HOXA11
homeobox A11, the group of HOXL subclass homeoboxes
Basic information
Region (hg38): 7:27181157-27185232
Previous symbols: [ "HOX1I", "HOX1" ]
Links
Phenotypes
GenCC
Source:
- radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (Limited), mode of inheritance: AD
- radio-ulnar synostosis-amegakaryocytic thrombocytopenia syndrome (Supportive), mode of inheritance: AD
- radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (Strong), mode of inheritance: AD
- radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (Limited), mode of inheritance: AD
- radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Radioulnar synostosis with amegakaryocytic thrombocytopenia 1 | AD | Hematologic | Individuals can have symptomatic thrombocytopenia and bone marrow failure manifesting in the neonatal period, requiring early bone marrow/umbilical cord stem cell transplantation | Hematologic; Musculoskeletal | 11101832; 11442476; 16765069; 20562651 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (44 variants)
- HOXA11-related_disorder (17 variants)
- Radioulnar_synostosis_with_amegakaryocytic_thrombocytopenia_1 (10 variants)
- not_provided (9 variants)
- Thrombocytopenia (1 variants)
- Abnormal_bleeding (1 variants)
- Mesomelic_dysplasia_with_urogenital_abnormalities (1 variants)
- Inherited_genitourinary_tract_anomalies (1 variants)
- Flexion_contracture (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOXA11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005523.6. 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 | 4 | |||||
| missense | 56 | 63 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 2 | 57 | 8 | 1 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HOXA11 | protein_coding | protein_coding | ENST00000006015 | 2 | 3714 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.943 | 0.0564 | 124889 | 0 | 1 | 124890 | 0.00000400 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.668 | 144 | 168 | 0.855 | 0.00000846 | 2012 |
| Missense in Polyphen | 41 | 69.611 | 0.58899 | 829 | ||
| Synonymous | -2.06 | 96 | 73.5 | 1.31 | 0.00000368 | 648 |
| Loss of Function | 2.79 | 0 | 9.08 | 0.00 | 4.44e-7 | 110 |
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) | 0.00000889 | 0.00000889 |
| 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.;
- Disease
- DISEASE: Radioulnar synostosis with amegakaryocytic thrombocytopenia 1 (RUSAT1) [MIM:605432]: The syndrome consists of an unusual association of bone marrow failure and skeletal defects. Patients have the same skeletal defects, the proximal fusion of the radius and ulna, resulting in extremely limited pronation and supination of the forearm. Some patients have also symptomatic thrombocytopenia, with bruising and bleeding problems since birth, necessitating correction by bone marrow or umbilical- cord stem-cell transplantation. {ECO:0000269|PubMed:11101832}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Transcriptional misregulation in cancer - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.230
Intolerance Scores
- loftool
- 0.216
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.63
Haploinsufficiency Scores
- pHI
- 0.375
- hipred
- Y
- hipred_score
- 0.837
- ghis
- 0.567
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.996
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hoxa11
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; limbs/digits/tail phenotype; skeleton phenotype; renal/urinary system phenotype; reproductive 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);
Gene ontology
- Biological process
- skeletal system development;metanephros development;branching involved in ureteric bud morphogenesis;organ induction;regulation of transcription by RNA polymerase II;multicellular organism development;spermatogenesis;single fertilization;mesodermal cell fate specification;male gonad development;anatomical structure morphogenesis;anterior/posterior pattern specification;dorsal/ventral pattern formation;proximal/distal pattern formation;positive regulation of cell development;embryonic limb morphogenesis;positive regulation of chondrocyte differentiation;embryonic forelimb morphogenesis;embryonic digit morphogenesis;positive regulation of transcription, DNA-templated;developmental growth;uterus development;embryonic skeletal joint morphogenesis;cartilage development involved in endochondral bone morphogenesis
- Cellular component
- nucleoplasm;transcription factor complex;protein-containing complex;protein-DNA complex
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding