HMX3

Chr 10

H6 family homeobox 3

Also known as: NKX-5.1, NKX5.1, Nkx5-1

NCBI Gene: 340784ENSG00000188620UniProt: Q8IZL8OMIM: 613380

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including embryo implantation; maternal process involved in female pregnancy; and neuromuscular process controlling balance. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIMResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant
This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.
0
Active trials
5
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.37
LOEUF
LOF
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.37LOEUF
pLI 0.920
Z-score 2.64
OE 0.00 (0.00–0.37)
Highly constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
0.91Z-score
OE missense 0.81 (0.70–0.93)
142 obs / 175.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.37)
0≤0.351.4
Missense OE?0.81 (0.70–0.93)
0≤0.61.4
Synonymous OE?1.16
0≤1.21.6
LoF obs/exp: 0 / 8.1Missense obs/exp: 142 / 175.9Syn Z: -1.12

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

HMX3 · protein map & ClinVar variants

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

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