LYPLA1

lysophospholipase 1, the group of Depalmitoylases

Basic information

Region (hg38): 8:54046366-54102017

Links

ENSG00000120992 ∙ NCBI:10434 ∙ OMIM:605599 ∙ HGNC:6737 ∙ Uniprot:O75608 ∙ 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 LYPLA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LYPLA1 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	1	12
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	2	1

Variants in LYPLA1

This is a list of pathogenic ClinVar variants found in the LYPLA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-54051026-T-A		not specified	Uncertain significance (Jan 04, 2022)
8-54051122-C-T		not specified	Uncertain significance (Mar 04, 2024)
8-54051141-G-A			Likely benign (Jul 01, 2023)
8-54051179-C-T		not specified	Likely benign (Jan 17, 2023)
8-54052660-G-A			Benign (May 24, 2018)
8-54052695-G-C		not specified	Uncertain significance (Dec 13, 2021)
8-54055098-T-C		not specified	Uncertain significance (Oct 06, 2022)
8-54055112-T-A		not specified	Uncertain significance (Nov 07, 2022)
8-54065770-T-C		not specified	Uncertain significance (Jul 09, 2021)
8-54100911-G-A		not specified	Uncertain significance (Feb 13, 2024)
8-54101781-G-A		not specified	Uncertain significance (Sep 14, 2022)
8-54101787-T-C		not specified	Uncertain significance (Jun 07, 2023)
8-54101817-C-T		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LYPLA1	protein_coding	protein_coding	ENST00000316963	9	55640

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000365	0.835	125725	0	22	125747	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	88	120	0.734	0.00000593	1482
Missense in Polyphen		17	32.457	0.52378		405
Synonymous	-0.416	45	41.6	1.08	0.00000221	434
Loss of Function	1.32	9	14.4	0.625	7.08e-7	171

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000319	0.000312
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes fatty acids from S-acylated cysteine residues in proteins such as trimeric G alpha proteins or HRAS. Has depalmitoylating activity toward KCNMA1. Has low lysophospholipase activity. {ECO:0000269|PubMed:20418879, ECO:0000269|PubMed:22399288}.
• Pathway: Glycerophospholipid metabolism - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Phospholipid Biosynthesis;Metabolism of nitric oxide;eNOS activation;eNOS activation and regulation;Metabolism (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.723
• rvis_EVS: 0.39
• rvis_percentile_EVS: 76.05

Haploinsufficiency Scores

• pHI: 0.657
• hipred: N
• hipred_score: 0.379
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lypla1

Gene ontology

• Biological process: protein depalmitoylation;fatty acid metabolic process;negative regulation of Golgi to plasma membrane protein transport;regulation of nitric-oxide synthase activity
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: lysophospholipase activity;palmitoyl-(protein) hydrolase activity;lipase activity;carboxylic ester hydrolase activity