HOXB4
homeobox B4, the group of HOXL subclass homeoboxes
Basic information
Region (hg38): 17:48575506-48578350
Previous symbols: [ "HOX2", "HOX2F" ]
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 HOXB4 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 | 20 | 20 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 20 | 0 | 0 |
Variants in HOXB4
This is a list of pathogenic ClinVar variants found in the HOXB4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-48576730-C-A | not specified | Uncertain significance (Apr 19, 2024) | ||
| 17-48576736-G-C | not specified | Uncertain significance (Jun 07, 2023) | ||
| 17-48576745-T-C | not specified | Uncertain significance (Mar 20, 2023) | ||
| 17-48576750-C-G | not specified | Uncertain significance (May 30, 2024) | ||
| 17-48576750-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 17-48576751-G-A | not specified | Uncertain significance (Sep 28, 2022) | ||
| 17-48576817-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 17-48577865-G-A | not specified | Uncertain significance (Jun 29, 2022) | ||
| 17-48577917-C-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 17-48577920-A-T | not specified | Uncertain significance (Dec 09, 2023) | ||
| 17-48577928-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
| 17-48578016-G-A | not specified | Uncertain significance (Jan 04, 2024) | ||
| 17-48578030-G-A | not specified | Uncertain significance (Jun 30, 2023) | ||
| 17-48578043-C-G | not specified | Uncertain significance (Jul 12, 2022) | ||
| 17-48578072-G-A | not specified | Uncertain significance (May 30, 2024) | ||
| 17-48578115-G-A | not specified | Uncertain significance (Jun 29, 2022) | ||
| 17-48578120-G-A | not specified | Uncertain significance (May 06, 2022) | ||
| 17-48578136-C-T | not specified | Uncertain significance (Jul 05, 2023) | ||
| 17-48578144-G-A | not specified | Uncertain significance (Mar 16, 2022) | ||
| 17-48578277-G-A | not specified | Uncertain significance (Dec 23, 2022) | ||
| 17-48578295-T-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 17-48578296-G-C | not specified | Uncertain significance (Jan 11, 2023) | ||
| 17-48578298-T-A | not specified | Uncertain significance (Aug 11, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HOXB4 | protein_coding | protein_coding | ENST00000332503 | 2 | 4599 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0598 | 0.875 | 125738 | 0 | 8 | 125746 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.550 | 106 | 123 | 0.861 | 0.00000557 | 1591 |
| Missense in Polyphen | 32 | 52.321 | 0.61161 | 598 | ||
| Synonymous | 0.161 | 52 | 53.5 | 0.972 | 0.00000242 | 534 |
| Loss of Function | 1.55 | 3 | 7.60 | 0.395 | 3.23e-7 | 90 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000181 | 0.000181 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000179 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.000163 | 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.;
- Pathway
- Activation of anterior HOX genes in hindbrain development during early embryogenesis
(Consensus)
Recessive Scores
- pRec
- 0.252
Intolerance Scores
- loftool
- 0.392
- rvis_EVS
- 0.3
- rvis_percentile_EVS
- 72.01
Haploinsufficiency Scores
- pHI
- 0.358
- hipred
- N
- hipred_score
- 0.272
- ghis
- 0.437
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.824
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hoxb4
- Phenotype
- immune system phenotype; skeleton phenotype; respiratory system 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); hematopoietic system 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); normal phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;skeletal system development;morphogenesis of an epithelial sheet;cell population proliferation;anterior/posterior pattern specification;positive regulation of transcription by RNA polymerase II;somatic stem cell division;spleen development;bone marrow development;embryonic skeletal system morphogenesis;definitive hemopoiesis;hematopoietic stem cell differentiation;positive regulation of stem cell differentiation
- Cellular component
- nucleus;centrosome
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;activating transcription factor binding