GENE REFERENCE / HGNC:9004

PITX1

paired like homeodomain 1

protein-coding gene5q31.1Gene information

What does this gene do?

The PITX1 gene provides instructions for making a protein that plays a critical role in the development of the legs and feet. The protein acts as a transcription factor, which means that it binds to specific regions of DNA and helps control the activity of particular genes. Specifically, the PITX1 protein regulates the activity of genes that direct the development of the bones and tissues in the legs, knees, ankles, and feet.

The PITX1 protein is also found in the embryonic structures called branchial arches that give rise to tissues in the face and neck and in the developing pituitary gland, which is a hormone-producing gland located at the base of the brain. Researchers suspect that the PITX1 protein may play a role in the formation of the pituitary gland and in the formation of certain tissues that are derived from the branchial arches, such as the roof of the mouth, the jaw, and parts of the inner ear.

Source: MedlinePlus, National Library of Medicine. Source publication: 2026-01-05. Source review: 2026-01.

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: 147
Submissions for variants in or overlapping this gene: 178
Submissions explicitly reporting this gene: 147
Alleles reported pathogenic / likely pathogenic: 11
VariationIDs with uncertain significance: 78
VariationIDs with conflicting classifications: 4

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 PITX1?

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 11 alleles in PITX1 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 PITX1.

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

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