HOXA3
homeobox A3, the group of HOXL subclass homeoboxes
Basic information
Region (hg38): 7:27106184-27152583
Previous symbols: [ "HOX1E", "HOX1" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (186 variants)
- not_provided (6 variants)
- HOXA4-related_disorder (6 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000153631.3. 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 | 1 | |||||
| missense | 63 | 66 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 63 | 4 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HOXA3 | protein_coding | protein_coding | ENST00000396352 | 2 | 46398 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.945 | 0.0555 | 125742 | 0 | 4 | 125746 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.281 | 264 | 277 | 0.952 | 0.0000167 | 2811 |
| Missense in Polyphen | 42 | 43.474 | 0.96609 | 389 | ||
| Synonymous | 0.0521 | 134 | 135 | 0.994 | 0.00000947 | 963 |
| Loss of Function | 3.16 | 1 | 13.5 | 0.0739 | 6.74e-7 | 141 |
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) | 0.0000365 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.;
- Pathway
- Activation of anterior HOX genes in hindbrain development during early embryogenesis
(Consensus)
Recessive Scores
- pRec
- 0.129
Intolerance Scores
- loftool
- 0.179
- rvis_EVS
- -0.01
- rvis_percentile_EVS
- 53.51
Haploinsufficiency Scores
- pHI
- 0.563
- hipred
- Y
- hipred_score
- 0.785
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.414
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hoxa3
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; muscle phenotype; craniofacial 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); 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); hematopoietic system phenotype; embryo phenotype; respiratory system phenotype; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail 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); digestive/alimentary phenotype;
Gene ontology
- Biological process
- angiogenesis;blood vessel remodeling;calcium ion transport;positive regulation of cell population proliferation;anterior/posterior pattern specification;specification of animal organ position;gene expression;magnesium ion homeostasis;glossopharyngeal nerve morphogenesis;bone mineralization;thyroid gland development;positive regulation of transcription by RNA polymerase II;thymus development;animal organ formation;embryonic skeletal system morphogenesis;cartilage development;negative regulation of calcium ion transport;phosphate ion homeostasis;calcium ion homeostasis;parathyroid gland development;positive regulation of receptor binding
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;HMG box domain binding