PLAAT4

phospholipase A and acyltransferase 4, the group of Phospholipase A and acyltransferase family

Basic information

Region (hg38): 11:63536808-63548808

Previous symbols: [ "RARRES3" ]

Links

ENSG00000133321 ∙ NCBI:5920 ∙ OMIM:605092 ∙ HGNC:9869 ∙ Uniprot:Q9UL19 ∙ 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 PLAAT4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAAT4 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			18	2		20
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in PLAAT4

This is a list of pathogenic ClinVar variants found in the PLAAT4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63539559-G-A		not specified	Uncertain significance (Feb 28, 2023)
11-63539561-C-G		not specified	Uncertain significance (Feb 07, 2025)
11-63539586-A-T		not specified	Uncertain significance (Oct 12, 2024)
11-63544632-G-A		not specified	Uncertain significance (Oct 30, 2023)
11-63544665-A-G		not specified	Likely benign (Oct 04, 2024)
11-63544692-C-T		not specified	Uncertain significance (Feb 15, 2023)
11-63544693-G-A		not specified	Uncertain significance (Jun 06, 2023)
11-63544726-G-A		not specified	Uncertain significance (Jan 19, 2025)
11-63544726-G-C		not specified	Uncertain significance (Jul 12, 2022)
11-63544755-CA-C			Likely benign (Dec 31, 2019)
11-63544761-C-T		not specified	Uncertain significance (Jun 29, 2022)
11-63544767-G-A		not specified	Uncertain significance (Aug 28, 2024)
11-63544767-G-C		not specified	Uncertain significance (Aug 15, 2023)
11-63544799-G-T		not specified	Uncertain significance (Nov 06, 2023)
11-63544875-T-G		not specified	Uncertain significance (Aug 30, 2021)
11-63544879-G-A		not specified	Likely benign (Apr 25, 2022)
11-63546176-G-T		not specified	Uncertain significance (Jul 17, 2024)
11-63546186-C-T		not specified	Uncertain significance (Oct 03, 2024)
11-63546212-T-A		not specified	Uncertain significance (Nov 30, 2022)
11-63546212-T-G		not specified	Uncertain significance (Feb 22, 2023)
11-63546216-C-G		not specified	Uncertain significance (Nov 25, 2024)
11-63546220-T-G		not specified	Uncertain significance (Aug 15, 2023)
11-63546252-C-T		not specified	Uncertain significance (Mar 06, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLAAT4	protein_coding	protein_coding	ENST00000255688	4	9654

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-7	0.0594	125593	0	20	125613	0.0000796

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.362	88	98.1	0.897	0.00000614	1062
Missense in Polyphen		19	27.888	0.6813		328
Synonymous	-0.149	39	37.8	1.03	0.00000231	321
Loss of Function	-1.03	9	6.23	1.45	2.64e-7	79

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000156	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000972	0.0000967
Middle Eastern	0.0000556	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

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. N- and O-acylation activity is hardly detectable. {ECO:0000269|PubMed:19615464}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE (Consensus)

Intolerance Scores

• loftool: 0.723
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.00106
• hipred: Y
• hipred_score: 0.554
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.559

Gene Damage Prediction

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

Gene ontology

• Biological process: phospholipid metabolic process;negative regulation of cell population proliferation;lipid catabolic process;phosphatidylethanolamine acyl-chain remodeling
• Cellular component: cytosol;integral component of membrane
• Molecular function: phospholipase A2 activity;protein binding;transferase activity, transferring acyl groups