PGLYRP1
peptidoglycan recognition protein 1, the group of Peptidoglycan recognition proteins
Basic information
Region (hg38): 19:46019153-46023053
Previous symbols: [ "TNFSF3L", "PGLYRP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGLYRP1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 15 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 15 | 1 | 0 |
Variants in PGLYRP1
This is a list of pathogenic ClinVar variants found in the PGLYRP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-46019249-G-A | not specified | Uncertain significance (Dec 21, 2022) | ||
| 19-46019317-C-T | not specified | Uncertain significance (Oct 10, 2023) | ||
| 19-46019589-C-T | not specified | Uncertain significance (Feb 08, 2023) | ||
| 19-46019609-C-T | not specified | Uncertain significance (Dec 13, 2022) | ||
| 19-46019610-G-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 19-46019616-C-T | not specified | Uncertain significance (Sep 30, 2021) | ||
| 19-46022745-C-T | not specified | Uncertain significance (Aug 16, 2021) | ||
| 19-46022753-C-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 19-46022754-A-G | not specified | Uncertain significance (Jun 10, 2024) | ||
| 19-46022775-A-G | not specified | Uncertain significance (Sep 07, 2022) | ||
| 19-46022792-G-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 19-46022810-G-C | not specified | Uncertain significance (Sep 06, 2022) | ||
| 19-46022825-C-G | not specified | Likely benign (Oct 03, 2022) | ||
| 19-46022834-G-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 19-46022894-G-A | not specified | Uncertain significance (Jun 28, 2022) | ||
| 19-46022916-G-A | not specified | Uncertain significance (Dec 18, 2023) | ||
| 19-46022979-G-A | not specified | Uncertain significance (Jun 21, 2022) | ||
| 19-46023015-G-A | not specified | Uncertain significance (Mar 02, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PGLYRP1 | protein_coding | protein_coding | ENST00000008938 | 3 | 3913 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000179 | 0.272 | 125709 | 0 | 19 | 125728 | 0.0000756 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.530 | 108 | 125 | 0.866 | 0.00000771 | 1250 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000180 | 0.000179 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000716 | 0.0000703 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000342 | 0.000326 |
dbNSFP
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}.;
- Pathway
- Neutrophil degranulation;toll-like receptor pathway;Antimicrobial peptides;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.0678
Intolerance Scores
- loftool
- 0.464
- rvis_EVS
- 0.46
- rvis_percentile_EVS
- 78.28
Haploinsufficiency Scores
- pHI
- 0.0248
- hipred
- N
- hipred_score
- 0.153
- ghis
- 0.391
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.0134
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Pglyrp1
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- pattern recognition receptor signaling pathway;peptidoglycan catabolic process;detection of bacterium;antimicrobial humoral response;killing of cells of other organism;negative regulation of interferon-gamma production;negative regulation of natural killer cell differentiation involved in immune response;neutrophil degranulation;growth of symbiont in host;innate immune response;negative regulation of inflammatory response;defense response to Gram-positive bacterium;positive regulation of cytolysis in other organism;antimicrobial humoral immune response mediated by antimicrobial peptide
- Cellular component
- extracellular region;extracellular space;specific granule lumen;extracellular exosome;phagocytic vesicle lumen;tertiary granule lumen
- Molecular function
- zinc ion binding;N-acetylmuramoyl-L-alanine amidase activity;peptidoglycan receptor activity;peptidoglycan binding