PLCL2

phospholipase C like 2, the group of C2 domain containing phospholipases|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:16802650-17090604

Previous symbols: [ "PLCE2" ]

Links

ENSG00000154822 ∙ NCBI:23228 ∙ OMIM:614276 ∙ HGNC:9064 ∙ Uniprot:Q9UPR0 ∙ 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 PLCL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCL2 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
missense					1	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	1	2

Variants in PLCL2

This is a list of pathogenic ClinVar variants found in the PLCL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-17010411-A-G		not specified	Likely benign (Jul 05, 2023)
3-17010708-C-T			Benign (Mar 03, 2015)
3-17011773-C-T		not specified	Likely benign (Apr 19, 2024)
3-17014786-C-T			Benign (Feb 09, 2018)
3-17089910-T-G			Benign (May 23, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCL2	protein_coding	protein_coding	ENST00000418129	5	287928

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000604	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.33	323	541	0.597	0.0000287	6684
Missense in Polyphen		64	200.95	0.31849		2546
Synonymous	-0.112	199	197	1.01	0.0000110	1860
Loss of Function	5.38	0	33.7	0.00	0.00000178	453

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an role in the regulation of Ins(1,4,5)P3 around the endoplasmic reticulum. {ECO:0000250}.
• Pathway: Proton Pump Inhibitor Pathway, Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.575
• hipred: Y
• hipred_score: 0.728
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.811

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plcl2
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: B cell proliferation involved in immune response;B-1a B cell differentiation;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 B cell receptor signaling pathway;negative regulation of cold-induced thermogenesis;positive regulation of receptor binding
• Cellular component: cytoplasm
• Molecular function: phosphatidylinositol phospholipase C activity;GABA receptor binding;inositol 1,4,5 trisphosphate binding