PLA2G2C

phospholipase A2 group IIC, the group of Phospholipases

Basic information

Region (hg38): 1:20161253-20186518

Previous symbols: [ "UBXN10-AS1" ]

Links

ENSG00000187980 ∙ NCBI:391013 ∙ ∙ HGNC:9032 ∙ Uniprot:Q5R387 ∙ 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 PLA2G2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G2C 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						0
missense			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	9	2	0

Variants in PLA2G2C

This is a list of pathogenic ClinVar variants found in the PLA2G2C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-20164016-C-T		not specified	Uncertain significance (May 31, 2023)
1-20164042-G-C		not specified	Uncertain significance (Jan 03, 2024)
1-20164052-T-G		not specified	Uncertain significance (Jan 15, 2025)
1-20164075-G-C		not specified	Uncertain significance (Mar 01, 2023)
1-20164115-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-20164133-G-A		not specified	Likely benign (Feb 17, 2022)
1-20164146-G-A		not specified	Uncertain significance (Sep 06, 2022)
1-20172856-T-C		not specified	Uncertain significance (Dec 12, 2024)
1-20172883-G-A		not specified	Likely benign (Jun 01, 2023)
1-20172891-G-T		not specified	Uncertain significance (Aug 11, 2022)
1-20175008-T-A		not specified	Uncertain significance (Jun 18, 2021)
1-20175050-A-C		not specified	Uncertain significance (Sep 14, 2023)
1-20175160-G-A		not specified	Uncertain significance (Nov 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G2C	protein_coding	protein_coding	ENST00000429261	4	16172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0357	0.840	80031	5986	38630	124647	0.199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0339	81	80.1	1.01	0.00000409	983
Missense in Polyphen		30	29.974	1.0009		391
Synonymous	0.0946	34	34.7	0.980	0.00000211	264
Loss of Function	1.23	3	6.33	0.474	2.67e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.384	0.381
Ashkenazi Jewish	0.205	0.206
East Asian	0.161	0.162
Finnish	0.198	0.196
European (Non-Finnish)	0.187	0.186
Middle Eastern	0.161	0.162
South Asian	0.369	0.364
Other	0.190	0.189

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inactive phospholipase. {ECO:0000305}.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Fat digestion and absorption - Homo sapiens (human);Vascular smooth muscle contraction - Homo sapiens (human);alpha-Linolenic acid metabolism - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);Pancreatic secretion - Homo sapiens (human);Ras Signaling (Consensus)

Recessive Scores

• pRec: 0.0678

Haploinsufficiency Scores

• pHI: 0.0676
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g2c

Gene ontology

• Biological process: phospholipid metabolic process;lipid catabolic process;arachidonic acid secretion
• Cellular component: extracellular region
• Molecular function: phospholipase A2 activity;calcium ion binding;phospholipid binding;calcium-dependent phospholipase A2 activity