HOXB9
Chr 17homeobox B9
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis
Clinical Summary— HOXB9
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Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.24) despite low pLI — interpret in context.
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Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.76LOEUF
pLI 0.312
Z-score 2.03
OE 0.24 (0.10–0.76)
Typical tolerance to LoF variation
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.29Z-score
OE missense 0.93 (0.81–1.08)
131 obs / 140.8 exp
Mild missense constraint
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.24 (0.10–0.76)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.93 (0.81–1.08)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.16
0≤1.21.6
LoF obs/exp: 2 / 8.3Missense obs/exp: 131 / 140.8Syn Z: -0.96
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
HOXB9 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
OMIM — Genotype-Phenotype Relationships
1 OMIM entry
HOMEOBOX B9; HOXB9
MIM #142964 · *
External Resources
Links to major genomics databases and tools
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
GalNAc-T14 promotes metastasis through Wnt dependent HOXB9 expression in lung adenocarcinoma.
Kwon OS et al.·Oncotarget
2015Meta-analysis
HOXB9 mediates resistance to chemotherapy and patient outcomes through the TGFβ pathway in pancreatic cancer.
Chiba N et al.·Oncotarget
2022
The E2F1-HOXB9/PBX2-CDK6 axis drives gastric tumorigenesis and serves as a therapeutic target in gastric cancer.
Zhang J et al.·J Pathol
2023
Identification of HOXB9 to predict prognosis of endometrial cancer based on comprehensive bioinformatics analysis.
Xu Y et al.·Eur J Med Res
2023
An E2F1-HOXB9 transcriptional circuit is associated with breast cancer progression.
Zhussupova A et al.·PLoS One
2014
HOXB9 expression promoting tumor cell proliferation and angiogenesis is associated with clinical outcomes in breast cancer patients.
Seki H et al.·Ann Surg Oncol
2012Cohort
PCAF-mediated acetylation of transcriptional factor HOXB9 suppresses lung adenocarcinoma progression by targeting oncogenic protein JMJD6.
Wan J et al.·Nucleic Acids Res
2016
HOXB9 enhances the ability of lung cancer cells to penetrate the blood-brain barrier.
Zheng H et al.·Aging (Albany NY)
2020
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
The miR-192-EGR1/HOXB9 Loop Regulates Glioma Cell Stemness and Malignant Phenotypes by Promoting Their Mesenchymal Transition.
Li GW et al.·J Cell Mol Med
2025Open Access
Endothelial HOXB9/SDC4 signaling exacerbates post-ischemic blood-brain and blood-spinal cord barrier disruption by promoting PKCα activation.
Wang LQ et al.·Brain Res Bull
2025
The miR-192/EGR1-HOXB9 loop inhibits immune evasion in glioma by arresting their NSC phenotypes.
Li GW et al.·Int Immunopharmacol
2025
TRIM11 modulates sepsis progression by promoting HOXB9 ubiquitination and inducing the NF-κB signaling pathway.
Gan J et al.·Mol Biol Rep
2025
The roles of HOXB9 and MMP12 in proliferation, migration, and invasion of human laryngeal cancer cells LCC and TU212.
Sun C et al.·Biochem Biophys Res Commun
2025
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Pan-cancer analysis of Homeobox B9 as a predictor for prognosis and immunotherapy in human tumors
Jin Q et al.·Aging (Albany NY)
2023
HOXB9 Overexpression Promotes Colorectal Cancer Progression and Is Associated with Worse Survival in Liver Resection Patients for Colorectal Liver Metastases
Martinou E et al.·Int J Mol Sci
2022Cohort
WT1 regulates HOXB9 gene expression in a bidirectional way.
Schmidt V et al.·Biochim Biophys Acta Gene Regul Mech
2021
HOXA9 versus HOXB9; particular focus on their controversial role in tumor pathogenesis.
Hjazi A et al.·J Appl Genet
2024
A Systematic Review on HOX Genes as Potential Biomarkers in Colorectal Cancer: An Emerging Role of HOXB9
Martinou E et al.·Int J Mol Sci
2021Review
Transcriptional Differences in Identical Twins With Different Reproductive Capacities: A Case Report
Campbell K et al.·Cureus
2023Case report
HOXB9 promotes laryngeal squamous cell carcinoma progression by upregulating MMP12.
Sun C et al.·Funct Integr Genomics
2024
Top 8 full-text resultsSearch PubTator3 ↗
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools