GENE REFERENCE / HGNC:4877

HESX1

HESX homeobox 1

protein-coding gene3p14.3Gene information

What does this gene do?

The HESX1 gene provides instructions for producing a protein that regulates the activity of other genes. On the basis of this action, the HESX1 protein is called a transcription factor. The HESX1 gene is part of a family of homeobox genes, which act during early embryonic development to control the formation of many body structures.

The HESX1 protein plays an important role in early brain development. In particular, it is essential for the formation of the pituitary, which is a gland at the base of the brain that produces several hormones. The HESX1 protein is also necessary for the development of structures at the front of the brain (the forebrain), including the nerves that carry visual information from the eyes to the brain (optic nerves).

The HESX1 protein interacts with other proteins, including the protein produced from the PROP1 gene, during embryonic development. Both the HESX1 protein and the PROP1 protein bind to DNA and control the activity of other genes. The HESX1 protein turns off (represses) genes, while the PROP1 protein turns on (activates) genes. These proteins work together to coordinate the development of certain parts of the brain.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-04-11. Source review: 2010-03.

ClinGen reviews

We found no matching ClinGen review in the data used here. This does not rule out a link between the gene and a condition.

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: 157
Submissions for variants in or overlapping this gene: 287
Submissions explicitly reporting this gene: 271
Alleles reported pathogenic / likely pathogenic: 23
VariationIDs with uncertain significance: 77
VariationIDs with conflicting classifications: 14

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 HESX1?

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 23 alleles in HESX1 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 HESX1.

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

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