DLX1
distal-less homeobox 1, the group of NKL subclass homeoboxes and pseudogenes
Basic information
Region (hg38): 2:172084740-172089677
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 DLX1 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in DLX1
This is a list of pathogenic ClinVar variants found in the DLX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-172085780-A-G | not specified | Uncertain significance (Mar 07, 2024) | ||
| 2-172085788-C-G | not specified | Uncertain significance (Dec 20, 2023) | ||
| 2-172085904-G-A | not specified | Uncertain significance (Nov 08, 2021) | ||
| 2-172085961-G-C | not specified | Uncertain significance (Jan 15, 2025) | ||
| 2-172085976-G-T | not specified | Uncertain significance (Jun 28, 2022) | ||
| 2-172088028-G-A | not specified | Uncertain significance (Mar 15, 2024) | ||
| 2-172088064-C-T | not specified | Uncertain significance (Nov 07, 2024) | ||
| 2-172088081-G-A | not specified | Uncertain significance (Jan 18, 2023) | ||
| 2-172088088-C-T | not specified | Uncertain significance (Nov 30, 2022) | ||
| 2-172088100-C-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 2-172088141-C-A | not specified | Uncertain significance (May 01, 2024) | ||
| 2-172088153-T-A | not specified | Uncertain significance (Mar 03, 2025) | ||
| 2-172088172-G-T | not specified | Uncertain significance (Nov 10, 2024) | ||
| 2-172088192-C-T | not specified | Uncertain significance (Dec 02, 2022) | ||
| 2-172088195-A-C | not specified | Uncertain significance (May 13, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DLX1 | protein_coding | protein_coding | ENST00000361725 | 3 | 4938 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.962 | 0.0376 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.82 | 80 | 141 | 0.569 | 0.00000629 | 1640 |
| Missense in Polyphen | 8 | 36.775 | 0.21754 | 474 | ||
| Synonymous | -2.06 | 80 | 59.7 | 1.34 | 0.00000288 | 514 |
| Loss of Function | 2.96 | 0 | 10.2 | 0.00 | 4.39e-7 | 118 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role as a transcriptional activator or repressor (PubMed:14671321). Inhibits several cytokine signaling pathways, such as TGFB1, activin-A/INHBA and BMP4 by interfering with the transcriptional stimulatory activity of transcription factors, such as MSX2, FAST2, SMAD2 and SMAD3 during hematopoietic cell differentiation (PubMed:14671321). Plays a role in terminal differentiation of interneurons, such as amacrine and bipolar cells in the developing retina (By similarity). Likely to play a regulatory role in the development of the ventral forebrain (By similarity). May play a role in craniofacial patterning and morphogenesis and may be involved in the early development of diencephalic subdivisions (By similarity). {ECO:0000250|UniProtKB:Q64317, ECO:0000269|PubMed:14671321}.;
- Pathway
- Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.203
Intolerance Scores
- loftool
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.28
Haploinsufficiency Scores
- pHI
- 0.151
- hipred
- Y
- hipred_score
- 0.875
- ghis
- 0.602
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.955
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Dlx1
- Phenotype
- craniofacial phenotype; growth/size/body region phenotype; digestive/alimentary phenotype; hearing/vestibular/ear 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); skeleton phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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);
Zebrafish Information Network
- Gene name
- dlx1a
- Affected structure
- ceratobranchial cartilage
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;proximal/distal pattern formation;subpallium development;hippocampus development;regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment;cerebral cortex GABAergic interneuron fate commitment;cell differentiation;negative regulation of BMP signaling pathway;odontogenesis of dentin-containing tooth;negative regulation of neuron apoptotic process;positive regulation of cell differentiation;negative regulation of Notch signaling pathway;positive regulation of transcription by RNA polymerase II;negative regulation of photoreceptor cell differentiation;embryonic skeletal system development;negative regulation of oligodendrocyte differentiation;cellular response to transforming growth factor beta stimulus;cellular response to BMP stimulus;positive regulation of amacrine cell differentiation;negative regulation of cellular response to transforming growth factor beta stimulus
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding