS1000070565 (20:9113235 A>C), RS1000071617 (20:9468817 A>C,G), RS1000074388 (20:9069546 T>C), RS1000083722 (20:9107126 T>G), RS1000084628 (20:9245613 C>T), RS1000087870 (20:9383016 G>A), RS1000091908 (20:9334273 T>C)

Disease associations

OMIM: gene MIM:600810 | disease phenotypes: MIM:614669, MIM:602483, MIM:613722, MIM:118450, MIM:620458, MIM:143890, MIM:215045, MIM:155720

GenCC curated gene-disease

DiseaseClassificationInheritance
auriculocondylar syndrome 2StrongAutosomal dominant
auriculocondylar syndrome 2BStrongAutosomal recessive
auriculocondylar syndromeSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (2)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
auriculocondylar syndrome 2DefinitiveAD
auriculocondylar syndrome 2DefinitiveAR

Mondo (11): auriculocondylar syndrome 2 (MONDO:0013845), prostate cancer (MONDO:0008315), long QT syndrome (MONDO:0002442), auriculocondylar syndrome 1 (MONDO:0011234), auriculocondylar syndrome (MONDO:0000107), developmental and epileptic encephalopathy, 12 (MONDO:0013389), Alagille syndrome due to a JAG1 point mutation (MONDO:0016862), auriculocondylar syndrome 2B (MONDO:0957544), familial hypercholesterolemia (MONDO:0005439), chondrodysplasia Blomstrand type (MONDO:0008970), uveal melanoma (MONDO:0006486)

Orphanet (6): Auriculocondylar syndrome (Orphanet:137888), Familial prostate cancer (Orphanet:1331), Alagille syndrome due to a JAG1 point mutation (Orphanet:261619), Alagille syndrome (Orphanet:52), Blomstrand lethal chondrodysplasia (Orphanet:50945), Uveal melanoma (Orphanet:39044)

HPO phenotypes

66 total (30 of 66 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000040Long penis
HP:0000160Narrow mouth
HP:0000162Glossoptosis
HP:0000171Microglossia
HP:0000175Cleft palate
HP:0000183Tongue muscle weakness
HP:0000193Bifid uvula
HP:0000256Macrocephaly
HP:0000293Full cheeks
HP:0000311Round face
HP:0000324Facial asymmetry
HP:0000341Narrow forehead
HP:0000347Micrognathia
HP:0000358Posteriorly rotated ears
HP:0000365Hearing impairment
HP:0000369Low-set ears
HP:0000377Abnormal pinna morphology
HP:0000384Preauricular skin tag
HP:0000402Stenosis of the external auditory canal
HP:0000506Telecanthus
HP:0000508Ptosis
HP:0000664Synophrys
HP:0000678Dental crowding
HP:0000689Dental malocclusion
HP:0000729Autistic behavior
HP:0001140Limbal dermoid
HP:0001252Hypotonia
HP:0001263Global developmental delay

GWAS associations

7 associations (top):

StudyTraitp-value
GCST000600_1Neutrophil count3.000000e-10
GCST003518_23Daytime sleep phenotypes6.000000e-07
GCST005023_39Initial pursuit acceleration4.000000e-07
GCST005026_13Initial pursuit acceleration in psychotic disorders9.000000e-08
GCST009391_1517Metabolite levels9.000000e-06
GCST009391_262Metabolite levels8.000000e-06
GCST010574_9Evening vs. morning chronotype (self-assessed)6.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004833neutrophil count
EFO:0007828daytime rest measurement
EFO:0008434initial pursuit acceleration
EFO:0010417triacylglycerol 52:5 measurement
EFO:0010426triacylglycerol 54:8 measurement
EFO:0008328chronotype measurement

MeSH disease descriptors (4)

DescriptorNameTree numbers
D008133Long QT SyndromeC14.280.067.565; C14.280.123.625; C16.131.240.400.715; C23.550.073.547
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750
C538270Auriculo-condylar syndrome (supp.)
C537914Chondrodysplasia, blomstrand type (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — Phosphoinositide-specific phospholipase C

CTD chemical–gene interactions

52 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases methylation, increases expression4
Benzo(a)pyreneaffects methylation, decreases methylation, increases expression3
Tobacco Smoke Pollutionaffects expression, decreases expression3
trichostatin Aaffects expression, increases expression2
perfluorooctane sulfonic aciddecreases expression, affects expression, affects cotreatment2
Nickeldecreases expression2
Particulate Matterdecreases expression2
aristolochic acid Idecreases expression1
FR900359decreases phosphorylation1
ammonium 2,3,3,3-tetrafluoro-2-(heptafluoropropoxy)-propanoateaffects cotreatment, affects expression1
methylmercuric chloridedecreases expression1
methylselenic acidincreases expression1
arseniteaffects binding, decreases reaction1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
perfluorooctanoic acidaffects cotreatment, affects expression1
zinc chromatedecreases expression, increases abundance1
aflatoxin B2increases methylation1
diallyl trisulfideincreases expression1
sphingosine 1-phosphatedecreases reaction, increases expression1
chromium hexavalent iondecreases expression, increases abundance1
2,2’,4,4’,5-brominated diphenyl etherdecreases expression1
abrineincreases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, increases expression1
perfluorobutanesulfonic acidaffects expression, affects cotreatment1
jinfukangaffects cotreatment, decreases expression1
Fingolimod Hydrochloridedecreases reaction, increases expression1
Sunitinibincreases expression1
Vorinostatdecreases expression1
Acetaminophendecreases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E0L7Ubigene HeLa PLCB4 KOCancer cell lineFemale
CVCL_TE24HAP1 PLCB4 (-) 1Cancer cell lineMale
CVCL_TE25HAP1 PLCB4 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer