PGLYRP4
protein-codingpeptidoglycan recognition protein 4, the group of Peptidoglycan recognition proteins
Gene summary
Summary: This gene encodes a peptidoglycan recognition protein, which belongs to the N-acetylmuramoyl-L-alanine amidase 2 family. These proteins are part of the innate immune system and recognize peptidoglycan, a ubiquitous component of bacterial cell walls. This antimicrobial protein binds to murein peptidoglycans of Gram-positive bacteria. [provided by RefSeq, Oct 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.7 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 PGLYRP4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020393.4. 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 | 2 | 2 | ||||
| missense | 52 | 3 | 55 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 55 | 3 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065126.2 | 8 | MANE Select | |
| Ensembl | ENSP00000352672.5 | 8 | MANE Select | |
| Ensembl | ENSP00000357728.3 | 8 | Standard | |
| Ensembl | ENSP00000357728.3 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
- protein heterodimerization activity
Cellular Component
- extracellular space
- membrane
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000359650
- Coding exons
- 8
- Length
- 18721
- Individuals with no LoFs
- 125402
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 345
- Defined
- 125748
- p
- 0.00138
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.00366 | 210 | 210 | 0.999 | 0.0000107 | 2409 |
| Missense (PolyPhen) | 67 | 73.778 | 0.90812 | 928 | ||
| Synonymous | -0.730 | 98 | 89.2 | 1.10 | 0.00000488 | 770 |
| Loss of Function | -0.897 | 20 | 16.1 | 1.24 | 6.86e-7 | 178 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00068 | 0.00068 | rare |
| Latino/Admixed American | 0.0021 | 0.0021 | notable |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00017 | 0.00016 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.0020 | 0.0020 | notable |
| South Asian | 0.00069 | 0.00065 | rare |
| Other | 0.0016 | 0.0016 | notable |
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:16354652}.;
Recessive Scores
- pRec
- 0.0909
Intolerance Scores
- RVIS EVS
- 1.26
- RVIS percentile EVS
- 93.58
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.425
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |