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

ENSG00000140332NCBI:7090OMIM:600190HGNC:11839Uniprot:Q04726AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TLE3 gene.

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
1
clinvar
5
clinvar
6
missense
39
clinvar
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)2333209
15-70050190-C-T Benign (Apr 04, 2018)788450
15-70051426-C-T not specified Uncertain significance (Nov 27, 2024)3456855
15-70051456-C-T not specified Uncertain significance (Nov 05, 2021)2380095
15-70052403-C-T TLE3-related condition Uncertain significance (Jul 16, 2024)3346974
15-70053282-C-T not specified Uncertain significance (Nov 11, 2024)3456858
15-70053353-A-G Benign (Apr 04, 2018)720142
15-70053356-T-C Benign (Apr 04, 2018)720143
15-70054475-T-C not specified Uncertain significance (Sep 16, 2021)2250068
15-70054512-G-A Benign (May 21, 2018)735181
15-70054603-G-C not specified Uncertain significance (Sep 21, 2021)2248786
15-70054666-C-T not specified • TLE3-related condition Uncertain significance (Oct 04, 2022)2316138
15-70054667-G-T not specified Uncertain significance (Dec 05, 2022)2332730
15-70055159-T-C not specified Uncertain significance (May 16, 2024)3326297
15-70056320-C-T not specified Uncertain significance (Dec 19, 2022)2342035
15-70056352-G-T not specified Uncertain significance (Mar 20, 2024)3326295
15-70057530-G-T not specified Uncertain significance (Nov 11, 2024)3456859
15-70057599-T-C not specified Uncertain significance (Nov 14, 2024)3456860
15-70057640-G-A not specified Uncertain significance (Feb 02, 2024)3177818
15-70057655-G-A not specified Uncertain significance (May 31, 2023)2570545
15-70058156-T-C not specified Uncertain significance (Jan 07, 2022)2270683
15-70058194-G-A not specified Uncertain significance (May 04, 2023)2508970
15-70058212-G-A not specified Uncertain significance (Aug 01, 2024)3456857
15-70058237-C-T not specified Uncertain significance (Dec 30, 2023)3177822
15-70058289-G-A Likely benign (Feb 01, 2023)2645496

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TLE3protein_codingprotein_codingENST00000558939 2050387
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.004.35e-7122336011223370.00000409
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.722464740.5190.00002875030
Missense in Polyphen78239.060.326282635
Synonymous-1.082252051.100.00001501496
Loss of Function5.91040.70.000.00000219445

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000009120.00000912
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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