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10 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
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HMX3
H6 family homeobox 3
Chromosome 10 · 10q26.13
NCBI Gene: 340784Ensembl: ENSG00000188620.11HGNC: HGNC:5019UniProt: A6NHT5
14PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA polymerase II transcription regulatory region sequence-specific DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specificregulation of transcription by RNA polymerase IInucleusneurodegenerative diseaseliver diseaserheumatic diseaseplacental retention
✦AI Summary

HMX3 is a transcription factor of the H6 family that functions as a sequence-specific DNA-binding regulator of RNA polymerase II transcription 1. Developmentally, HMX3 is essential for inner ear morphogenesis, particularly controlling semicircular canal formation, and is required for hypothalamic-pituitary axis development 2. The gene is expressed in vestibular tissues and knockout mouse models demonstrate its necessity for normal vestibular function 2. Mechanistically, HMX3 establishes cell identity through mutually repressive interactions with other transcription factors. In kidney collecting ducts, HMX3 and HMX2 antagonistically regulate intercalated cell subtype specification; HMX3 promotes type B intercalated cell differentiation while being suppressed by Dmrt2, which instead promotes type A cell fate 3, 4. Post-translationally, USP38 directly interacts with HMX3 to stabilize its protein levels via deubiquitination 5. Clinically, HMX3 dysregulation is implicated in multiple disease contexts. In pediatric acute myelomonocytic leukemia with KMT2A::MLLT3 fusion lacking MECOM expression, HMX3 functions as a leukemia-specific vulnerability by driving cancer-associated E2F and MYC programs; HMX3 silencing induces cell cycle arrest and apoptosis 1. In colorectal cancer, HMX3 is significantly downregulated and acts as a tumor suppressor; overexpression suppresses proliferation, migration, and invasion while correlating with improved patient survival 5. Rare HMX3 variants associate with non-syndromic vestibular dysfunction and potentially superior semicircular canal dehiscence 2, 6.

Sources cited
1
HMX3 is a transcription factor of the H6 family that functions as a sequence-specific DNA-binding regulator of RNA polymerase II transcription .
PMID: 39633068
2
Developmentally, HMX3 is essential for inner ear morphogenesis, particularly controlling semicircular canal formation, and is required for hypothalamic-pituitary axis development .
PMID: 37107589
3
In kidney collecting ducts, HMX3 and HMX2 antagonistically regulate intercalated cell subtype specification; HMX3 promotes type B intercalated cell differentiation while being suppressed by Dmrt2, which instead promotes type A cell fate , .
PMID: 40354537
4
In kidney collecting ducts, HMX3 and HMX2 antagonistically regulate intercalated cell subtype specification; HMX3 promotes type B intercalated cell differentiation while being suppressed by Dmrt2, which instead promotes type A cell fate , .
PMID: 41051882
5
Post-translationally, USP38 directly interacts with HMX3 to stabilize its protein levels via deubiquitination .
PMID: 36204976
6
Rare HMX3 variants associate with non-syndromic vestibular dysfunction and potentially superior semicircular canal dehiscence , .
PMID: 22779713
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.48Moderate
liver diseaseOpen Targets
0.34Weak
rheumatic diseaseOpen Targets
0.22Weak
placental retentionOpen Targets
0.13Weak
diverticular diseaseOpen Targets
0.12Weak
premature birthOpen Targets
0.12Weak
alcohol drinkingOpen Targets
0.11Weak
thyroid cancerOpen Targets
0.10Suggestive
hearing loss, autosomal recessiveOpen Targets
0.09Suggestive
hearing loss, autosomal dominant 87Open Targets
0.08Suggestive
hearing loss, autosomal dominant 80Open Targets
0.08Suggestive
insomniaOpen Targets
0.08Suggestive
hearing loss, autosomal dominant 85Open Targets
0.07Suggestive
hearing loss, autosomal dominant 75Open Targets
0.07Suggestive
X-linked nonsyndromic hearing lossOpen Targets
0.07Suggestive
deafnessOpen Targets
0.07Suggestive
autosomal dominant nonsyndromic hearing lossOpen Targets
0.07Suggestive
hearing loss, autosomal dominant 86Open Targets
0.07Suggestive
autosomal recessive nonsyndromic hearing loss 4Open Targets
0.07Suggestive
hearing loss, autosomal dominant 77Open Targets
0.06Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
HINFPProtein interaction78%PPP1R21Protein interaction78%WNT7AProtein interaction75%HMX2Co-mentioned in literature40%DMRT2Co-mentioned in literature20%SHROOM2Shared pathway8%
Tissue Expression6 tissues
Brain
100%
Heart
0%
Ovary
0%
Bone Marrow
0%
Liver
0%
Lung
0%
Gene Interaction Network
Click a node to explore
HMX3HINFPPPP1R21WNT7AHMX2DMRT2SHROOM2
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt A6NHT5
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
1.08LoF Tolerant
pLIⓘ
0.02Tolerant
Observed/Expected LoF0.60 [0.35–1.08]
RankingsWhere HMX3 stands among ~20K protein-coding genes
  • #15,890of 20,598
    Most Researched14
  • #10,906of 17,882
    Most Constrained (LOEUF)1.08
Genes detectedHMX3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
HMX3 is a critical vulnerability in MECOM-negative KMT2A::MLLT3 acute myelomonocytic leukemia.
PMID: 39633068
Leukemia · 2025
1.00
2
USP38 inhibits colorectal cancer cell proliferation and migration via downregulating HMX3 ubiquitylation.
PMID: 36204976
Cell Cycle · 2023
0.90
3
Gene homologs on human chromosome 15q21-q26 and a chicken microchromosome identify a new conserved segment.
PMID: 9166590
Mamm Genome · 1997
0.80
4
Rare Coding Variants in Patients with Non-Syndromic Vestibular Dysfunction.
PMID: 37107589
Genes (Basel) · 2023
0.70
5
Dmrt2 and Hmx2 direct intercalated cell diversity in the mammalian kidney through antagonistic and supporting regulatory processes.
PMID: 40354537
Proc Natl Acad Sci U S A · 2025
0.60