PGLYRP1
protein-codingpeptidoglycan recognition protein 1, the group of Peptidoglycan recognition proteins
Gene summary
Enables several functions, including Hsp70 protein binding activity; peptidoglycan binding activity; and peptidoglycan immune receptor activity. Involved in antimicrobial humoral immune response mediated by antimicrobial peptide; defense response to Gram-positive bacterium; and detection of bacterium. Located in extracellular exosome. Is active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]
- TNFSF3L
- PGLYRP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~3.9 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 PGLYRP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005091.3. 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 | 35 | 3 | 38 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 3 | 0 | 39 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005082.1 | 3 | MANE Select | |
| Ensembl | ENSP00000008938.3 | 3 | MANE Select | |
| Ensembl | ENSP00000773442.1 | 2 | Standard | |
| Ensembl | ENSP00000801229.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- toll-like receptor pathway
- Antimicrobial peptides
- Innate Immune System
- Immune System
Biological Process
- pattern recognition receptor signaling pathway
- peptidoglycan catabolic process
- detection of bacterium
- antimicrobial humoral response
- killing of cells of other organism
Molecular Function
- zinc ion binding
- N-acetylmuramoyl-L-alanine amidase activity
- peptidoglycan receptor activity
- peptidoglycan binding
Cellular Component
- extracellular region
- extracellular space
- specific granule lumen
- extracellular exosome
- phagocytic vesicle lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000008938
- Coding exons
- 3
- Length
- 3913
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 19
- Defined
- 125728
- p
- 0.0000756
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.530 | 108 | 125 | 0.866 | 0.00000771 | 1250 |
| Missense (PolyPhen) | 42 | 53.555 | 0.78424 | 526 | ||
| Synonymous | 1.59 | 36 | 50.4 | 0.715 | 0.00000317 | 404 |
| Loss of Function | -0.118 | 7 | 6.67 | 1.05 | 2.86e-7 | 69 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000072 | 0.000070 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00034 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Pattern receptor that binds to murein peptidoglycans (PGN) of Gram-positive bacteria. Has bactericidal activity towards Gram-positive bacteria. May kill Gram-positive bacteria by interfering with peptidoglycan biosynthesis. Binds also to Gram- negative bacteria, and has bacteriostatic activity towards Gram- negative bacteria. Plays a role in innate immunity. {ECO:0000269|PubMed:11461926, ECO:0000269|PubMed:16354652}.;
Recessive Scores
- pRec
- 0.0678
Intolerance Scores
- LoFtool
- 0.464
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0134
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |