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Human HOXA1 syndromes is characterized by deafness, central hypoventilation, congenital ocular paralysis and developmental retardation. Cardiac anomalies and paralysis of the vocal chords may also be present. Six cases have been reported so far. Transmission is thought to be autosomal recessive.
Features include very common findings: Inner ear hearing loss (sensorineural hearing impairment); and common findings: Central hypoventilation, Delayed gross motor development, and Internal carotid artery hypoplasia. 7 total HPO annotations.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 2 | Seizure, Delayed gross motor development |
Ears | 1 | Inner ear hearing loss (sensorineural hearing impairment) |
Lungs and breathing | 1 | Central hypoventilation |
Muscles | 1 | Delayed gross motor development |
HOXA1-related disorders are characterized by ocular motility disorder (horizontal gaze palsy with or without Duane syndrome), bilateral sensorineural deafness, variable cerebrovascular malformations (predominantly involving the carotid arteries), motor developmental delay, central hypoventilation, and intellectual disability. To date, 34 individuals have been identified with biallelic pathogenic variants in HOXA1 [, , , , , , , ]. Two overlapping phenotypes have been described: Athabascan brain stem dysgenesis syndrome (ABDS) and Bosley-Salih-Alorainy syndrome (BSAS). Table 2. HOXA1-Related Disorders: Frequency of Selected Features by Phenotype Feature | % of Persons w/Feature by Phenotype1 ABDS | BSAS
Horizontal gaze palsy w/ or w/o Duane syndrome | 14/14 | 18/20 |
|---|---|---|
Sensorineural deafness | 13/14 | 19/20 |
Cerebrovascular anomalies involving the carotid artery | 3/3 | 13/13 |
Motor delay | 12/14 | 13/20 |
HOXA1 encodes homeobox A1 (335 aa). Sequence-specific transcription factor. Highest expression in Esophagus Mucosa (3.6 TPM) and Cells Cultured fibroblasts (2.8 TPM).
Human HOXA1 syndromes is associated with mutations in the HOXA1 gene on chromosome 7.
The HOXA1 protein participates in HOXA1 gene is transcribed, Retinoic acid activates HOXA1 chromatin, and Retinoic acid activates HOXB1 chromatin pathways.
HOXA1 is classified as a druggable target (Transcription Factor category) with score 0.0.
No genotype-phenotype correlations have been identified. Central hypoventilation has only been reported in individuals with ABDS, and high altitude is a suspected contributing factor .
Source: GeneReviews — "HOXA1-Related Disorders"
HOXA1-related disorders should be suspected in probands with the following clinical and imaging findings and family history.
Clinical findings
Ocular motility disorder: horizontal gaze palsy with or without Duane syndrome (also referred to as Duane retraction syndrome)
Bilateral sensorineural deafness
Developmental delay
Intellectual disability
Central hypoventilation while awake or asleep requiring supplemental oxygen and/or mechanical ventilatory support
Congenital heart malformations, cerebrovascular malformations
Facial paresis, vocal cord paresis, and swallowing dysfunction leading to recurrent aspiration and pneumonia
Seizure disorder
Neurobehavioral/psychiatric manifestations
Imaging findings
Source: GeneReviews — "HOXA1-Related Disorders"
Athabascan brain stem dysgenesis syndrome (ABDS), most commonly reported in individuals of Navajo and Apache descent, must be distinguished from overlapping disorders with horizontal gaze palsy, sensorineural deafness, and/or central hypoventilation. Of note, the differential diagnosis of central hypoventilation includes congenital central hypoventilation syndrome (CCHS) and other conditions associated with central hypoventilation in early infancy such as primary neuromuscular, pulmonary, or cardiac disease; brain stem lesion; hypoxic ischemic encephalopathy, asphyxia, infarction, and infection; and severe prematurity (see CCHS, Differential Diagnosis). Bosley-Salih-Alorainy syndrome (BSAS), most commonly reported in individuals from Middle Eastern populations, must be distinguished from overlapping disorders with sensorineural deafness, horizontal gaze palsy, and/or carotid artery anomalies Table 3. Genes of Interest in the Differential Diagnosis of HOXA1-Related Disorders
Gene | Disorder | MOI | Features of Disorder |
|---|---|---|---|
Genetic testing for HOXA1 is available. Testing is considered confirmatory for diagnosis.
Biomarker and diagnostic research for human HOXA1 syndromes has been reported in the published literature.
No approved treatments are currently available for human HOXA1 syndromes. The disease remains an area of unmet medical need.
No clinical practice guidelines for HOXA1-related disorders have been published. In the absence of published guidelines, the following recommendations are based on the authors' personal experience managing individuals with this disorder. Evaluations Following Initial Diagnosis To establish the extent of disease and needs in an individual diagnosed with a HOXA1-related disorder, the evaluations summarized (if not performed as part of the evaluation that led to the diagnosis) are recommended. Table 4. HOXA1-Related Disorders: Recommended Evaluations Following Initial Diagnosis
System/Concern | Evaluation | Comment |
|---|---|---|
Auditory | Brain stem auditory evoked response test | To assess for hearing impairment |
Cerebrovascular | Neck brain MR TOF angiogram | To assess for anomaly of carotid artery other arteries Neurologic |
Development | Developmental assessment incl Vineland Adaptive Behavior scale | To incl motor, adaptive, cognitive, speech-language eval; Eval for early intervention/ special education Neurobehavioral/ |
Psychiatric | Neuropsychiatric eval | For persons age 12 mos: screening for concerns incl behavioral issues /or findings suggestive of ASD Respiratory system |
Genetic counseling | By genetics professionals1 |
Source: GeneReviews — "HOXA1-Related Disorders"
It seems prudent to avoid high altitude, especially among individuals with ABDS, based on a few case studies , but this needs further study and confirmation. In addition, practical limitations would make avoiding high altitude challenging. Avoid risk factors leading to stroke (lifestyle and drugs).
Source: GeneReviews — "HOXA1-Related Disorders"
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "HOXA1-Related Disorders"
1 trial found
To monitor existing manifestations, the individual's response to supportive care, and the emergence of new manifestations, the evaluations summarized in are recommended. Table 6. HOXA1-Related Disorders: Recommended Surveillance
System/Concern | Evaluation | Frequency |
|---|---|---|
Ophthalmologic | Ophthalmologic exam | Every 6-12 mos; Assessment of visual acuity ocular alignment; Orthoptic eval (if applicable); Fundoscopic exam |
Cerebrovascular anomalies | Surveillance as recommended by neurologist /or vascular surgeon | Frequency per neurologist /or vascular surgeon Neurodevelopmental |
(in ABDS) | Respiratory eval (pulmonary function tests, sleep studies) | Annually; Assess for signs of central hypoventilation.; Monitor for respiratory manifestations or complications. |
Source: GeneReviews — "HOXA1-Related Disorders"
Phenotype severity distribution: 1 very common feature, 3 common features.
Estimated prevalence: <1 in 1,000,000 (VERY_RARE).
1 clinical trial registered, 1 recruiting. Interventions under study include other interventions. Research is primarily sponsored by academic and government institutions.
3 publications have been identified in PubMed for human HOXA1 syndromes. Research spans Diagnostic / Biomarker (33%), Review / Meta-Analysis (33%), and Basic Science / Preclinical (33%).
Aufderheide K (2026). [PMID: 41870107](https://pubmed.ncbi.nlm.nih.gov/41870107/). *International ophthalmology clinics*. [Review / Meta-Analysis]
Feng Z (2026). [PMID: 41580430](https://pubmed.ncbi.nlm.nih.gov/41580430/). *Nature communications*. [Basic Science / Preclinical]
Hao L (2024). [PMID: 39483475](https://pubmed.ncbi.nlm.nih.gov/39483475/). *Frontiers in immunology*. [Diagnostic / Biomarker]
Data assembled from 8 of 12 sources · Last updated Sep 20, 2026, 9:39 AM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Intellectual disability
13/13 |
3/20 |
Autism spectrum disorder | NA | 3/20 |
Central hypoventilation | 12/14 | 0/20 |
Congenital heart disease | 10/14 | 5/20 |
Facial paresis or twitching | 7/14 | 5/20 |
Seizures | 4/14 | 2/20 Based on , , , , , , ABDS = Athabascan brain stem dysgenesis syndrome; BSAS = Bosley-Salih-Alorainy syndrome; NA = not applicable 1. Ocular motility disorder. |
Source: GeneReviews — "HOXA1-Related Disorders"
AD1 |
Central hypoventilation, restricted eye movements |
Autonomic nervous system dysregulation, Hirschsprung disease |
CHN1 | CHN1-related isolated Duane syndrome | AD | Variable severity of ocular abduction/adduction |
FOXI3 | Craniofacial microsomia 2 (OMIM 620444) | ADAR | Carotid artery anomalies, deafness |
KIF21A | KIF21A-related CFEOM | AD | Variable vertical horizontal eye movements |
MAFB | MAFB-related isolated Duane syndrome | AD | Variable severity of ocular abduction/adduction |
PHOX2A | PHOX2A-related CFEOM | AR | Variable vertical horizontal eye movements |
PLXND1REV3L(unknown in most affected persons)2 | Moebius syndrome2 (OMIM 157900) | Unknown in most; AD in small # of persons2 | Limited ocular abduction facial weakness |
ROBO3 | ROBO3-related horizontal gaze palsy w/progressive scoliosis (OMIM 607313) | AR | Horizontal gaze paralysis |
SALL4 | SALL4-related disorders incl Duane-radial ray syndrome (DRRS) acro-renal-ocular syndrome (AROS) | AD | Duane ocular anomaly |
TUBB3 | TUBB3-related CFEOM | AD | Variable vertical horizontal eye movements |
Source: GeneReviews — "HOXA1-Related Disorders"
To obtain a pedigree inform affected persons their families re nature, MOI, implications of a HOXA1-related disorder to facilitate medical personal decision making Family support
resources | By clinicians, wider care team, family support organizations | Assessment of family social structure to determine need for:; Community or such as Parent to Parent; Social work involvement for parental support; Home nursing referral ASD = autism spectrum disorder; MOI = mode of inheritance; TOF = time-of-flight 1. |
HOXA1-Related Disorders: Treatment of Manifestations Manifestation/Concern | Treatment | Considerations/Other Duane syndrome/ Horizontal gaze palsy |