PLBD1
protein-codingphospholipase B domain containing 1
Gene summary
Enables aminopeptidase activity. Involved in lysosomal protein catabolic process. Located in lysosome and obsolete extracellular space. [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 ~64.2 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 PLBD1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024829.6. 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 | 79 | 5 | 84 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 83 | 5 | 0 | 88 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079105.4 | 11 | MANE Select | |
| Ensembl | ENSP00000240617.5 | 11 | MANE Select | |
| Ensembl | ENSP00000438367.1 | 4 | Standard | |
| Ensembl | ENSP00000441278.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Acyl chain remodelling of PI
- Metabolism of lipids
- Metabolism
- Acyl chain remodelling of PC
- Glycerophospholipid biosynthesis
Biological Process
- phospholipid metabolic process
- lipid catabolic process
- phosphatidylinositol acyl-chain remodeling
- phosphatidylcholine acyl-chain remodeling
- phosphatidylethanolamine acyl-chain remodeling
Molecular Function
- lysophospholipase activity
- phospholipase A2 activity
Cellular Component
- extracellular space
- lysosome
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000240617
- Coding exons
- 11
- Length
- 64689
- Individuals with no LoFs
- 125564
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 184
- Defined
- 125748
- p
- 0.000732
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.778 | 253 | 290 | 0.872 | 0.0000146 | 3616 |
| Missense (PolyPhen) | 112 | 143.67 | 0.77956 | 1734 | ||
| Synonymous | -0.0913 | 106 | 105 | 1.01 | 0.00000512 | 1031 |
| Loss of Function | 0.440 | 26 | 28.5 | 0.911 | 0.00000149 | 336 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.00044 | 0.00043 | rare |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.0010 | 0.0010 | notable |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00071 | 0.00070 | rare |
| South Asian | 0.0018 | 0.0018 | notable |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: In view of the small size of the putative binding pocket, it has been proposed that it may act as an amidase or a peptidase (By similarity). Exhibits a weak phospholipase activity, acting on various phospholipids, including phosphatidylcholine, phosphatidylinositol, phosphatidylethanolamine and lysophospholipids. {ECO:0000250, ECO:0000269|PubMed:19019078}.;
Intolerance Scores
- LoFtool
- 0.909
- RVIS EVS
- 0.53
- RVIS percentile EVS
- 80.88
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.125
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |