NKX2-3

Chr 10

NK2 homeobox 3

Also known as: CSX3, NK2.3, NKX2.3, NKX2C, NKX4-3

NCBI Gene: 159296ENSG00000119919UniProt: Q8TAU0

This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]

ResearchGenerating 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
6
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.32
LOEUF· LoF intol.
LOF
Mechanism· predicted
Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.32LOEUF
pLI 0.950
Z-score 2.85
OE 0.00 (0.00–0.32)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
0.81Z-score
OE missense 0.82 (0.72–0.95)
137 obs / 166.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.00 (0.00–0.32)
0≤0.351.4
Missense OE?0.82 (0.72–0.95)
0≤0.61.4
Synonymous OE?0.87
0≤1.21.6
LoF obs/exp: 0 / 9.5Missense obs/exp: 137 / 166.3Syn Z: 0.90

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

NKX2-3 · 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