PRTN3
proteinase 3, the group of Granule associated serine proteases of immune defence
Basic information
Region (hg38): 19:840999-848175
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (34 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRTN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000002777.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 31 | 36 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 31 | 8 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRTN3 | protein_coding | protein_coding | ENST00000234347 | 5 | 7213 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000380 | 0.394 | 124663 | 0 | 19 | 124682 | 0.0000762 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.153 | 140 | 145 | 0.964 | 0.00000845 | 1598 |
| Missense in Polyphen | 35 | 51.675 | 0.67731 | 618 | ||
| Synonymous | -0.637 | 68 | 61.6 | 1.10 | 0.00000349 | 544 |
| Loss of Function | 0.233 | 7 | 7.70 | 0.909 | 4.12e-7 | 80 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000978 | 0.0000930 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000501 | 0.000375 |
| European (Non-Finnish) | 0.0000606 | 0.0000533 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000705 | 0.0000328 |
| Other | 0.000357 | 0.000329 |
dbNSFP
Source:
- Function
- FUNCTION: Serine protease that degrades elastin, fibronectin, laminin, vitronectin, and collagen types I, III, and IV (in vitro) (PubMed:3198760, PubMed:2033050, PubMed:28240246). By cleaving and activating receptor F2RL1/PAR-2, enhances endothelial cell barrier function and thus vascular integrity during neutrophil transendothelial migration (PubMed:23202369). May play a role in neutrophil transendothelial migration, probably when associated with CD177 (PubMed:22266279). {ECO:0000269|PubMed:2033050, ECO:0000269|PubMed:22266279, ECO:0000269|PubMed:23202369, ECO:0000269|PubMed:28240246, ECO:0000269|PubMed:3198760}.;
- Disease
- DISEASE: Note=Is the major autoantigen in anti-neutrophil cytoplasmic autoantibody (ANCA)-associated vasculitis (Wegener's granulomatosis) (PubMed:2377228, PubMed:2679910). This complex, systemic disease is characterized by granulomatous inflammation with necrotizing lesions in the respiratory tract, glomerulonephritis, vasculitis, and anti-neutrophil cytoplasmatic autoantibodies detected in patient sera (PubMed:2377228, PubMed:2679910). PRTN3 causes emphysema when administered by tracheal insufflation to hamsters (PubMed:3198760). {ECO:0000269|PubMed:3198760, ECO:0000303|PubMed:2377228, ECO:0000303|PubMed:2679910}.;
- Pathway
- Neutrophil degranulation;Other interleukin signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Antimicrobial peptides;Innate Immune System;Immune System;Hemostasis;Common Pathway of Fibrin Clot Formation;Formation of Fibrin Clot (Clotting Cascade);C-MYB transcription factor network
(Consensus)
Intolerance Scores
- loftool
- 0.378
- rvis_EVS
- 0.46
- rvis_percentile_EVS
- 78.46
Haploinsufficiency Scores
- pHI
- 0.146
- hipred
- N
- hipred_score
- 0.372
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.591
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prtn3
- Phenotype
- hematopoietic system phenotype; immune system phenotype; cellular phenotype;
Gene ontology
- Biological process
- proteolysis;membrane protein ectodomain proteolysis;phagocytosis;blood coagulation;positive regulation of cell population proliferation;cytokine-mediated signaling pathway;antimicrobial humoral response;collagen catabolic process;neutrophil degranulation;positive regulation of GTPase activity;cell-cell junction maintenance;negative regulation of phagocytosis;neutrophil extravasation;mature conventional dendritic cell differentiation
- Cellular component
- extracellular region;extracellular space;cytosol;plasma membrane;azurophil granule lumen;plasma membrane raft;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- serine-type endopeptidase activity;signaling receptor binding;protein binding;serine-type peptidase activity;enzyme binding