PLA1A

phospholipase A1 member A, the group of Phospholipases

Basic information

Region (hg38): 3:119597875-119629811

Links

ENSG00000144837 ∙ NCBI:51365 ∙ OMIM:607460 ∙ HGNC:17661 ∙ Uniprot:Q53H76 ∙ 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 PLA1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLA1A 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					3	3
missense			19	1	1	21
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	1	4

Variants in PLA1A

This is a list of pathogenic ClinVar variants found in the PLA1A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-119606791-C-A		not specified	Uncertain significance (Oct 12, 2021)
3-119606863-C-T		not specified	Uncertain significance (Aug 13, 2021)
3-119606941-A-G		not specified	Uncertain significance (Jan 23, 2024)
3-119608801-A-G		not specified	Uncertain significance (Sep 02, 2024)
3-119608829-C-T		not specified	Uncertain significance (Mar 12, 2024)
3-119608865-G-A		not specified	Uncertain significance (Dec 06, 2022)
3-119608937-A-G		not specified	Likely benign (Dec 20, 2023)
3-119609469-T-A		not specified	Uncertain significance (Mar 25, 2024)
3-119613040-T-C		not specified	Uncertain significance (May 10, 2024)
3-119613065-G-A		not specified	Uncertain significance (Jan 09, 2024)
3-119616021-T-G		not specified	Uncertain significance (Jun 29, 2023)
3-119616032-G-A		not specified	Uncertain significance (Aug 13, 2021)
3-119616047-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-119618049-G-A		not specified	Uncertain significance (Mar 21, 2022)
3-119618071-C-G		not specified	Uncertain significance (Jan 26, 2023)
3-119618071-C-T			Benign (Mar 29, 2018)
3-119618133-C-A		not specified	Uncertain significance (Dec 03, 2024)
3-119619597-G-A			Benign (Mar 29, 2018)
3-119619622-C-A		not specified	Uncertain significance (Sep 22, 2023)
3-119625183-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
3-119628713-A-G			Benign (Mar 29, 2018)
3-119628721-G-A		not specified	Uncertain significance (Apr 09, 2024)
3-119628778-A-T		not specified	Uncertain significance (Oct 28, 2024)
3-119628796-G-A		not specified	Uncertain significance (Dec 17, 2023)
3-119628844-C-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLA1A	protein_coding	protein_coding	ENST00000273371	11	31970

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.37e-11	0.190	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.286	244	257	0.950	0.0000139	2970
Missense in Polyphen		87	88.237	0.98598		1036
Synonymous	-0.234	100	97.1	1.03	0.00000548	887
Loss of Function	0.714	18	21.6	0.834	0.00000100	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000868	0.000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000264	0.000264
Middle Eastern	0.000163	0.000163
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes the ester bond at the sn-1 position of glycerophospholipids and produces 2-acyl lysophospholipids. Hydrolyzes phosphatidylserine (PS) in the form of liposomes and 1- acyl-2 lysophosphatidylserine (lyso-PS), but not triolein, phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidic acid (PA) or phosphatidylinositol (PI). Isoform 2 hydrolyzes lyso-PS but not PS. Hydrolysis of lyso-PS in peritoneal mast cells activated by receptors for IgE leads to stimulate histamine production. {ECO:0000269|PubMed:10196188}.
• Pathway: Ras signaling pathway - Homo sapiens (human);Ras Signaling;Metabolism of lipids;Metabolism;Acyl chain remodelling of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

• pRec: 0.157

Intolerance Scores

• loftool: 0.212
• rvis_EVS: 0.89
• rvis_percentile_EVS: 89.24

Haploinsufficiency Scores

• pHI: 0.0835
• hipred: N
• hipred_score: 0.199
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pla1a

Gene ontology

• Biological process: lipid metabolic process;phosphatidylserine metabolic process;lipid catabolic process;phosphatidylserine acyl-chain remodeling
• Cellular component: acrosomal membrane;extracellular region
• Molecular function: phospholipase A1 activity;phosphatidylserine 1-acylhydrolase activity