NKX3-2
Chr 4ARNK3 homeobox 2
Also known as: BAPX1, NKX3.2, NKX3B, SMMD
NKX3-2 encodes a transcriptional repressor that negatively regulates chondrocyte maturation and is required for proper middle ear development and distal stomach morphogenesis. Mutations cause spondylo-megaepiphyseal-metaphyseal dysplasia, a skeletal dysplasia inherited in an autosomal recessive pattern. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.631).
Primary Disease Associations & Inheritance
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Tolerant to missense variation
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
271 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 5 | 0 | 57 | 0 | 62 |
Likely Pathogenic | 2 | 0 | 3 | 0 | 5 |
VUS | 0 | 99 | 11 | 0 | 110 |
Likely Benign | 0 | 7 | 9 | 54 | 70 |
Benign | 0 | 1 | 3 | 6 | 10 |
Conflicting | — | 6 | |||
| Total | 7 | 107 | 83 | 60 | 263 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
NKX3-2 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools