PLAAT1

phospholipase A and acyltransferase 1, the group of Phospholipase A and acyltransferase family

Basic information

Region (hg38): 3:193241128-193277738

Previous symbols: [ "HRASLS" ]

Links

ENSG00000127252 ∙ NCBI:57110 ∙ OMIM:606487 ∙ HGNC:14922 ∙ Uniprot:Q9HDD0 ∙ 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 PLAAT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLAAT1 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					1	1
missense			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	1

Variants in PLAAT1

This is a list of pathogenic ClinVar variants found in the PLAAT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-193255654-G-A		not specified	Uncertain significance (Mar 29, 2022)
3-193255723-C-T		not specified	Uncertain significance (Oct 12, 2024)
3-193255762-G-A		not specified	Uncertain significance (Mar 28, 2024)
3-193263047-G-T		not specified	Uncertain significance (Feb 21, 2024)
3-193263053-G-A		not specified	Uncertain significance (Jul 26, 2024)
3-193263087-A-G		not specified	Uncertain significance (Dec 03, 2021)
3-193263104-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-193263105-C-T		not specified	Uncertain significance (Dec 03, 2024)
3-193263132-G-A		not specified	Uncertain significance (Feb 28, 2023)
3-193263133-G-A			Benign (Apr 04, 2018)
3-193263134-T-C		not specified	Uncertain significance (Sep 01, 2021)
3-193263201-C-G		not specified	Uncertain significance (Oct 12, 2024)
3-193263209-C-T		not specified	Uncertain significance (Nov 14, 2023)
3-193270625-G-A		not specified	Likely benign (Sep 26, 2023)
3-193270696-A-C		not specified	Uncertain significance (Jan 09, 2024)
3-193275045-CA-C			Benign (Jun 23, 2018)
3-193275056-A-G		not specified	Uncertain significance (Jun 02, 2023)
3-193275070-G-C		not specified	Uncertain significance (Nov 13, 2024)
3-193275109-T-C		not specified	Uncertain significance (Feb 28, 2024)
3-193275141-G-C		not specified	Uncertain significance (Dec 09, 2023)
3-193275158-C-T		not specified	Uncertain significance (Nov 13, 2024)
3-193275178-T-C		not specified	Uncertain significance (Dec 08, 2023)
3-193275247-A-C		not specified	Uncertain significance (Aug 16, 2021)
3-193276755-C-T		not specified	Uncertain significance (Aug 02, 2021)
3-193276770-A-G		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLAAT1	protein_coding	protein_coding	ENST00000264735	4	36614

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000250	0.549	125267	3	477	125747	0.00191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0796	95	97.2	0.977	0.00000539	1734
Missense in Polyphen		57	53.616	1.0631		611
Synonymous	0.464	35	38.7	0.905	0.00000239	586
Loss of Function	0.488	6	7.44	0.807	3.98e-7	127

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00267	0.00266
Ashkenazi Jewish	0.000415	0.000397
East Asian	0.000708	0.000707
Finnish	0.000559	0.000554
European (Non-Finnish)	0.00323	0.00311
Middle Eastern	0.000708	0.000707
South Asian	0.000794	0.000686
Other	0.00228	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Exhibits calcium-independent phospholipase activity towards phosphatidylcholine (PC) and phosphatidylethanolamine (PE). Also shows acyltransferase activities, transferring an acyl group of PCs to the amino group of PEs and the hydroxyl group of lyso PCs. {ECO:0000269|PubMed:21880860}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Acyl chain remodelling of PE (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0727
• hipred: N
• hipred_score: 0.146
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hrasls

Gene ontology

• Biological process: lipid catabolic process;phosphatidylcholine metabolic process
• Cellular component: nuclear envelope lumen;cytoplasm;integral component of membrane
• Molecular function: phospholipase A2 activity;O-acyltransferase activity;phospholipase A1 activity;N-acyltransferase activity