HOXA5
homeobox A5, the group of HOXL subclass homeoboxes
Basic information
Region (hg38): 7:27141052-27143681
Previous symbols: [ "HOX1C", "HOX1" ]
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 HOXA5 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 | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 1 |
Variants in HOXA5
This is a list of pathogenic ClinVar variants found in the HOXA5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-27141860-G-A | not specified | Uncertain significance (Jul 16, 2021) | ||
| 7-27141866-A-G | not specified | Uncertain significance (Apr 23, 2024) | ||
| 7-27142058-C-G | not specified | Uncertain significance (Aug 23, 2021) | ||
| 7-27143130-C-T | not specified | Uncertain significance (Feb 09, 2022) | ||
| 7-27143180-A-G | not specified | Uncertain significance (Sep 25, 2024) | ||
| 7-27143204-G-A | Uncertain significance (Jun 01, 2024) | |||
| 7-27143268-T-A | not specified | Uncertain significance (Feb 13, 2024) | ||
| 7-27143336-G-A | not specified | Uncertain significance (Oct 24, 2024) | ||
| 7-27143364-C-G | not specified | Uncertain significance (May 24, 2023) | ||
| 7-27143388-C-T | not specified | Uncertain significance (Sep 25, 2024) | ||
| 7-27143448-G-C | not specified | Uncertain significance (Dec 28, 2023) | ||
| 7-27143477-C-T | not specified | Uncertain significance (Oct 16, 2024) | ||
| 7-27143485-G-T | not specified | Uncertain significance (Oct 16, 2024) | ||
| 7-27143527-A-G | Benign (Apr 13, 2018) | |||
| 7-27143563-A-T | not specified | Uncertain significance (Mar 19, 2024) | ||
| 7-27143577-C-G | not specified | Uncertain significance (Aug 21, 2023) | ||
| 7-27143602-G-C | not specified | Uncertain significance (Aug 15, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HOXA5 | protein_coding | protein_coding | ENST00000222726 | 2 | 2617 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00297 | 0.825 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.860 | 136 | 167 | 0.813 | 0.00000863 | 1777 |
| Missense in Polyphen | 39 | 60.651 | 0.64302 | 681 | ||
| Synonymous | -0.0606 | 71 | 70.4 | 1.01 | 0.00000361 | 526 |
| Loss of Function | 1.13 | 5 | 8.55 | 0.585 | 3.66e-7 | 96 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000905 | 0.0000905 |
| Ashkenazi Jewish | 0.000110 | 0.0000992 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000956 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
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. Also binds to its own promoter. Binds specifically to the motif 5'-CYYNATTA[TG]Y-3'.;
- Pathway
- miR-targeted genes in lymphocytes - TarBase
(Consensus)
Recessive Scores
- pRec
- 0.215
Intolerance Scores
- loftool
- rvis_EVS
- -0.27
- rvis_percentile_EVS
- 33.97
Haploinsufficiency Scores
- pHI
- 0.992
- hipred
- Y
- hipred_score
- 0.651
- ghis
- 0.580
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.985
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hoxa5
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype; vision/eye phenotype; craniofacial phenotype; normal 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); reproductive system phenotype; hematopoietic system phenotype; respiratory system phenotype; immune system phenotype; skeleton phenotype; hearing/vestibular/ear phenotype; digestive/alimentary phenotype;
Gene ontology
- Biological process
- respiratory system process;anterior/posterior pattern specification;positive regulation of receptor biosynthetic process;cell migration;negative regulation of angiogenesis;thyroid gland development;regulation of mammary gland epithelial cell proliferation;multicellular organism growth;positive regulation of apoptotic process;positive regulation of myeloid cell differentiation;negative regulation of erythrocyte differentiation;positive regulation of transcription by RNA polymerase II;lung alveolus development;embryonic skeletal system morphogenesis;bronchiole development;epithelial tube branching involved in lung morphogenesis;lung goblet cell differentiation;lung-associated mesenchyme development;trachea cartilage morphogenesis;intestinal epithelial cell maturation;mesenchymal-epithelial cell signaling;mammary gland epithelial cell differentiation;mammary gland alveolus development;cell-cell signaling involved in mammary gland development
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding