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Gene

NKX2-1

NK2 homeobox 1

Summary

Cytogenetic location
14q13.3
Coordinates
Chromosome 14: 36,516,397–36,520,232 (GRCh38)
Exons
3 exons across 3.8 kb
Protein
401 amino acids
Inheritance
Autosomal dominant
Also known as
TTF-1, TTF1
Previous symbols
NKX2A, BCH, TITF1
MANE Select transcript
ENST00000354822.7NM_001079668.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Congenital Hypothyroidism

    • NKX2-1-related choreoathetosis and congenital hypothyroidismAutosomal dominant

      Brain-lung-thyroid syndrome: congenital hypothyroidism with childhood chorea and, in some, breathing problems, caused by NKX2-1 variants.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How NKX2-1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 14, with a bracket where NKX2-1 sits. NKX2-1 and 5 genes near it on chromosome 14, from 36,018,315 to 37,018,314.Chromosome 1414q13.3p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3336.2 Mb36.4 Mb36.6 Mb36.8 Mb37 MbMBIP: 36,298,231–36,320,680, reverse strandMBIPSFTA3: 36,473,207–36,521,149, reverse strandSFTA3NKX2-1: 36,516,397–36,520,232, reverse strandNKX2-1NKX2-8: 36,580,004–36,582,614, reverse strandNKX2-8PAX9: 36,657,568–36,679,362, forward strandPAX9SLC25A21: 36,677,921–37,172,743, reverse strandSLC25A21Diagram of NKX2-1: 3 exons on the reverse strand of chromosome 14Exon 3: 50 known disease-causing sitesExon 2: 20 known disease-causing sitesExon 1: 1 known disease-causing siteExon 3: 36,516,397–36,518,020, 1,624 basesExon 2: 36,518,985–36,519,370, 386 basesExon 1: 36,520,053–36,520,232, 180 bases3215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 2.2 kb of the gene's 3.8 kb; 1,206 of those bases code for the protein.

How a genome test reads NKX2-1

73

positions in NKX2-1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 3.8 kb of NKX2-1, introns included, not only the 2.2 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). NKX2-1 gene: NK2 homeobox 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/nkx2-1

Vancouver

Dante Labs. NKX2-1 gene: NK2 homeobox 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nkx2-1

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