TLX1
Basic information
Region (hg38): 10:101131300-101137789
Previous symbols: [ "TCL3", "HOX11" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (39 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005521.4. 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 | 37 | 39 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 37 | 2 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TLX1 | protein_coding | protein_coding | ENST00000370196 | 3 | 8289 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.742 | 0.256 | 123490 | 0 | 2 | 123492 | 0.00000810 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.93 | 85 | 152 | 0.560 | 0.00000709 | 2053 |
| Missense in Polyphen | 19 | 52.994 | 0.35853 | 638 | ||
| Synonymous | 0.560 | 64 | 70.0 | 0.915 | 0.00000342 | 708 |
| Loss of Function | 2.44 | 1 | 8.80 | 0.114 | 3.81e-7 | 110 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000549 | 0.0000546 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000911 | 0.00000910 |
| Middle Eastern | 0.0000549 | 0.0000546 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Controls the genesis of the spleen. Binds to the DNA sequence 5'-GGCGGTAAGTGG-3'.;
- Disease
- DISEASE: Note=A chromosomal aberration involving TLX1 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(10;14)(q24;q11) with TCRD. {ECO:0000269|PubMed:1676542, ECO:0000269|PubMed:1681546, ECO:0000269|PubMed:1717256}.;
- Pathway
- Transcriptional misregulation in cancer - Homo sapiens (human);Cell Differentiation - Index expanded;Cell Differentiation - Index
(Consensus)
Recessive Scores
- pRec
- 0.232
Intolerance Scores
- loftool
- 0.138
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.471
- hipred
- Y
- hipred_score
- 0.736
- ghis
- 0.423
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.891
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tlx1
- Phenotype
- cellular phenotype; hematopoietic system phenotype; 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); immune system phenotype;
Gene ontology
- Biological process
- multicellular organism development;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding