PTX3
protein-codingpentraxin 3, the group of Long pentraxins
Gene summary
This gene encodes a member of the pentraxin protein family. The expression of this protein is induced by inflammatory cytokines in response to inflammatory stimuli in several mesenchymal and epithelial cell types, particularly endothelial cells and mononuclear phagocytes. The protein promotes fibrocyte differentiation and is involved in regulating inflammation and complement activation. It also plays a role in angiogenesis and tissue remodeling. The protein serves as a biomarker for several inflammatory conditions. [provided by RefSeq, Jun 2016]
- TNFAIP5
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.8 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 PTX3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002852.4. 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 | 11 | 11 | ||||
| missense | 61 | 6 | 1 | 68 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 61 | 17 | 1 | 79 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002843.2 | 3 | MANE Select | |
| Ensembl | ENSP00000295927.3 | 3 | MANE Select | |
| Ensembl | ENSP00000640445.1 | 2 | Standard | |
| Ensembl | ENSP00000640445.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Human Complement System
- Lung fibrosis
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- ovarian cumulus expansion
- response to yeast
- inflammatory response
- opsonization
- extracellular matrix organization
Molecular Function
- complement component C1q binding
- (1->3)-beta-D-glucan binding
- protein binding
- identical protein binding
- virion binding
Cellular Component
- extracellular region
- extracellular space
- extracellular matrix
- specific granule lumen
- tertiary granule lumen
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000295927
- Coding exons
- 3
- Length
- 6840
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 23
- Defined
- 125748
- p
- 0.0000915
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0494 | 190 | 188 | 1.01 | 0.00000911 | 2424 |
| Missense (PolyPhen) | 58 | 63.304 | 0.91622 | 819 | ||
| Synonymous | 0.525 | 72 | 77.9 | 0.924 | 0.00000393 | 785 |
| Loss of Function | 1.07 | 8 | 12.0 | 0.667 | 5.90e-7 | 141 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000088 | 0.000088 | rare |
| South Asian | 0.00025 | 0.00023 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the regulation of innate resistance to pathogens, inflammatory reactions, possibly clearance of self- components and female fertility. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.134
Intolerance Scores
- LoFtool
- 0.612
- RVIS EVS
- 1.04
- RVIS percentile EVS
- 91.21
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0942
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |