TLE3
TLE family member 3, transcriptional corepressor, the group of WD repeat domain containing|Wnt enhanceosome complex|TLE family|MicroRNA protein coding host genes
Basic information
Region (hg38): 15:70047790-70098176
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLE3 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 | 6 | |||||
| missense | 39 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 39 | 1 | 5 |
Variants in TLE3
This is a list of pathogenic ClinVar variants found in the TLE3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-70050164-G-A | not specified | Uncertain significance (Dec 06, 2022) | ||
| 15-70050190-C-T | Benign (Apr 04, 2018) | |||
| 15-70051426-C-T | not specified | Uncertain significance (Nov 27, 2024) | ||
| 15-70051456-C-T | not specified | Uncertain significance (Nov 05, 2021) | ||
| 15-70052403-C-T | TLE3-related condition | Uncertain significance (Jul 16, 2024) | ||
| 15-70053282-C-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| 15-70053353-A-G | Benign (Apr 04, 2018) | |||
| 15-70053356-T-C | Benign (Apr 04, 2018) | |||
| 15-70054475-T-C | not specified | Uncertain significance (Sep 16, 2021) | ||
| 15-70054512-G-A | Benign (May 21, 2018) | |||
| 15-70054603-G-C | not specified | Uncertain significance (Sep 21, 2021) | ||
| 15-70054666-C-T | not specified • TLE3-related condition | Uncertain significance (Oct 04, 2022) | ||
| 15-70054667-G-T | not specified | Uncertain significance (Dec 05, 2022) | ||
| 15-70055159-T-C | not specified | Uncertain significance (May 16, 2024) | ||
| 15-70056320-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 15-70056352-G-T | not specified | Uncertain significance (Mar 20, 2024) | ||
| 15-70057530-G-T | not specified | Uncertain significance (Nov 11, 2024) | ||
| 15-70057599-T-C | not specified | Uncertain significance (Nov 14, 2024) | ||
| 15-70057640-G-A | not specified | Uncertain significance (Feb 02, 2024) | ||
| 15-70057655-G-A | not specified | Uncertain significance (May 31, 2023) | ||
| 15-70058156-T-C | not specified | Uncertain significance (Jan 07, 2022) | ||
| 15-70058194-G-A | not specified | Uncertain significance (May 04, 2023) | ||
| 15-70058212-G-A | not specified | Uncertain significance (Aug 01, 2024) | ||
| 15-70058237-C-T | not specified | Uncertain significance (Dec 30, 2023) | ||
| 15-70058289-G-A | Likely benign (Feb 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TLE3 | protein_coding | protein_coding | ENST00000558939 | 20 | 50387 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 4.35e-7 | 122336 | 0 | 1 | 122337 | 0.00000409 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.72 | 246 | 474 | 0.519 | 0.0000287 | 5030 |
| Missense in Polyphen | 78 | 239.06 | 0.32628 | 2635 | ||
| Synonymous | -1.08 | 225 | 205 | 1.10 | 0.0000150 | 1496 |
| Loss of Function | 5.91 | 0 | 40.7 | 0.00 | 0.00000219 | 445 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000912 | 0.00000912 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional corepressor that binds to a number of transcription factors. Inhibits the transcriptional activation mediated by CTNNB1 and TCF family members in Wnt signaling. The effects of full-length TLE family members may be modulated by association with dominant-negative AES (By similarity). {ECO:0000250}.;
- Pathway
- White fat cell differentiation;White fat cell differentiation;Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;Repression of WNT target genes;Notch;Signaling by NOTCH1;Signaling by NOTCH;TGF-beta super family signaling pathway canonical;Deactivation of the beta-catenin transactivating complex;Wnt Canonical;Formation of the beta-catenin:TCF transactivating complex;TCF dependent signaling in response to WNT;Wnt Mammals;NOTCH1 Intracellular Domain Regulates Transcription
(Consensus)
Recessive Scores
- pRec
- 0.148
Intolerance Scores
- loftool
- 0.864
- rvis_EVS
- -1.02
- rvis_percentile_EVS
- 8
Haploinsufficiency Scores
- pHI
- 0.670
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.593
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.976
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tle3
- Phenotype
- embryo 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); cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- tle3a
- Affected structure
- neural tube
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;signal transduction;animal organ morphogenesis;Wnt signaling pathway;negative regulation of canonical Wnt signaling pathway;negative regulation of cold-induced thermogenesis;negative regulation of nucleic acid-templated transcription;beta-catenin-TCF complex assembly
- Cellular component
- nucleus;nucleoplasm;transcription factor complex;beta-catenin-TCF complex
- Molecular function
- transcription corepressor activity;protein binding;repressing transcription factor binding