LIPG

lipase G, endothelial type, the group of Lipases

Basic information

Region (hg38): 18:49560699-49599185

Links

ENSG00000101670 ∙ NCBI:9388 ∙ OMIM:603684 ∙ HGNC:6623 ∙ Uniprot:Q9Y5X9 ∙ 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 LIPG gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIPG 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	32	3	36
missense			51	5	8	64
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			3			3
splice region			1	4	1	6
non coding			1	6	5	12
Total	0	0	58	43	16

Variants in LIPG

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

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

Position	Type	Phenotype	Significance	ClinVar
18-49562308-G-T		LIPG-related disorder	Likely benign (Aug 29, 2019)
18-49562320-C-A			Benign (Jan 31, 2024)
18-49562344-C-T			Likely benign (Aug 19, 2023)
18-49562371-C-T			Benign (Jan 31, 2024)
18-49562377-A-C			Likely benign (Oct 17, 2021)
18-49562378-C-T		not specified	Uncertain significance (Dec 13, 2022)
18-49562384-G-A			Benign (Jan 31, 2024)
18-49562419-G-A			Likely benign (Oct 14, 2022)
18-49565330-A-C			Uncertain significance (Oct 04, 2023)
18-49565334-A-C			Benign (Dec 26, 2023)
18-49565335-A-C		not specified	Uncertain significance (Nov 29, 2023)
18-49565352-G-A			Uncertain significance (Apr 28, 2021)
18-49565379-C-T			Uncertain significance (May 09, 2023)
18-49565400-C-G			Uncertain significance (Jun 27, 2022)
18-49565423-C-T			Likely benign (Oct 28, 2023)
18-49565437-C-T			Benign (Nov 15, 2023)
18-49565448-T-C			Uncertain significance (Mar 02, 2023)
18-49565490-G-A			Uncertain significance (Nov 23, 2022)
18-49565506-C-T			Likely benign (Nov 28, 2023)
18-49567426-C-G			Benign (Jan 24, 2024)
18-49567444-G-T			Uncertain significance (May 18, 2022)
18-49567447-C-T			Likely benign (Oct 20, 2023)
18-49567453-C-T			Likely benign (Oct 18, 2023)
18-49567478-G-A			Uncertain significance (May 25, 2022)
18-49567490-C-T		not specified	Uncertain significance (Apr 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LIPG	protein_coding	protein_coding	ENST00000261292	10	32204

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-10	0.295	125673	0	75	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.857	257	299	0.860	0.0000190	3319
Missense in Polyphen		103	130.55	0.78895		1471
Synonymous	-1.20	134	117	1.14	0.00000808	945
Loss of Function	0.907	18	22.7	0.794	0.00000116	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00208	0.00208
European (Non-Finnish)	0.000132	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has phospholipase and triglyceride lipase activities. Hydrolyzes high density lipoproteins (HDL) more efficiently than other lipoproteins. Binds heparin.
• Pathway: Glycerolipid metabolism - Homo sapiens (human);Cholesterol metabolism - Homo sapiens (human);HDL remodeling;Transport of small molecules;Glycerophospholipid metabolism;triacylglycerol degradation;Plasma lipoprotein assembly, remodeling, and clearance;Plasma lipoprotein remodeling (Consensus)

Recessive Scores

• pRec: 0.336

Intolerance Scores

• loftool: 0.249
• rvis_EVS: 0.49
• rvis_percentile_EVS: 79.46

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.615
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lipg
• Phenotype: homeostasis/metabolism phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: lipid metabolic process;response to nutrient;cell population proliferation;phospholipid catabolic process;positive regulation of high-density lipoprotein particle clearance;positive regulation of cholesterol transport;high-density lipoprotein particle remodeling;cholesterol homeostasis;reverse cholesterol transport;regulation of lipoprotein metabolic process;phospholipid homeostasis
• Cellular component: extracellular region;extracellular space;early endosome;Golgi apparatus;cell surface
• Molecular function: lipoprotein lipase activity;phospholipase activity;heparin binding;phospholipase A1 activity