PLCH2

phospholipase C eta 2, the group of EF-hand domain containing|Phospholipases

Basic information

Region (hg38): 1:2425980-2505532

Previous symbols: [ "PLCL4" ]

Links

ENSG00000149527 ∙ NCBI:9651 ∙ OMIM:612836 ∙ HGNC:29037 ∙ Uniprot:O75038 ∙ 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 PLCH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCH2 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				9	8	17
missense			125	14	3	142
nonsense			1			1
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding				1	3	4
Total	0	0	126	24	15

Variants in PLCH2

This is a list of pathogenic ClinVar variants found in the PLCH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-2476595-G-T		not specified	Uncertain significance (Sep 14, 2022)
1-2476603-G-A		See cases	Uncertain significance (Sep 13, 2019)
1-2476606-C-T			Benign (Jul 31, 2018)
1-2476610-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-2476619-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-2476620-G-A		not specified	Uncertain significance (Jul 16, 2024)
1-2476632-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-2476647-C-T		not specified	Uncertain significance (Sep 14, 2023)
1-2476671-G-C			Benign (Jan 12, 2018)
1-2476673-A-T		not specified	Uncertain significance (Jul 16, 2024)
1-2476706-C-G		not specified	Uncertain significance (Jul 20, 2021)
1-2478526-C-T		not specified	Uncertain significance (Aug 22, 2023)
1-2478527-G-A		not specified	Uncertain significance (Sep 12, 2023)
1-2478571-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-2479739-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-2479770-G-A		not specified	Uncertain significance (Nov 24, 2024)
1-2479811-G-A		not specified	Uncertain significance (Sep 01, 2021)
1-2479840-C-T			Benign (Dec 31, 2019)
1-2479841-G-A		not specified	Uncertain significance (Mar 25, 2024)
1-2479850-C-T		not specified	Uncertain significance (Nov 07, 2024)
1-2479853-G-A		not specified	Uncertain significance (Aug 01, 2024)
1-2479855-G-T		not specified	Uncertain significance (Jul 08, 2022)
1-2479857-C-T		not specified	Uncertain significance (Jul 27, 2024)
1-2479913-C-T		not specified	Uncertain significance (Sep 20, 2024)
1-2479914-G-A		not specified	Uncertain significance (Oct 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCH2	protein_coding	protein_coding	ENST00000449969	22	79551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-18	0.487	124841	0	64	124905	0.000256

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	615	707	0.869	0.0000471	7339
Missense in Polyphen		227	303.28	0.74848		3100
Synonymous	-1.50	331	298	1.11	0.0000218	2205
Loss of Function	1.80	35	48.6	0.721	0.00000236	559

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000413	0.000408
Ashkenazi Jewish	0.000205	0.000199
East Asian	0.00101	0.00100
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000266	0.000256
Middle Eastern	0.00101	0.00100
South Asian	0.000165	0.000163
Other	0.000169	0.000165

dbNSFP

Source: dbNSFP

• 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 phospholipase activity is very sensitive to calcium. May be important for formation and maintenance of the neuronal network in the postnatal brain (By similarity). {ECO:0000250}.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;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 (Consensus)

Recessive Scores

• pRec: 0.101

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.540
• ghis: 0.601

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.394

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Plch2
• Phenotype: normal phenotype

Gene ontology

• Biological process: biological_process;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;inositol phosphate metabolic process;phosphatidylinositol metabolic process;phosphatidylinositol-mediated signaling;release of sequestered calcium ion into cytosol
• Cellular component: cellular_component;cytoplasm;plasma membrane
• Molecular function: molecular_function;phosphatidylinositol phospholipase C activity;calcium ion binding