PLA2G12A

phospholipase A2 group XIIA, the group of Phospholipases

Basic information

Region (hg38): 4:109709988-109730070

Previous symbols: [ "PLA2G12" ]

Links

ENSG00000123739 ∙ NCBI:81579 ∙ OMIM:611652 ∙ HGNC:18554 ∙ Uniprot:Q9BZM1 ∙ 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 PLA2G12A gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G12A 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in PLA2G12A

This is a list of pathogenic ClinVar variants found in the PLA2G12A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-109714457-T-C		not specified	Uncertain significance (Jun 13, 2023)
4-109717562-G-A		not specified	Uncertain significance (Jul 30, 2023)
4-109717607-C-A		not specified	Uncertain significance (Jun 06, 2023)
4-109717648-A-C		not specified	Uncertain significance (Aug 02, 2022)
4-109717684-C-G		not specified	Uncertain significance (Dec 21, 2023)
4-109717707-T-C		not specified	Uncertain significance (Aug 02, 2023)
4-109717709-T-C		not specified	Uncertain significance (Jun 07, 2023)
4-109718729-T-C		not specified	Uncertain significance (Mar 20, 2023)
4-109718742-G-A		not specified	Uncertain significance (Jan 26, 2023)
4-109729632-C-T		not specified	Uncertain significance (May 31, 2023)
4-109729648-G-C		not specified	Uncertain significance (Feb 13, 2024)
4-109729650-C-T		not specified	Uncertain significance (Apr 07, 2022)
4-109729793-C-A		not specified	Uncertain significance (Jan 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G12A	protein_coding	protein_coding	ENST00000243501	4	20089

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000379	0.639	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.199	112	106	1.05	0.00000508	1226
Missense in Polyphen		43	46.851	0.9178		561
Synonymous	0.782	36	42.5	0.847	0.00000215	367
Loss of Function	0.694	6	8.14	0.737	4.28e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000391
Ashkenazi Jewish	0.00	0.00
East Asian	0.00266	0.00267
Finnish	0.00	0.00
European (Non-Finnish)	0.0000442	0.0000439
Middle Eastern	0.00266	0.00267
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PA2 catalyzes the calcium-dependent hydrolysis of the 2- acyl groups in 3-sn-phosphoglycerides. Does not exhibit detectable activity toward sn-2-arachidonoyl- or linoleoyl- phosphatidylcholine or -phosphatidylethanolamine. {ECO:0000269|PubMed:12522102}.
• 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;Acyl chain remodelling of PI;Acyl chain remodelling of PG;Metabolism of lipids;Metabolism;phospholipases;Acyl chain remodelling of PC;Linoleate metabolism;Glycerophospholipid metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE;Synthesis of PA;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.390
• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.350
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.229

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g12a

Gene ontology

• Biological process: phosphatidic acid biosynthetic process;biological_process;lipid catabolic process;phosphatidylglycerol acyl-chain remodeling;phosphatidylinositol acyl-chain remodeling;phosphatidylserine acyl-chain remodeling;phosphatidylcholine acyl-chain remodeling;phosphatidylethanolamine acyl-chain remodeling;arachidonic acid secretion
• Cellular component: extracellular region;cytoplasm
• Molecular function: phospholipase A2 activity;calcium ion binding;calcium-dependent phospholipase A2 activity;phospholipase A2 activity (consuming 1,2-dipalmitoylphosphatidylcholine);phospholipase A2 activity consuming 1,2-dioleoylphosphatidylethanolamine)