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.

• not_specified (25 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000004585.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			23	2		25
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	3	0

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