PNLIPRP1
protein-codingpancreatic lipase related protein 1
Gene summary
Predicted to enable calcium ion binding activity; 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. Biomarker of prostate cancer. [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 ~18.8 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 PNLIPRP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006229.4. 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 | 0 | |||||
| missense | 65 | 3 | 68 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 65 | 3 | 0 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006220.1 | 12 | MANE Select | |
| Ensembl | ENSP00000351695.4 | 12 | MANE Select | |
| RefSeq | NP_001290064.1 | 12 | Standard | |
| Ensembl | ENSP00000431207.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glycerolipid metabolism - Homo sapiens (human)
- Fat digestion and absorption - Homo sapiens (human)
- Pancreatic secretion - Homo sapiens (human)
- Glycerophospholipid metabolism
- Digestion of dietary lipid
Biological Process
- lipid metabolic process
Molecular Function
- triglyceride lipase activity
- calcium ion binding
- lipase activity
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000528052
- Coding exons
- 12
- Length
- 18791
- Individuals with no LoFs
- 125498
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 249
- Defined
- 125748
- p
- 0.000995
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0831 | 264 | 260 | 1.01 | 0.0000135 | 3082 |
| Missense (PolyPhen) | 88 | 85.304 | 1.0316 | 1021 | ||
| Synonymous | -0.776 | 112 | 102 | 1.10 | 0.00000588 | 875 |
| Loss of Function | 0.640 | 22 | 25.5 | 0.863 | 0.00000135 | 288 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0030 | 0.0030 | notable |
| Latino/Admixed American | 0.00099 | 0.00098 | rare |
| Ashkenazi Jewish | 0.00050 | 0.00050 | rare |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.00046 | 0.00046 | rare |
| European (Non-Finnish) | 0.0011 | 0.0011 | notable |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0.0018 | 0.0016 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as inhibitor of dietary triglyceride digestion. Lacks detectable lipase activity towards triglycerides, diglycerides, phosphatidylcholine, galactolipids or cholesterol esters (in vitro) (By similarity). {ECO:0000250, ECO:0000269|PubMed:19824014}.;
Recessive Scores
- pRec
- 0.121
Intolerance Scores
- RVIS EVS
- 0.15
- RVIS percentile EVS
- 64.74
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0766
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |