GENE REFERENCE / HGNC:11825

NKX2-1

NK2 homeobox 1

protein-coding gene14q13.3Gene information

What does this gene do?

The NKX2-1 gene provides instructions for making a protein called homeobox protein Nkx-2.1, which is a member of the homeobox protein family. Homeobox proteins direct the formation of body structures during early embryonic development. Homeobox protein Nkx-2.1 is particularly involved in the development and function of the brain, lungs, and thyroid gland. The thyroid is a butterfly shaped gland in the lower neck that makes hormones to help regulate a wide variety of critical body functions, including growth and brain development.

Homeobox protein Nkx-2.1 functions as a transcription factor, which means it attaches to DNA and controls the activity (expression) of other genes. In the brain, homeobox protein Nkx-2.1 regulates genes that play a role in the development and movement (migration) of specialized nerve cells (neurons), called interneurons, to their proper location. Interneurons relay signals between other neurons. In the lungs, homeobox protein Nkx-2.1 controls development of lung structures and regulates the expression of surfactant genes, which provide instructions for producing surfactant proteins. Together with certain fats, these proteins form surfactant, which lines the lung tissue and makes breathing easy. In the thyroid gland, homeobox protein Nkx-2.1 controls genes that are critical in the production of thyroid hormones.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2017-01.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
NKX2-1 related choreoathetosis and congenital hypothyroidism with or without pulmonary dysfunctionMONDO:0100520 · Evaluated 2023-07-27	Autosomal dominant	DefinitiveSyndromic Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 476
Submissions for variants in or overlapping this gene: 654
Submissions explicitly reporting this gene: 592
Alleles reported pathogenic / likely pathogenic: 142
VariationIDs with uncertain significance: 173
VariationIDs with conflicting classifications: 17

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about NKX2-1?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 142 alleles in NKX2-1 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in NKX2-1.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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