NKX3-2 Chromosome 4
NK3 homeobox 2
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What This Gene Does
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in cell differentiation; negative regulation of chondrocyte differentiation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including intestinal epithelial cell development; middle ear morphogenesis; and skeletal system development. Predicted to be located in chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Gene Info
Gene Group
NKL subclass homeoboxes and pseudogenes
Locus Type
gene with protein product
Location
4p15.33
Ensembl
ENSG00000109705
Associated Conditions (4)
Connective tissue disorder
Inborn genetic diseases
NKX3-2-related disorder
Spondylo-megaepiphyseal-metaphyseal dysplasia
Key Variants
RS202191746
Conflicting classifications of pathogenicity
Connective tissue disorder, Inborn genetic diseases, Connective tissue disorder
Health Risk
RS371597026
Conflicting classifications of pathogenicity
Connective tissue disorder, NKX3-2-related disorder, Connective tissue disorder
Health Risk
RS528413999
Conflicting classifications of pathogenicity
Inborn genetic diseases, Inborn genetic diseases
Health Risk
RS559539989
Conflicting classifications of pathogenicity
NKX3-2-related disorder, Inborn genetic diseases, NKX3-2-related disorder
Health Risk
RS577849807
Conflicting classifications of pathogenicity
NKX3-2-related disorder, Inborn genetic diseases, NKX3-2-related disorder
Health Risk
RS921673580
Conflicting classifications of pathogenicity
Health Risk
RS2109005842
Likely pathogenic
Connective tissue disorder, Connective tissue disorder
Health Risk
RS2474462219
Pathogenic
Health Risk
RS606231352
Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia
Health Risk
RS606231353
Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia
Health Risk
RS606231354
Pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia
Health Risk
RS1560165127
Pathogenic/Likely pathogenic
Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia
Health Risk
All Variants (12)
| RSID | Category | Clinical Significance | Conditions |
|---|---|---|---|
| RS202191746 | Health Risk | Conflicting classifications of pathogenicity | Connective tissue disorder, Inborn genetic diseases, Connective tissue disorder |
| RS371597026 | Health Risk | Conflicting classifications of pathogenicity | Connective tissue disorder, NKX3-2-related disorder, Connective tissue disorder |
| RS528413999 | Health Risk | Conflicting classifications of pathogenicity | Inborn genetic diseases, Inborn genetic diseases |
| RS559539989 | Health Risk | Conflicting classifications of pathogenicity | NKX3-2-related disorder, Inborn genetic diseases, NKX3-2-related disorder |
| RS577849807 | Health Risk | Conflicting classifications of pathogenicity | NKX3-2-related disorder, Inborn genetic diseases, NKX3-2-related disorder |
| RS921673580 | Health Risk | Conflicting classifications of pathogenicity | — |
| RS2109005842 | Health Risk | Likely pathogenic | Connective tissue disorder, Connective tissue disorder |
| RS2474462219 | Health Risk | Pathogenic | — |
| RS606231352 | Health Risk | Pathogenic | Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia |
| RS606231353 | Health Risk | Pathogenic | Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia |
| RS606231354 | Health Risk | Pathogenic | Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia |
| RS1560165127 | Health Risk | Pathogenic/Likely pathogenic | Spondylo-megaepiphyseal-metaphyseal dysplasia, Spondylo-megaepiphyseal-metaphyseal dysplasia |