TOX3
Basic information
Region (hg38): 16:52436417-52547802
Previous symbols: [ "TNRC9" ]
Links
Phenotypes
GenCC
Source:
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 TOX3 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 | |||||
missense | 27 | 31 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 27 | 2 | 3 |
Variants in TOX3
This is a list of pathogenic ClinVar variants found in the TOX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
16-52439246-T-A | not specified | Uncertain significance (Dec 07, 2021) | ||
16-52439280-G-A | not specified | Uncertain significance (Mar 28, 2023) | ||
16-52439295-G-C | not specified | Uncertain significance (May 20, 2024) | ||
16-52439298-G-A | not specified | Uncertain significance (Jan 23, 2024) | ||
16-52439314-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
16-52439332-A-T | not specified | Uncertain significance (May 23, 2023) | ||
16-52439334-G-C | not specified | Uncertain significance (Mar 13, 2023) | ||
16-52439418-C-T | not specified | Likely benign (Jan 29, 2024) | ||
16-52439419-G-A | Benign (Jul 17, 2018) | |||
16-52439430-T-A | not specified | Uncertain significance (Jun 07, 2023) | ||
16-52439433-T-A | not specified | Uncertain significance (Jun 07, 2023) | ||
16-52439457-T-C | not specified | Uncertain significance (Apr 08, 2024) | ||
16-52439504-G-T | not specified | Uncertain significance (Jan 17, 2023) | ||
16-52439588-C-G | not specified | Uncertain significance (Nov 14, 2023) | ||
16-52439670-G-A | not specified | Uncertain significance (Feb 11, 2022) | ||
16-52439718-G-T | not specified | Uncertain significance (Jan 19, 2024) | ||
16-52439730-G-A | not specified | Uncertain significance (Jun 28, 2023) | ||
16-52439739-T-C | not specified | Uncertain significance (Mar 20, 2023) | ||
16-52439743-C-T | not specified | Uncertain significance (Dec 03, 2024) | ||
16-52439771-G-T | not specified | Uncertain significance (Mar 05, 2024) | ||
16-52439807-G-A | Benign (Dec 31, 2019) | |||
16-52439862-T-C | not specified | Uncertain significance (Jun 16, 2024) | ||
16-52439863-G-A | not specified | Uncertain significance (Dec 03, 2024) | ||
16-52439898-G-A | not specified | Uncertain significance (Sep 29, 2022) | ||
16-52439934-C-T | not specified | Uncertain significance (Dec 04, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TOX3 | protein_coding | protein_coding | ENST00000219746 | 7 | 109798 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000504 | 124686 | 0 | 6 | 124692 | 0.0000241 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.16 | 252 | 310 | 0.814 | 0.0000161 | 3781 |
Missense in Polyphen | 74 | 108.56 | 0.68164 | 1366 | ||
Synonymous | 0.0363 | 122 | 123 | 0.996 | 0.00000703 | 1109 |
Loss of Function | 4.57 | 1 | 26.3 | 0.0381 | 0.00000114 | 277 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000104 | 0.0000935 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000359 | 0.0000354 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional coactivator of the p300/CBP-mediated transcription complex. Activates transactivation through cAMP response element (CRE) sites. Protects against cell death by inducing antiapoptotic and repressing pro-apoptotic transcripts. Stimulates transcription from the estrogen-responsive or BCL-2 promoters. Required for depolarization-induced transcription activation of the C-FOS promoter in neurons. Associates with chromatin to the estrogen-responsive C3 promoter region. {ECO:0000269|PubMed:21172805}.;
- Pathway
- Mesodermal Commitment Pathway;Ectoderm Differentiation
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.33
- rvis_percentile_EVS
- 73.61
Haploinsufficiency Scores
- pHI
- 0.955
- hipred
- Y
- hipred_score
- 0.643
- ghis
- 0.452
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.262
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tox3
- 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); homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- regulation of transcription by RNA polymerase II;apoptotic process;regulation of apoptotic process;negative regulation of neuron apoptotic process;positive regulation of transcription, DNA-templated
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;protein binding;estrogen response element binding;protein homodimerization activity;phosphoprotein binding