PLA2G4C

phospholipase A2 group IVC, the group of Phospholipases

Basic information

Region (hg38): 19:48047843-48110817

Links

ENSG00000105499 ∙ NCBI:8605 ∙ OMIM:603602 ∙ HGNC:9037 ∙ Uniprot:Q9UP65 ∙ 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 PLA2G4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G4C 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					2	2
missense			45	2	2	49
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	4

Variants in PLA2G4C

This is a list of pathogenic ClinVar variants found in the PLA2G4C region.

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

Position	Type	Phenotype	Significance	ClinVar
19-48048348-C-T		not specified	Uncertain significance (Sep 14, 2022)
19-48052998-C-T		not specified	Uncertain significance (Sep 12, 2023)
19-48053000-G-T		not specified	Uncertain significance (Aug 02, 2021)
19-48053037-T-C		not specified	Uncertain significance (Oct 27, 2021)
19-48053050-C-A		not specified	Uncertain significance (Dec 03, 2024)
19-48053067-A-C		not specified	Uncertain significance (Mar 31, 2022)
19-48053114-G-A		not specified	Uncertain significance (Feb 14, 2024)
19-48053118-C-T		not specified	Uncertain significance (Apr 08, 2024)
19-48053135-G-T		not specified	Uncertain significance (Dec 06, 2024)
19-48053137-C-A		not specified	Uncertain significance (Jun 09, 2022)
19-48054887-C-A		not specified	Uncertain significance (Oct 05, 2023)
19-48054892-A-G		not specified	Likely benign (Sep 27, 2024)
19-48054912-C-T		not specified	Uncertain significance (Oct 26, 2022)
19-48054953-T-C		not specified	Uncertain significance (May 03, 2023)
19-48054989-C-T		not specified	Uncertain significance (Dec 22, 2023)
19-48055042-C-T		not specified	Uncertain significance (Mar 04, 2024)
19-48062024-C-T			Benign (Apr 04, 2018)
19-48062050-C-T		not specified	Uncertain significance (Oct 07, 2024)
19-48062066-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-48062095-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-48062123-G-A		not specified	Uncertain significance (Sep 08, 2023)
19-48067817-G-A		not specified	Uncertain significance (Mar 01, 2024)
19-48067831-C-G		not specified	Uncertain significance (Sep 06, 2022)
19-48067839-C-T		not specified	Uncertain significance (Jan 16, 2024)
19-48067875-T-C		not specified	Likely benign (Dec 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G4C	protein_coding	protein_coding	ENST00000599111	17	62975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-13	0.553	125612	0	136	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.174	300	309	0.972	0.0000167	3571
Missense in Polyphen		85	84.54	1.0054		1008
Synonymous	-1.00	140	126	1.11	0.00000763	1062
Loss of Function	1.53	25	34.7	0.720	0.00000181	379

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00428	0.00429
Ashkenazi Jewish	0.00	0.00
East Asian	0.000654	0.000653
Finnish	0.000277	0.000277
European (Non-Finnish)	0.000300	0.000299
Middle Eastern	0.000654	0.000653
South Asian	0.000131	0.000131
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has a preference for arachidonic acid at the sn-2 position of phosphatidylcholine as compared with palmitic acid. {ECO:0000269|PubMed:10085124, ECO:0000269|PubMed:9705332}.
• Pathway: Inflammatory mediator regulation of TRP channels - Homo sapiens (human);Platelet activation - Homo sapiens (human);Oxytocin signaling pathway - Homo sapiens (human);Fc epsilon RI signaling pathway - Homo sapiens (human);Ether lipid metabolism - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Long-term depression - Homo sapiens (human);GnRH signaling pathway - Homo sapiens (human);Necroptosis - 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);MAPK signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Ovarian steroidogenesis - Homo sapiens (human);MAPK Signaling Pathway;Ras Signaling;Acyl chain remodelling of PI;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC;Acyl chain remodelling of PE;Hydrolysis of LPE;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0690

Intolerance Scores

• loftool: 0.938
• rvis_EVS: 2.45
• rvis_percentile_EVS: 98.57

Haploinsufficiency Scores

• pHI: 0.0611
• hipred: N
• hipred_score: 0.145
• ghis: 0.385

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.910

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g4c

Gene ontology

• Biological process: phospholipid metabolic process;inflammatory response;parturition;arachidonic acid metabolic process;intracellular signal transduction;phosphatidylinositol acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;glycerophospholipid catabolic process
• Cellular component: nuclear envelope;nucleoplasm;cytoplasm;endoplasmic reticulum membrane;cytosol;cell cortex;membrane
• Molecular function: lysophospholipase activity;phospholipase A2 activity;calcium ion binding;phospholipid binding;calcium-dependent phospholipid binding;phospholipase A1 activity;calcium-dependent phospholipase A2 activity;calcium-independent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)