PLAAT2

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

Basic information

Region (hg38): 11:63552770-63563379

Previous symbols: [ "HRASLS2" ]

Links

ENSG00000133328 ∙ NCBI:54979 ∙ OMIM:613866 ∙ HGNC:17824 ∙ Uniprot:Q9NWW9 ∙ 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 PLAAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAAT2 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in PLAAT2

This is a list of pathogenic ClinVar variants found in the PLAAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63552999-T-G		not specified	Likely benign (Oct 04, 2024)
11-63553014-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-63558403-G-A		not specified	Uncertain significance (Dec 03, 2024)
11-63558415-A-G		not specified	Uncertain significance (Mar 25, 2024)
11-63558418-G-A		not specified	Uncertain significance (Jun 22, 2024)
11-63558439-C-T		not specified	Uncertain significance (Aug 28, 2023)
11-63558453-G-T		not specified	Uncertain significance (Dec 09, 2024)
11-63558639-G-A		not specified	Uncertain significance (Dec 11, 2024)
11-63560090-G-A		not specified	Uncertain significance (Dec 04, 2024)
11-63560180-G-A		not specified	Likely benign (Jul 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLAAT2	protein_coding	protein_coding	ENST00000255695	4	10614

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000678	0.304	125744	0	4	125748	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.868	76	100	0.756	0.00000609	1027
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000331	0.0000327
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE (Consensus)

Recessive Scores

• pRec: 0.0472

Intolerance Scores

• loftool: 0.613
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.0102
• hipred: N
• hipred_score: 0.139
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0115

Gene Damage Prediction

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

Gene ontology

• Biological process: lipid catabolic process;phosphatidylethanolamine acyl-chain remodeling
• Cellular component: cytosol;integral component of membrane
• Molecular function: transferase activity, transferring acyl groups;hydrolase activity