PNLIPRP3
protein-codingpancreatic lipase related protein 3, the group of Lipases
Gene summary
Predicted to enable glycerophospholipid phospholipase A1 activity and lipoprotein lipase activity. Predicted to be involved in several processes, including cholesterol homeostasis; high-density lipoprotein particle remodeling; and triglyceride catabolic process. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~50.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PNLIPRP3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001011709.3. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 56 | 4 | 60 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 56 | 5 | 0 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001011709.2 | 12 | MANE Select | |
| Ensembl | ENSP00000358232.3 | 12 | MANE Select | |
| Ensembl | ENSP00000809522.1 | 12 | Standard | |
| RefSeq | XP_011537578.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerolipid metabolism - Homo sapiens (human)
- triacylglycerol degradation
- Digestion of dietary lipid
- Digestion
- Digestion and absorption
Biological Process
- lipid catabolic process
Molecular Function
- triglyceride lipase activity
Cellular Component
- extracellular region
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369230
- Coding exons
- 12
- Length
- 50091
- Individuals with no LoFs
- 114132
- Homozygous LoFs
- 382
- Heterozygous LoFs
- 11232
- Defined
- 125746
- p
- 0.0473
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0586 | 251 | 248 | 1.01 | 0.0000123 | 3072 |
| Missense (PolyPhen) | 78 | 78.502 | 0.9936 | 922 | ||
| Synonymous | 0.177 | 82 | 84.1 | 0.975 | 0.00000420 | 847 |
| Loss of Function | 0.865 | 19 | 23.5 | 0.807 | 0.00000117 | 300 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.13 | 0.072 | notable |
| Latino/Admixed American | 0.029 | 0.026 | notable |
| Ashkenazi Jewish | 0.076 | 0.076 | notable |
| East Asian | 0.0011 | 0.0011 | notable |
| Finnish | 0.088 | 0.088 | notable |
| European (Non-Finnish) | 0.057 | 0.057 | notable |
| South Asian | 0.016 | 0.015 | notable |
| Other | 0.054 | 0.052 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0654
Intolerance Scores
- LoFtool
- 0.370
- RVIS EVS
- 1.31
- RVIS percentile EVS
- 94.01
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.122
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |