PLCL1

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

Basic information

Region (hg38): 2:197804592-198572581

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.

• Inborn genetic diseases (39 variants)
• not provided (9 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.

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			1	1	2	4
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	41	2	2

Variants in PLCL1

This is a list of pathogenic ClinVar variants found in the PLCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-197805106-G-C		not specified	Uncertain significance (Apr 28, 2022)
2-197805143-A-C		not specified	Uncertain significance (Jun 11, 2021)
2-197805148-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-197805167-C-T		not specified	Uncertain significance (Mar 24, 2023)
2-197805170-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-197805200-T-A		not specified	Uncertain significance (Nov 22, 2022)
2-197805206-C-T		not specified	Uncertain significance (Dec 27, 2022)
2-197805275-C-T		not specified	Uncertain significance (Feb 27, 2023)
2-198083919-T-A		not specified	Uncertain significance (Jun 16, 2023)
2-198084019-C-G		not specified	Uncertain significance (Jan 10, 2022)
2-198084144-T-A		not specified	Uncertain significance (Jan 26, 2022)
2-198084238-T-C		not specified	Uncertain significance (Nov 03, 2023)
2-198084250-A-G		not specified	Uncertain significance (Oct 04, 2022)
2-198084292-A-T		not specified	Uncertain significance (Sep 12, 2023)
2-198084322-A-G		not specified	Uncertain significance (Aug 05, 2023)
2-198084337-A-G		not specified	Uncertain significance (Nov 07, 2022)
2-198084350-C-T			Likely benign (Apr 01, 2024)
2-198084407-G-A		not specified	Uncertain significance (Dec 20, 2021)
2-198084526-C-A		not specified	Uncertain significance (Jun 12, 2023)
2-198084554-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-198084617-G-A		not specified	Uncertain significance (Jun 09, 2022)
2-198084653-A-G		not specified	Uncertain significance (Feb 17, 2024)
2-198084920-T-A			Uncertain significance (Sep 01, 2023)
2-198084922-C-A			Uncertain significance (Sep 01, 2023)
2-198084922-C-G		not specified	Uncertain significance (Mar 06, 2023)

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