PLA2G15

phospholipase A2 group XV, the group of Phospholipases

Basic information

Region (hg38): 16:68245304-68261058

Previous symbols: [ "LYPLA3" ]

Links

ENSG00000103066 ∙ NCBI:23659 ∙ OMIM:609362 ∙ HGNC:17163 ∙ Uniprot:Q8NCC3 ∙ 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 PLA2G15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA2G15 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in PLA2G15

This is a list of pathogenic ClinVar variants found in the PLA2G15 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-68245443-G-T		not specified	Uncertain significance (Jun 28, 2022)
16-68245469-G-A		not specified	Uncertain significance (May 13, 2024)
16-68245518-C-T		not specified	Uncertain significance (Jul 14, 2021)
16-68245529-G-A		not specified	Uncertain significance (Oct 03, 2022)
16-68245541-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-68249385-A-G		not specified	Uncertain significance (Dec 28, 2022)
16-68249396-C-G		not specified	Uncertain significance (Apr 01, 2024)
16-68249427-T-G		not specified	Uncertain significance (May 31, 2023)
16-68254974-C-T		not specified	Uncertain significance (Oct 20, 2023)
16-68254975-G-A		not specified	Uncertain significance (May 09, 2024)
16-68255332-C-G		not specified	Uncertain significance (Dec 18, 2023)
16-68255333-G-A		not specified	Uncertain significance (Mar 28, 2024)
16-68255374-G-A		not specified	Uncertain significance (Jun 07, 2023)
16-68255795-C-T		not specified	Uncertain significance (Mar 29, 2022)
16-68255874-C-T		not specified	Uncertain significance (Jun 05, 2024)
16-68255888-C-A		not specified	Uncertain significance (May 15, 2024)
16-68255891-C-T		not specified	Uncertain significance (Sep 26, 2022)
16-68255903-G-T		not specified	Uncertain significance (May 04, 2023)
16-68259157-C-T		not specified	Uncertain significance (Apr 07, 2022)
16-68259331-G-C		not specified	Uncertain significance (Aug 21, 2023)
16-68259349-C-T		not specified	Uncertain significance (Mar 14, 2023)
16-68259383-T-C		not specified	Uncertain significance (Jul 25, 2023)
16-68259394-G-A		not specified	Uncertain significance (Feb 09, 2023)
16-68259499-G-A		not specified	Uncertain significance (Mar 23, 2022)
16-68259547-C-T		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA2G15	protein_coding	protein_coding	ENST00000219345	6	15755

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.378	0.621	125713	0	20	125733	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.751	226	260	0.869	0.0000161	2642
Missense in Polyphen		105	119.93	0.87549		1285
Synonymous	1.13	95	110	0.863	0.00000666	856
Loss of Function	3.04	4	17.9	0.224	8.47e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has transacylase and calcium-independent phospholipase A2 activity (PubMed:20410020, PubMed:23958596). Catalyzes the formation of 1-O-acyl-N-acetylsphingosine and the concomitant release of a lyso-phospholipid (PubMed:11790796, PubMed:25727495). Has high activity with 1-palmitoyl-2-oleoyl-sn-glycero-3- phosphocholine (POPC) and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), catalyzing the transfer of oleic acid to N-acetyl- sphingosine. Required for normal phospholipid degradation in alveolar and peritoneal macrophages and in spleen (By similarity). May have weak lysophospholipase activity (PubMed:10092508). {ECO:0000250|UniProtKB:Q8VEB4, ECO:0000269|PubMed:10092508, ECO:0000269|PubMed:11790796, ECO:0000269|PubMed:20410020, ECO:0000269|PubMed:23958596, ECO:0000269|PubMed:25727495}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Lysosome - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of lipids;Metabolism;Glycerophospholipid metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Hydrolysis of LPC (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.143
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.56

Haploinsufficiency Scores

• pHI: 0.0932
• hipred: Y
• hipred_score: 0.563
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla2g15
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; renal/urinary system phenotype; immune system phenotype; respiratory system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: phospholipid metabolic process;glycerophospholipid metabolic process;ceramide metabolic process;fatty acid catabolic process;phosphatidylcholine catabolic process;phosphatidylethanolamine catabolic process
• Cellular component: extracellular region;extracellular space;nucleoplasm;lysosome;membrane;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: lysophospholipase activity;phospholipid binding;O-acyltransferase activity;calcium-independent phospholipase A2 activity