HOXD3
Basic information
Region (hg38): 2:176136612-176173102
Previous symbols: [ "HOX4A", "HOX4", "HOX1D" ]
Links
Phenotypes
GenCC
Source:
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 HOXD3 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 | 25 | 26 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 25 | 1 | 1 |
Variants in HOXD3
This is a list of pathogenic ClinVar variants found in the HOXD3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-176151697-G-A | Likely benign (Aug 16, 2018) | |||
2-176151724-G-C | not specified | Uncertain significance (Dec 15, 2023) | ||
2-176151731-G-A | not specified | Uncertain significance (Jul 08, 2022) | ||
2-176151746-G-A | not specified | Uncertain significance (Aug 26, 2024) | ||
2-176151751-G-T | not specified | Uncertain significance (May 23, 2024) | ||
2-176151760-G-C | not specified | Uncertain significance (Nov 11, 2024) | ||
2-176151768-C-T | Benign (Feb 16, 2018) | |||
2-176151776-C-A | not specified | Uncertain significance (Feb 10, 2022) | ||
2-176151793-C-T | not specified | Uncertain significance (Aug 17, 2021) | ||
2-176151808-G-A | not specified | Uncertain significance (May 30, 2022) | ||
2-176151875-A-T | Leukemia, acute lymphoblastic, susceptibility to | Uncertain significance (Apr 01, 2005) | ||
2-176151907-C-A | not specified | Uncertain significance (Sep 01, 2021) | ||
2-176151944-C-A | not specified | Uncertain significance (Jul 12, 2023) | ||
2-176151982-G-C | not specified | Uncertain significance (Sep 22, 2023) | ||
2-176152025-C-T | not specified | Uncertain significance (Mar 15, 2024) | ||
2-176152033-T-C | not specified | Uncertain significance (Feb 28, 2024) | ||
2-176152036-C-A | not specified | Uncertain significance (Aug 21, 2024) | ||
2-176152048-A-G | not specified | Uncertain significance (Dec 03, 2024) | ||
2-176152054-C-A | not specified | Uncertain significance (Aug 26, 2024) | ||
2-176152072-G-T | Benign (Jun 29, 2018) | |||
2-176152722-G-A | not specified | Uncertain significance (Jul 19, 2023) | ||
2-176152725-G-A | not specified | Uncertain significance (May 31, 2023) | ||
2-176152761-G-T | not specified | Uncertain significance (Nov 21, 2022) | ||
2-176152812-A-G | not specified | Uncertain significance (Dec 02, 2024) | ||
2-176152867-C-G | not specified | Uncertain significance (Dec 06, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
HOXD3 | protein_coding | protein_coding | ENST00000468418 | 2 | 36491 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.441 | 0.558 | 125743 | 0 | 4 | 125747 | 0.0000159 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.09 | 207 | 256 | 0.809 | 0.0000125 | 2763 |
Missense in Polyphen | 76 | 78.572 | 0.96726 | 747 | ||
Synonymous | 0.644 | 104 | 113 | 0.923 | 0.00000576 | 908 |
Loss of Function | 2.75 | 3 | 14.1 | 0.212 | 6.69e-7 | 154 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.000102 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00000881 | 0.00000879 |
Middle Eastern | 0.0000544 | 0.0000544 |
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
- 0.205
Intolerance Scores
- loftool
- 0.0697
- rvis_EVS
- 0.11
- rvis_percentile_EVS
- 61.73
Haploinsufficiency Scores
- pHI
- 0.307
- hipred
- Y
- hipred_score
- 0.735
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.976
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hoxd3
- 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; skeleton phenotype; embryo phenotype; respiratory 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); 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; endocrine/exocrine gland phenotype; craniofacial phenotype; cellular phenotype;
Gene ontology
- Biological process
- transcription, DNA-templated;cell-matrix adhesion;Notch signaling pathway;anterior/posterior pattern specification;positive regulation of gene expression;glossopharyngeal nerve morphogenesis;thyroid gland development;positive regulation of neuron differentiation;positive regulation of transcription by RNA polymerase II;embryonic skeletal system morphogenesis;cartilage development
- Cellular component
- nucleus;nucleoplasm;aggresome;nuclear body
- 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;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding