HOXA10

Chr 7

homeobox A10

Also known as: HOX1, HOX1.8, HOX1H, PL

NCBI Gene: 3206ENSG00000253293UniProt: P31260

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 that may regulate gene expression, morphogenesis, and differentiation. More specifically, it may function in fertility, embryo viability, and regulation of hematopoietic lineage commitment. Alternatively spliced transcript variants have been described. Read-through transcription also exists between this gene and the downstream homeobox A9 (HOXA9) gene. [provided by RefSeq, Mar 2011]

125
ClinVar variants
31
Pathogenic / LP
0.88
pLI score
0
Active trials
Clinical Summary— HOXA10
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.88) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
31 Pathogenic / Likely Pathogenic· 83 VUS of 125 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
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.
0.42LOEUF
pLI 0.885
Z-score 2.86
OE 0.09 (0.03–0.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

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.
-1.07Z-score
OE missense 1.21 (1.09–1.34)
258 obs / 214.0 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.0.09 (0.03–0.42)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.21 (1.09–1.34)
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.1.30
0≤1.21.6
LoF obs/exp: 1 / 11.4Missense obs/exp: 258 / 214.0Syn Z: -2.35

ClinVar Variant Classifications

125 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic28
Likely Pathogenic3
VUS83
Likely Benign6
Benign5
28
Pathogenic
3
Likely Pathogenic
83
VUS
6
Likely Benign
5
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
80
3
0
83
Likely Benign
0
0
1
5
6
Benign
0
1
1
3
5
Total081368125

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

View in ClinVar →

Protein Context — Lollipop Plot

HOXA10 · 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 A10; HOXA10
MIM #142957 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
HOXA10 expression profiling in prostate cancer.
Hatanaka Y et al.·Prostate
2019Meta-analysis
The role of the Hoxa10/HOXA10 gene in the etiology of endometriosis and its related infertility: a review.
Zanatta A et al.·J Assist Reprod Genet
2010Review
HBO1 is required for the maintenance of leukaemia stem cells.
MacPherson L et al.·Nature
2020
IKAROS and MENIN coordinate therapeutically actionable leukemogenic gene expression in MLL-r acute myeloid leukemia.
Aubrey BJ et al.·Nat Cancer
2022
Advances in the Pathophysiology of Thin Endometrium.
Niu Y et al.·Reprod Sci
2025Review
Uterine receptivity and implantation: the regulation and action of insulin-like growth factor binding protein-1 (IGFBP-1), HOXA10 and forkhead transcription factor-1 (FOXO-1) in the baboon endometrium.
Kim JJ et al.·Reprod Biol Endocrinol
2004Review
Polycystic ovary syndrome: Endometrial markers.
Piltonen TT·Best Pract Res Clin Obstet Gynaecol
2016Review
Precision Therapeutic and Preventive Molecular Strategies for Endometriosis-Associated Infertility.
Limam I et al.·Int J Mol Sci
2025Review
Generation of epithelial-stromal assembloids as an advanced in vitro model of impaired adenomyosis-related endometrial receptivity.
Stratopoulou CA et al.·Fertil Steril
2025Functional
Clinicopathologic and molecular characteristics of gastric cancer showing gastric and intestinal mucin phenotype.
Oue N et al.·Cancer Sci
2015Review
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

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools