Skip to content
Use your HSA or FSA funds

Gene

NKX2-5

NK2 homeobox 5

Summary

Cytogenetic location
5q35.1
Coordinates
Chromosome 5: 173,232,109–173,235,206 (GRCh38)
Exons
2 exons across 3.1 kb
Protein
324 amino acids
Inheritance
Autosomal dominant
Also known as
CSX1, NKX2.5, NKX4-1
Previous symbols
CSX, NKX2E
MANE Select transcript
ENST00000329198.5NM_004387.4
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 reports relevant to this gene

  • Congenital Hypothyroidism

    • A thyroid hormone deficiency present from birth.

      • 1 GenCC submitter rates it definitive or strong

  • Inherited Congenital Heart Defects

    • Atrial Septal Defect

      A hole between the upper chambers of the heart; inherited forms are caused by genes such as NKX2-5, GATA4, TBX20, MYH6 and ACTC1, and NKX2-5 forms also carry a risk of progressive heart block.

      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing about it supports heart imaging and, for NKX2-5, regular ECG checks.

  • Syndromic and Metabolic Cardiomyopathies

    • NKX2-5-Related Heart DiseaseAutosomal dominant

      A condition caused by changes in NKX2-5 that can combine congenital heart defects such as atrial septal defect with progressive conduction disease and cardiomyopathy.

      • ClinGen rates the link definitive
      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing about it supports regular rhythm monitoring, as conduction disease can progress and need a pacemaker.

  • Tetralogy of Fallot

    • Autosomal dominant

      Tetralogy of Fallot is a congenital cardiac malformation that consists of an interventricular communication, also known as a ventricular septal defect, obstruction of the right ventricular outflow tract, override of the ventricular septum by the aortic root, and right ventricular hypertrophy.

      • 1 GenCC submitter rates it definitive or strong

  • Thyroid Cancer

    • Hypothyroidism

      Abnormally low levels of thyroid hormone.

      • 1 GenCC submitter rates it definitive or strong
    • Thyroid Gland Disorder

      A disease involving the thyroid gland.

      • 1 GenCC submitter rates 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 NKX2-5 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 5, with a bracket where NKX2-5 sits. NKX2-5 and 8 genes near it on chromosome 5, from 172,733,658 to 173,733,657.Chromosome 55q35.1p15.33p15.32p15.31p15.2p15.1p14.3p14.2p14.1p13.3p13.2p13.1p12p11q11.1q11.2q12.1q12.2q12.3q13.1q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q31.1q31.2q31.3q32q33.1q33.2q33.3q34q35.1q35.2q35.3172.8 Mb173 Mb173.2 Mb173.4 Mb173.6 MbDUSP1: 172,766,992–172,771,198, reverse strandDUSP1ERGIC1: 172,834,251–172,952,792, forward strandERGIC1RPL26L1: 172,954,004–172,974,768, forward strandRPL26L1ATP6V0E1: 172,983,755–173,037,672, forward strandATP6V0E1CREBRF: 173,056,323–173,139,640, forward strandCREBRFBNIP1: 173,144,442–173,164,397, forward strandBNIP1NKX2-5: 173,232,109–173,235,206, reverse strandNKX2-5STC2: 173,314,708–173,328,447, reverse strandSTC2BOD1: 173,603,722–173,616,694, reverse strandBOD1Diagram of NKX2-5: 2 exons on the reverse strand of chromosome 5Exon 2: 58 known disease-causing sitesExon 1: 21 known disease-causing sitesExon 2: 173,232,109–173,233,209, 1,101 basesExon 1: 173,234,750–173,235,206, 457 bases215′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 1.6 kb of the gene's 3.1 kb; 975 of those bases code for the protein.

How a genome test reads NKX2-5

81

positions in NKX2-5 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 3.1 kb of NKX2-5, introns included, not only the 1.6 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.). NKX2-5 gene: NK2 homeobox 5. Retrieved 17 October 2026, from https://dantelabs.com/genes/nkx2-5

Vancouver

Dante Labs. NKX2-5 gene: NK2 homeobox 5 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/nkx2-5

One test. A lifetime of answers.

From $449Free shipping · Results in 6–8 weeks

Get my Genome Test