HOXB2

Chr 17

homeobox B2

Also known as: HOX2, HOX2H, Hox-2.8, K8

NCBI Gene: 3212UniProt: P14652

This gene is a member of the Antp homeobox family and encodes a nuclear protein with a homeobox DNA-binding domain. It is included in a cluster of homeobox B genes located on chromosome 17. The encoded protein functions as a sequence-specific transcription factor that is involved in development. Increased expression of this gene is associated with pancreatic cancer. [provided by RefSeq, Jul 2008]

0
Active trials
79
ClinVar variants
10
Pathogenic / LP
-1.6
Missense Z
1.33
LOEUF
7
Pubs (2 yr)
Clinical Summary— HOXB2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
10 Pathogenic / Likely Pathogenic· 67 VUS of 79 total submissions
Some data sources returned errors (1)

ensembl: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
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.
1.33LOEUF
pLI 0.000
Z-score 0.84
OE 0.71 (0.40–1.33)
Tolerant

Highly tolerant — LoF variants common in population

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.
-1.57Z-score
OE missense 1.31 (1.18–1.45)
270 obs / 206.4 exp
Tolerant

Tolerant to missense variation

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.0.71 (0.40–1.33)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.31 (1.18–1.45)
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.1.09
0≤1.21.6
LoF obs/exp: 7 / 9.9Missense obs/exp: 270 / 206.4Syn Z: -0.69

ClinVar Variant Classifications

79 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic9
Likely Pathogenic1
VUS67
Likely Benign2
9
Pathogenic
1
Likely Pathogenic
67
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
9
0
9
Likely Pathogenic
0
0
1
0
1
VUS
0
65
2
0
67
Likely Benign
0
2
0
0
2
Benign
0
0
0
0
0
Total06712079

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

HOXB2 · 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

OMIM
HOMEOBOX B2; HOXB2
MIM #142967 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The homeoprotein HOXB2 limits triple-negative breast carcinogenesis via extracellular matrix remodeling.
Oh JH et al.·Int J Biol Sci
2024Functional
HOXB2 increases the proliferation and invasiveness of colon cancer cells through the upregulation of CCT6A.
Yang X et al.·Mol Med Rep
2022
Ectopic expression of hoxb2 after retinoic acid treatment or mRNA injection: disruption of hindbrain and craniofacial morphogenesis in zebrafish embryos.
Yan YL et al.·Dev Dyn
1998Functional
The role of HOXB2 and HOXB3 in acute myeloid leukemia.
Lindblad O et al.·Biochem Biophys Res Commun
2015
LINC00662 promotes cell viability and metastasis in esophageal squamous cell carcinoma by sponging miR-340-5p and upregulating HOXB2.
Zhang Z et al.·Thorac Cancer
2020
High expression of homeobox B2 predicts poor survival of colon adenocarcinoma by enhancing tumor proliferation and invasion.
Li S et al.·Ir J Med Sci
2023
Expression of HOXB2, a retinoic acid signaling target in pancreatic cancer and pancreatic intraepithelial neoplasia.
Segara D et al.·Clin Cancer Res
2005
Comprehensive analysis of single-cell transcriptomics and genetic factors reveals the mechanisms and preventive strategies for the progression from pulmonary fibrosis to lung cancer.
Gu J et al.·Int Immunopharmacol
2024Functional
A potential tumor marker: Chaperonin containing TCP‑1 controls the development of malignant tumors (Review).
Zheng L et al.·Int J Oncol
2023Review
Identification of methylated genes associated with aggressive bladder cancer.
Marsit CJ et al.·PLoS One
2010
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Transcriptome sequencing of facial adipose tissue reveals alterations in mRNAs of hemifacial microsomia
Liu B et al.·Front Pediatr
2023
Identification of HOX signatures contributing to oral cancer phenotype
Padam KSR et al.·Sci Rep
2022
Epigenetic characterization of sarcopenia-associated genes based on machine learning and network screening
Chen Y et al.·Eur J Med Res
2024
HOXB2 is a prognostic biomarker and correlated with immune infiltration in colorectal cancer and glioma.
Liu Z et al.·Discov Oncol
2026
Estrogen suppresses HOXB2 expression via ERalpha in breast cancer cells.
Kumar A et al.·Gene
2021
RETRACTION NOTICE: miR-4324 functions as a tumor suppressor in colorectal cancer by targeting HOXB2
·J Int Med Res
2021
Homeobox B2 promotes malignant behavior and contributes to the radioresistance of nasopharyngeal carcinoma by regulating forkhead box protein O1
Chen J et al.·Int J Med Sci
2024
SHP2 promotes osteosarcoma via regulating STAT3/TET3/HOXB2 signaling
Yang H et al.·Sci Rep
2026
Top 8 full-text resultsSearch PubTator3 ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients