ENPP3
ectonucleotide pyrophosphatase/phosphodiesterase 3, the group of CD molecules|Ectonucleotide pyrophosphatase/phosphodiesterase family
Basic information
Region (hg38): 6:131628442-131747418
Previous symbols: [ "PDNP3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (234 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENPP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005021.5. 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 | 1 | |||||
| missense | 101 | 108 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 101 | 6 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ENPP3 | protein_coding | protein_coding | ENST00000414305 | 25 | 118972 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.47e-23 | 0.0532 | 125073 | 1 | 672 | 125746 | 0.00268 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0744 | 463 | 468 | 0.990 | 0.0000229 | 5805 |
| Missense in Polyphen | 175 | 192.54 | 0.90889 | 2439 | ||
| Synonymous | -0.491 | 169 | 161 | 1.05 | 0.00000805 | 1557 |
| Loss of Function | 1.40 | 41 | 51.9 | 0.790 | 0.00000260 | 647 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00482 | 0.00482 |
| Ashkenazi Jewish | 0.000697 | 0.000695 |
| East Asian | 0.00158 | 0.00152 |
| Finnish | 0.00208 | 0.00208 |
| European (Non-Finnish) | 0.00278 | 0.00277 |
| Middle Eastern | 0.00158 | 0.00152 |
| South Asian | 0.00504 | 0.00494 |
| Other | 0.00261 | 0.00261 |
dbNSFP
Source:
- Function
- FUNCTION: Hydrolase that metabolizes extracellular nucleotides, including ATP, GTP, UTP and CTP (PubMed:29717535). Limits mast cell and basophil responses during inflammation and during the chronic phases of allergic responses by eliminating the extracellular ATP that functions as signaling molecule and activates basophils and mast cells and induces the release of inflammatory cytokines. Metabolizes extracellular ATP in the lumen of the small intestine, and thereby prevents ATP-induced apoptosis of intestinal plasmacytoid dendritic cells (By similarity). Has also alkaline phosphodiesterase activity (PubMed:11342463). {ECO:0000250|UniProtKB:Q6DYE8, ECO:0000269|PubMed:11342463, ECO:0000269|PubMed:29717535}.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Starch and sucrose metabolism - Homo sapiens (human);Pantothenate and CoA biosynthesis - Homo sapiens (human);Riboflavin metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);IL-3 Signaling Pathway;Pathways in clear cell renal cell carcinoma;Pyrimidine metabolism;Vitamin B2 (riboflavin) metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Vitamin B5 - CoA biosynthesis from pantothenate;Nicotinate Nicotinamide metabolism;Pyrimidine metabolism
(Consensus)
Recessive Scores
- pRec
- 0.423
Intolerance Scores
- loftool
- 0.935
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 75.68
Haploinsufficiency Scores
- pHI
- 0.130
- hipred
- N
- hipred_score
- 0.254
- ghis
- 0.379
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.599
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Enpp3
- Phenotype
- digestive/alimentary phenotype; immune system phenotype; respiratory system phenotype; hematopoietic system 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); growth/size/body region phenotype;
Gene ontology
- Biological process
- basophil activation involved in immune response;pyrimidine nucleotide metabolic process;phosphate-containing compound metabolic process;receptor-mediated endocytosis;nucleoside triphosphate catabolic process;inorganic diphosphate transport;negative regulation of mast cell activation involved in immune response;ATP metabolic process;negative regulation of inflammatory response;negative regulation of mast cell proliferation;nucleic acid phosphodiester bond hydrolysis
- Cellular component
- external side of plasma membrane;integral component of membrane;apical plasma membrane;perinuclear region of cytoplasm;extracellular exosome
- Molecular function
- nucleic acid binding;phosphodiesterase I activity;scavenger receptor activity;calcium ion binding;zinc ion binding;polysaccharide binding;NADH pyrophosphatase activity;nucleoside-triphosphate diphosphatase activity