HOXA9

Chr 7

homeobox A9

Also known as: ABD-B, HOX1, HOX1.7, HOX1G

NCBI Gene: 3205ENSG00000078399UniProt: P31269

In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. This gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila. A specific translocation event which causes a fusion between this gene and the NUP98 gene has been associated with myeloid leukemogenesis. Read-through transcription exists between this gene and the upstream homeobox A10 (HOXA10) gene.[provided by RefSeq, Mar 2011]

96
ClinVar variants
31
Pathogenic / LP
0.00
pLI score
4
Active trials
Clinical Summary— HOXA9
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
31 Pathogenic / Likely Pathogenic· 64 VUS of 96 total submissions
💊
Clinical Trials
4 active or recruiting trials — potential therapeutic options may be available
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

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.
1.62LOEUF
pLI 0.000
Z-score 0.30
OE 0.89 (0.50–1.62)
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.
-0.06Z-score
OE missense 1.01 (0.89–1.16)
157 obs / 155.0 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.0.89 (0.50–1.62)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.01 (0.89–1.16)
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.1.42
0≤1.21.6
LoF obs/exp: 7 / 7.9Missense obs/exp: 157 / 155.0Syn Z: -2.68

ClinVar Variant Classifications

96 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic28
Likely Pathogenic3
VUS64
Benign1
28
Pathogenic
3
Likely Pathogenic
64
VUS
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
28
0
28
Likely Pathogenic
0
0
3
0
3
VUS
0
61
3
0
64
Likely Benign
0
0
0
0
0
Benign
0
0
0
1
1
Total06134196

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

View in ClinVar →

Protein Context — Lollipop Plot

HOXA9 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype

OMIM

No OMIM entries found.

Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Mapping human haematopoietic stem cells from haemogenic endothelium to birth.
Calvanese V et al.·Nature
2022
Effective Menin inhibitor-based combinations against AML with MLL rearrangement or NPM1 mutation (NPM1c).
Fiskus W et al.·Blood Cancer J
2022
KAT6A and KAT7 Histone Acetyltransferase Complexes Are Molecular Dependencies and Therapeutic Targets in NUP98-Rearranged Acute Myeloid Leukemia.
Michmerhuizen NL et al.·Cancer Discov
2025
HOXA9 Regulome and Pharmacological Interventions in Leukemia.
Aryal S et al.·Adv Exp Med Biol
2024Review
Loss of the stress sensor GADD45A promotes stem cell activity and ferroptosis resistance in LGR4/HOXA9-dependent AML.
Hassan N et al.·Blood
2024
HBO1 is required for the maintenance of leukaemia stem cells.
MacPherson L et al.·Nature
2020
HOXA9 promotes proliferation, metastasis and prevents apoptosis in hepatocellular carcinoma.
Bao G et al.·J Cancer Res Clin Oncol
2024
Efficacy, Safety, and Biomarker Analysis of Neoadjuvant Camrelizumab and Apatinib in Patients With Resectable NSCLC: A Phase 2 Clinical Trial.
Zhao J et al.·J Thorac Oncol
2023Clinical trial
Oncogenic role of RARG rearrangements in acute myeloid leukemia resembling acute promyelocytic leukemia.
Wang F et al.·Nat Commun
2025
The E3 ubiquitin ligase Herc1 modulates the response to nucleoside analogs in acute myeloid leukemia.
Jankovic M et al.·Blood Adv
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Epithelial Ovarian CancerCirculating Tumor DNADNA Methylation

ctDNA Methylation for Epithelial Ovarian Cancer

RECRUITING
NCT05801263Lei LiStarted 2023-03-24
CDO1 and HOXA9 methylation assay
ALL, AdultAML, AdultAcute Leukaemia

A Study of BN104 in the Treatment of Acute Leukemia

ACTIVE NOT RECRUITING
NCT06052813Phase PHASE1, PHASE2Institut de Recherches Internationales Servier (I.R.I.S.)Started 2023-10-19
BN104 monotherapyBN104 monotherapyBN104 monotherapy - rp2d
Acute Myeloid Leukemia

BN104 in Combination With Chemotherapy or Targeted Agents for Acute Myeloid Leukemia

RECRUITING
NCT06746519Phase PHASE1, PHASE2Chen SuningStarted 2024-12-25
BN104 combined Intensive Chemotherapy or Venetoclax/Azacitidine
Epithelial Ovarian CancerCirculating Tumor DNADNA Methylation

ctDNA Methylation for Detecting Ovarian Cancer

RECRUITING
NCT05801276Lei LiStarted 2023-03-24
Methylation assay

External Resources

Links to major genomics databases and tools