TLX3
Basic information
Region (hg38): 5:171309247-171312139
Previous symbols: [ "HOX11L2" ]
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 TLX3 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in TLX3
This is a list of pathogenic ClinVar variants found in the TLX3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-171309462-C-T | not specified | Uncertain significance (Apr 22, 2022) | ||
| 5-171309468-C-A | not specified | Uncertain significance (May 13, 2024) | ||
| 5-171309522-G-A | not specified | Uncertain significance (Jul 25, 2023) | ||
| 5-171309553-T-C | not specified | Uncertain significance (Nov 10, 2022) | ||
| 5-171309564-G-C | not specified | Uncertain significance (Oct 17, 2023) | ||
| 5-171309715-T-C | not specified | Uncertain significance (May 01, 2022) | ||
| 5-171309762-C-T | not specified | Uncertain significance (Jul 14, 2021) | ||
| 5-171310152-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 5-171310299-C-A | not specified | Uncertain significance (Mar 28, 2024) | ||
| 5-171311418-A-G | Hereditary breast ovarian cancer syndrome | Uncertain significance (Aug 01, 2020) | ||
| 5-171311450-C-A | not specified | Uncertain significance (Mar 29, 2022) | ||
| 5-171311576-C-T | not specified | Uncertain significance (Jul 21, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TLX3 | protein_coding | protein_coding | ENST00000296921 | 3 | 2851 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.260 | 0.716 | 122477 | 0 | 1 | 122478 | 0.00000408 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.40 | 119 | 170 | 0.698 | 0.00000777 | 1842 |
| Missense in Polyphen | 20 | 34.404 | 0.58132 | 369 | ||
| Synonymous | -0.941 | 85 | 74.7 | 1.14 | 0.00000353 | 609 |
| Loss of Function | 1.90 | 2 | 7.66 | 0.261 | 3.29e-7 | 82 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000640 | 0.0000640 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Pathway
- Transcriptional misregulation in cancer - Homo sapiens (human);Cell Differentiation - Index expanded;Cell Differentiation - Index;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways
(Consensus)
Recessive Scores
- pRec
- 0.163
Intolerance Scores
- loftool
- 0.0391
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.2
Haploinsufficiency Scores
- pHI
- 0.690
- hipred
- Y
- hipred_score
- 0.665
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.974
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tlx3
- Phenotype
- homeostasis/metabolism phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); 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); neoplasm;
Gene ontology
- Biological process
- neuron migration;regulation of respiratory gaseous exchange by neurological system process;regulation of transcription by RNA polymerase II;central nervous system development;respiratory gaseous exchange;negative regulation of neuron differentiation;neuron fate specification
- Cellular component
- nucleoplasm
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding