PLCL1

phospholipase C like 1 (inactive), the group of Protein phosphatase 1 regulatory subunits|C2 domain containing phospholipases

Basic information

Region (hg38): 2:197804593-198572581

Previous symbols: [ "PLCE" ]

Links

ENSG00000115896

∙ NCBI:5334 ∙ OMIM:600597 ∙ HGNC:9063 ∙ Uniprot:Q15111 ∙ 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 PLCL1 gene.

not_specified (110 variants)
not_provided (10 variants)
Autism_spectrum_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006226.4. 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			1 clinvar	1 clinvar	2 clinvar	4
missense			113 clinvar	2 clinvar		115
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	114	3	2

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCL1	protein_coding	protein_coding	ENST00000428675	6	767880

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0121	0.988	125713	0	29	125742	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.86	437	561	0.779	0.0000302	7257
Missense in Polyphen		109	207.98	0.52409		2550
Synonymous	-0.698	213	200	1.06	0.0000112	2074
Loss of Function	4.09	11	38.3	0.287	0.00000230	477

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000244	0.000242
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Involved in an inositol phospholipid-based intracellular signaling cascade. Shows no PLC activity to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol. Component in the phospho-dependent endocytosis process of GABA A receptor (By similarity). Regulates the turnover of receptors and thus contributes to the maintenance of GABA-mediated synaptic inhibition. Its aberrant expression could contribute to the genesis and progression of lung carcinoma. Acts as an inhibitor of PPP1C. {ECO:0000250, ECO:0000269|PubMed:17254016}.;
Pathway: GABAergic synapse - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;GPR40 Pathway (Consensus)

Recessive Scores

pRec: 0.115

Intolerance Scores

loftool: 0.683
rvis_EVS: -0.24
rvis_percentile_EVS: 36.28

Haploinsufficiency Scores

pHI: 0.412
hipred: Y
hipred_score: 0.614
ghis: 0.485

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.418

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Plcl1
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; 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); 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; 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: lipid metabolic process;gamma-aminobutyric acid signaling pathway;regulation of synaptic transmission, GABAergic;inositol trisphosphate biosynthetic process;regulation of peptidyl-serine phosphorylation;intracellular signal transduction;negative regulation of cold-induced thermogenesis;positive regulation of receptor binding
Cellular component: cytoplasm;plasma membrane
Molecular function: phosphatidylinositol phospholipase C activity;phospholipase C activity;inositol 1,4,5 trisphosphate binding