PLA1A

protein-coding

phospholipase A1 member A, the group of Phospholipases

Gene summary

The protein encoded by this gene is a phospholipase that hydrolyzes fatty acids at the sn-1 position of phosphatidylserine and 1-acyl-2-lysophosphatidylserine. This secreted protein hydrolyzes phosphatidylserine in liposomes. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2011]

MANE transcript

NM_015900.4

Inheritance

—

ClinVar variants

P:1U:59B:7

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr3:119,597,875-119,629,811

External References & Databases

Ensembl (ENSG00000144837)

Transcript & Mutation Effects

hg38 • Region Span ~31.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLA1A variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 55

not providedTotal: 4

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Familial hypercholesterolemiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015900.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		3 clinvar	5
missense	1 clinvar		55 clinvar	3 clinvar	1 clinvar	60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	59	3	4	67

Highest pathogenic variant AF is 6.9250444e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015900.4	RefSeq	NP_056984.1	11	MANE Select
ENST00000273371.9	Ensembl	ENSP00000273371.4	11	MANE Select
NM_001206960.2	RefSeq	NP_001193889.1	11	Standard
NM_001206961.2	RefSeq	NP_001193890.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ras signaling pathway - Homo sapiens (human)
Ras Signaling
Metabolism of lipids
Metabolism
Acyl chain remodelling of PS

Biological Process

lipid metabolic process
phosphatidylserine metabolic process
lipid catabolic process
phosphatidylserine acyl-chain remodeling

Molecular Function

phospholipase A1 activity
phosphatidylserine 1-acylhydrolase activity

Cellular Component

acrosomal membrane
extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273371
Coding exons: 11
Length: 31970
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.286	244	257	0.950	0.0000139	2970
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00049	0.00049	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00026	0.00026	rare
South Asian	0.000065	0.000065	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.157

Intolerance Scores

LoFtool: 0.212
RVIS EVS: 0.89
RVIS percentile EVS: 89.24

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.943

Gene Damage Prediction

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