SLPI
secretory leukocyte peptidase inhibitor, the group of WAP four-disulfide core domain containing
Basic information
Region (hg38): 20:45252239-45254564
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Otitis media, susceptibility to (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLPI 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 1 | 0 | 8 | 0 | 0 |
Variants in SLPI
This is a list of pathogenic ClinVar variants found in the SLPI region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-45253001-C-A | Otitis media, susceptibility to | Pathogenic (Jul 14, 2023) | ||
| 20-45253033-C-A | not specified | Uncertain significance (Dec 25, 2024) | ||
| 20-45253040-A-G | not specified | Uncertain significance (Jun 09, 2022) | ||
| 20-45253041-T-C | not specified | Uncertain significance (Jan 09, 2024) | ||
| 20-45253070-C-A | not specified | Uncertain significance (Dec 03, 2024) | ||
| 20-45253091-G-C | not specified | Uncertain significance (Nov 22, 2022) | ||
| 20-45253091-G-T | not specified | Uncertain significance (Jan 24, 2025) | ||
| 20-45253110-A-G | not specified | Uncertain significance (Feb 22, 2025) | ||
| 20-45253599-C-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 20-45254192-G-A | Type 2 diabetes mellitus | Benign (-) | ||
| 20-45254495-T-G | not specified | Uncertain significance (Mar 25, 2024) | ||
| 20-45254500-A-T | not specified | Uncertain significance (Feb 12, 2025) | ||
| 20-45254532-G-T | not specified | Uncertain significance (Jan 23, 2024) | ||
| 20-45254533-C-T | not specified | Uncertain significance (Apr 28, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLPI | protein_coding | protein_coding | ENST00000338380 | 4 | 2326 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000897 | 0.584 | 125641 | 0 | 93 | 125734 | 0.000370 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.0423 | 71 | 72.0 | 0.986 | 0.00000343 | 865 |
| Missense in Polyphen | 25 | 22.805 | 1.0963 | 295 | ||
| Synonymous | -1.08 | 32 | 25.1 | 1.27 | 0.00000125 | 241 |
| Loss of Function | 0.471 | 5 | 6.27 | 0.797 | 2.63e-7 | 83 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000500 | 0.000499 |
| Ashkenazi Jewish | 0.00556 | 0.00557 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.000115 | 0.000114 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000131 | 0.000131 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Acid-stable proteinase inhibitor with strong affinities for trypsin, chymotrypsin, elastase, and cathepsin G (PubMed:3533531, PubMed:3462719, PubMed:2039600, PubMed:2110563, PubMed:10702419, PubMed:24121345). Modulates the inflammatory and immune responses after bacterial infection, and after infection by the intracellular parasite L.major. Down-regulates responses to bacterial lipopolysaccharide (LPS) (By similarity). Plays a role in regulating the activation of NF-kappa-B and inflammatory responses (PubMed:10702419, PubMed:24352879). Has antimicrobial activity against mycobacteria, but not against salmonella. Contributes to normal resistance against infection by M.tuberculosis. Required for normal resistance to infection by L.major. Required for normal wound healing, probably by preventing tissue damage by limiting protease activity (By similarity). Together with ELANE, required for normal differentiation and proliferation of bone marrow myeloid cells (PubMed:24352879). {ECO:0000250|UniProtKB:P97430, ECO:0000269|PubMed:10702419, ECO:0000269|PubMed:2039600, ECO:0000269|PubMed:2110563, ECO:0000269|PubMed:24121345, ECO:0000269|PubMed:24352879, ECO:0000269|PubMed:3462719, ECO:0000269|PubMed:3533531, ECO:0000305}.;
- Pathway
- Neutrophil degranulation;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.411
Intolerance Scores
- loftool
- 0.587
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.0743
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.438
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.752
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slpi
- Phenotype
- homeostasis/metabolism 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; immune system phenotype;
Gene ontology
- Biological process
- immune response;negative regulation of endopeptidase activity;antibacterial humoral response;negative regulation of protein binding;response to lipopolysaccharide;modification of morphology or physiology of other organism;neutrophil degranulation;negative regulation of viral genome replication;innate immune response
- Cellular component
- extracellular region;extracellular space;specific granule lumen;collagen-containing extracellular matrix;extracellular exosome
- Molecular function
- DNA binding;mRNA binding;endopeptidase inhibitor activity;serine-type endopeptidase inhibitor activity;protein binding;enzyme binding