PLAAT2

protein-coding

phospholipase A and acyltransferase 2, the group of Phospholipase A and acyltransferase family

Gene summary

The protein encoded by this gene has both phospholipase and acyltransferase activities and acts as a tumor suppressor. The encoded protein can hydrolyze dipalmitoylated phosphatidylcholine (PC) to palmitic acid and lyso-PC. In addition, this protein can catalyze the N-acylation of phosphatidylethanolamine and can catalyze the O-acylation of lyso-PC to form PC. [provided by RefSeq, Jul 2016]

Previous symbols:

HRASLS2

MANE transcript

NM_017878.2

Inheritance

—

ClinVar variants

U:16B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.09

Max pathogenic AF

—

Genomic locus

chr11:63,552,770-63,563,379

External References & Databases

Ensembl (ENSG00000133328)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 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 PLAAT2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017878.2. 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						0
missense			16 clinvar	2 clinvar		18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	16	2	0	18

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017878.2	RefSeq	NP_060348.1	4	MANE Select
ENST00000255695.2	Ensembl	ENSP00000255695.1	4	MANE Select
ENST00000947707.1	Ensembl	ENSP00000617766.1	3	Standard
ENST00000947707.2	Ensembl	ENSP00000617766.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of lipids
Metabolism
Glycerophospholipid biosynthesis
Phospholipid metabolism
Acyl chain remodelling of PE

Biological Process

lipid catabolic process
phosphatidylethanolamine acyl-chain remodeling

Molecular Function

transferase activity, transferring acyl groups
hydrolase activity

Cellular Component

cytosol
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000255695
Coding exons: 4
Length: 10614
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.868	76	100	0.756	0.00000609	1027
Missense (PolyPhen)		23	33.192	0.69295		321
Synonymous	0.369	40	43.1	0.929	0.00000274	357
Loss of Function	-0.187	6	5.53	1.09	2.33e-7	75

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Exhibits PLA1/2 activity, catalyzing the calcium- independent hydrolysis of acyl groups in various phosphatidylcholines (PC) and phosphatidylethanolamine (PE). For most substrates, PLA1 activity is much higher than PLA2 activity. Catalyzes N-acylation of PE using both sn-1 and sn-2 palmitoyl groups of PC as acyl donor. Also catalyzes O-acylation converting lyso-PC into PC. {ECO:0000269|PubMed:19615464, ECO:0000269|PubMed:22605381}.;

Recessive Scores

pRec: 0.0472

Intolerance Scores

LoFtool: 0.613
RVIS EVS: 0.08
RVIS percentile EVS: 60.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0115

Gene Damage Prediction

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