GeneBe

LIPC

protein-coding

lipase C, hepatic type, the group of Lipases

Gene summary

Enables glycerophospholipid phospholipase A1 activity and triacylglycerol lipase activity. Involved in several processes, including cholesterol homeostasis; plasma lipoprotein particle remodeling; and triglyceride catabolic process. Located in obsolete extracellular space. Implicated in several diseases, including Alzheimer's disease; coronary artery disease; familial combined hyperlipidemia; peripheral vascular disease; and type 2 diabetes mellitus. Biomarker of hyperinsulinism; obesity; and type 1 diabetes mellitus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_000236.3

Inheritance

AR, SD

ClinVar variants

P:4U:183B:68

Top phenotype

Hepatic lipase deficiency

gnomAD constraint

pLI —, LoF o/e 0.59

Max pathogenic AF

—

Genomic locus

chr15:58,410,569-58,569,844

External References & Databases

Ensembl (ENSG00000166035)NCBI Gene (3990)OMIM (151670)HGNC:6619GenCCUniProt (P11150)AlphaFoldClinVar (LIPC)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~159.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

hyperlipidemia due to hepatic triglyceride lipase deficiencySTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0013533

Submitter: Laboratory for Molecular Medicine

This gene-disease relationship has undergone rapid assessment. Classifications are based on preliminary review of gene-disease validity during analysis of genomic sequencing results.

hyperlipidemia due to hepatic triglyceride lipase deficiencyLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0013533

Submitter: Labcorp Genetics (formerly Invitae)

hyperlipidemia due to hepatic triglyceride lipase deficiencyLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0013533

Submitter: Ambry Genetics

hyperlipidemia due to hepatic triglyceride lipase deficiencySTRONG

Inheritance Pattern: SD

Disease ID:MONDO:0013533

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Hepatic lipase deficiencyAR

Manifestation: Cardiovascular

Intervention: Cardiovascular

Rationale: Surveillance and treatment for cholesterol and cardiovascular perturbations may decrease morbidity and mortality

Refs: 1883393; 1671786; 12777476; 19428034Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LIPC variants in ClinVar

9 Conditions Cataloged
not providedTotal: 216
not specifiedTotal: 74
Hyperlipidemia due to hepatic triglyceride lipase deficiencyTotal: 59
Type 2 diabetes mellitusTotal: 20
High density lipoprotein cholesterol level quantitative trait locus 12Total: 13
LIPC-related disorderTotal: 7
Abnormal circulating lipid concentrationTotal: 2
HIGH DENSITY LIPOPROTEIN CHOLESTEROL LEVEL QUANTITATIVE TRAIT LOCUS 6Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000236.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
8
clinvar
56
clinvar
1
clinvar
 65
missense
1
clinvar
1
clinvar
162
clinvar
11
clinvar
 175
nonsense
1
clinvar
3
clinvar
 4
start loss
0
frameshift
7
clinvar
 7
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
 4
Total22183671255

Highest pathogenic variant AF is 0.000009292621

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000236.3RefSeqNP_000227.29MANE Select
ENST00000299022.10EnsemblENSP00000299022.59MANE Select
ENST00000356113.10EnsemblENSP00000348425.69Standard
ENST00000356113.11EnsemblENSP00000348425.69Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Glycerolipid metabolism - Homo sapiens (human)
  • Cholesterol metabolism - Homo sapiens (human)
  • Statin Pathway, Pharmacodynamics
  • Familial lipoprotein lipase deficiency
  • Glycerolipid Metabolism

Biological Process

  • fatty acid biosynthetic process
  • cholesterol metabolic process
  • triglyceride catabolic process
  • very-low-density lipoprotein particle remodeling
  • intermediate-density lipoprotein particle remodeling

Molecular Function

  • phospholipase activity
  • triglyceride lipase activity
  • heparin binding
  • low-density lipoprotein particle binding
  • apolipoprotein binding

Cellular Component

  • extracellular region
  • extracellular space
  • endoplasmic reticulum lumen
  • high-density lipoprotein particle

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000356113
Coding exons
9
Length
158384
Individuals with no LoFs
125607
Homozygous LoFs
0
Heterozygous LoFs
141
Defined
125748
p
0.000561
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.9193352911.150.00001933261
Missense (PolyPhen)121105.631.14551237
Synonymous-1.801481231.210.00000939969
Loss of Function1.821423.50.5950.00000136249

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00120.0012notable
Latino/Admixed American0.000350.00035rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000440.00044rare
Finnish00.0absent
European (Non-Finnish)0.000770.00076rare
South Asian0.000170.00016rare
Other0.00130.0013notable

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Hepatic lipase has the capacity to catalyze hydrolysis of phospholipids, mono-, di-, and triglycerides, and acyl-CoA thioesters. It is an important enzyme in HDL metabolism. Hepatic lipase binds heparin.;
Disease
DISEASE: Hepatic lipase deficiency (HL deficiency) [MIM:614025]: A disorder characterized by elevated levels of beta-migrating very low density lipoproteins, and abnormally triglyceride-rich low and high density lipoproteins. {ECO:0000269|PubMed:10660332, ECO:0000269|PubMed:1301939}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.361

Intolerance Scores

LoFtool
0.189
RVIS EVS
-0.71
RVIS percentile EVS
14.78

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
N
Indispensability score
0.457

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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