GENE REFERENCE / HGNC:9005

PITX2

paired like homeodomain 2

protein-coding gene4q25Gene information

What does this gene do?

The PITX2 gene provides instructions for making a protein that attaches (binds) to specific regions of DNA and regulates the activity of other genes. On the basis of this action, the PITX2 protein is called a transcription factor. The PITX2 gene is part of a family of homeobox genes, which act during early embryonic development to control the formation of many parts of the body.

The PITX2 protein plays a critical role in early development, particularly in the formation of structures in the front part of the eye (the anterior segment). These structures include the colored part of the eye (the iris), the lens of the eye, and the clear front covering of the eye (the cornea). Studies suggest that the PITX2 protein also has functions in the adult eye, such as helping cells respond to oxidative stress. Oxidative stress occurs when unstable molecules called free radicals accumulate to levels that can damage or kill cells.

The PITX2 protein is also involved in the normal development of other parts of the body, including the teeth, heart, and abdominal organs.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-04-19. Source review: 2014-01.

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
anterior segment dysgenesis 4MONDO:0007662 · Evaluated 2025-07-17	Autosomal dominant	DefinitiveGlaucoma and Neuro-Ophthalmology 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: 306
Submissions for variants in or overlapping this gene: 767
Submissions explicitly reporting this gene: 724
Alleles reported pathogenic / likely pathogenic: 90
VariationIDs with uncertain significance: 105
VariationIDs with conflicting classifications: 15

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 PITX2?

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 90 alleles in PITX2 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 PITX2.

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

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