TSLP
Basic information
Region (hg38): 5:111070062-111078026
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSLP gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033035.5. 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 | 0 | |||||
| missense | 21 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 21 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TSLP | protein_coding | protein_coding | ENST00000344895 | 4 | 7963 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00404 | 0.668 | 125735 | 0 | 12 | 125747 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.491 | 100 | 87.1 | 1.15 | 0.00000423 | 1038 |
| Missense in Polyphen | 28 | 22.662 | 1.2355 | 282 | ||
| Synonymous | -1.68 | 45 | 32.8 | 1.37 | 0.00000159 | 294 |
| Loss of Function | 0.602 | 4 | 5.53 | 0.724 | 2.32e-7 | 69 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000547 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000882 | 0.0000879 |
| Middle Eastern | 0.0000547 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Isoform 1: Cytokine that induces the release of T-cell- attracting chemokines from monocytes and, in particular, enhances the maturation of CD11c(+) dendritic cells. Can induce allergic inflammation by directly activating mast cells. {ECO:0000269|PubMed:11418668, ECO:0000269|PubMed:11480573, ECO:0000269|PubMed:17242164}.;
- Pathway
- Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway;Development and heterogeneity of the ILC family
(Consensus)
Recessive Scores
- pRec
- 0.0705
Intolerance Scores
- loftool
- 0.373
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.141
- hipred
- N
- hipred_score
- 0.221
- ghis
- 0.450
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tslp
- Phenotype
- immune system 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; respiratory system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- positive regulation of cytokine-mediated signaling pathway;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of chemokine production;positive regulation of interleukin-10 production;positive regulation of interleukin-13 production;positive regulation of interleukin-5 production;positive regulation of interleukin-6 production;positive regulation of mast cell activation;interleukin-7-mediated signaling pathway;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of apoptotic process;positive regulation of inflammatory response;positive regulation of chemokine (C-C motif) ligand 1 production;positive regulation of granulocyte colony-stimulating factor production;positive regulation of STAT cascade;positive regulation of interleukin-5 secretion
- Cellular component
- extracellular region;extracellular space
- Molecular function
- cytokine activity;interleukin-7 receptor binding