LIPI

lipase I, the group of Lipases

Basic information

Region (hg38): 21:14108813-14210955

Links

ENSG00000188992 ∙ NCBI:149998 ∙ OMIM:609252 ∙ HGNC:18821 ∙ Uniprot:Q6XZB0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypertriglyceridemia (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypertriglyceridemia, familial	AD	Cardiovascular	Surveillance and treatment for cholesterol and cardiovascular perturbations may decrease morbidity and mortality	Cardiovascular	12719377

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LIPI gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPI 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			2	8	3	13
missense			44	4	7	55
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel					1	1
splice donor/acceptor (+/-2bp)			1			1
splice region			3	4	2	9
non coding			3	4	9	16
Total	0	0	52	16	20

Variants in LIPI

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

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

Position	Type	Phenotype	Significance	ClinVar
21-14109008-T-G			Likely benign (Mar 23, 2021)
21-14109044-G-T			Benign (Feb 01, 2024)
21-14109045-T-A			Uncertain significance (Jan 15, 2022)
21-14109049-T-C		not specified	Uncertain significance (Apr 23, 2024)
21-14109073-G-T		not specified	Uncertain significance (Jun 10, 2024)
21-14109087-AAG-A			Benign (Jul 17, 2023)
21-14144627-C-T			Benign (Jan 31, 2024)
21-14144655-A-A			Benign (Feb 01, 2024)
21-14144707-T-C		not specified	Uncertain significance (Jun 19, 2024)
21-14144714-A-G			Benign (Sep 19, 2022)
21-14144719-A-G		not specified	Uncertain significance (May 15, 2024)
21-14144736-A-C		not specified	Uncertain significance (Aug 17, 2022)
21-14144737-A-C			Uncertain significance (Oct 27, 2022)
21-14144737-A-T		not specified	Uncertain significance (May 23, 2024)
21-14144819-C-T			Likely benign (Nov 05, 2022)
21-14152595-T-C		not specified	Likely benign (Mar 22, 2022)
21-14152600-C-T			Benign (Jan 31, 2024)
21-14152617-T-G			Uncertain significance (Oct 07, 2021)
21-14152629-C-T			Benign (Mar 29, 2023)
21-14152645-G-T			Uncertain significance (Sep 04, 2023)
21-14152657-A-C		not specified	Uncertain significance (Apr 08, 2024)
21-14152661-T-G		not specified	Uncertain significance (Jan 08, 2024)
21-14152684-G-C		not specified	Uncertain significance (Jan 23, 2024)
21-14152687-A-G			Uncertain significance (Jan 18, 2023)
21-14163406-G-A			Benign (Jan 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPI	protein_coding	protein_coding	ENST00000344577	10	102033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-19	0.000321	125692	0	47	125739	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.365	261	245	1.07	0.0000112	3179
Missense in Polyphen		100	92.14	1.0853		1184
Synonymous	-0.516	93	86.9	1.07	0.00000413	862
Loss of Function	-1.06	26	20.8	1.25	8.66e-7	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000548	0.000543
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000381	0.000381
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000160	0.000158
Middle Eastern	0.000381	0.000381
South Asian	0.000197	0.000196
Other	0.000500	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes specifically phosphatidic acid (PA) to produce 2-acyl lysophosphatidic acid (LPA; a potent bioactive lipid mediator) and fatty acid. Does not hydrolyze other phospholipids, like phosphatidylserine (PS), phosphatidylcholine (PC) and phosphatidylethanolamine (PE) or triacylglycerol (TG). {ECO:0000269|PubMed:12963729}.
• Pathway: Metabolism of lipids;Metabolism;Glycerophospholipid biosynthesis;Phospholipid metabolism;Synthesis of PA (Consensus)

Intolerance Scores

• loftool: 0.241
• rvis_EVS: 1.2
• rvis_percentile_EVS: 92.95

Haploinsufficiency Scores

• pHI: 0.192
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.124

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lipi
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: phosphatidic acid biosynthetic process;lipid catabolic process
• Cellular component: extracellular region;plasma membrane
• Molecular function: phospholipase activity;heparin binding;carboxylic ester hydrolase activity