GENE REFERENCE / HGNC:691

PHOX2A

paired like homeobox 2A

protein-coding gene11q13.4Gene information

What does this gene do?

The PHOX2A gene provides instructions for making a protein that is found in the nervous system. This protein acts early in development to help promote the formation of nerve cells (neurons) and regulate the process by which the neurons mature to carry out specific functions (differentiation).

Most of researchers' knowledge about the PHOX2A protein comes from studies in animals. From these studies, it is clear that the protein plays a critical role in the development of the autonomic nervous system, which controls involuntary body functions such as breathing, blood pressure, heart rate, and digestion. The PHOX2A protein is also involved in the formation of certain nerves in the head and face (cranial nerves). Specifically, it appears to be critical for the development and function of cranial nerves III and IV, which emerge from the brain and control many of the muscles that surround the eyes (extraocular muscles). These muscles direct eye movement and determine the position of the eyes.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2019-10.

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: 59
Submissions for variants in or overlapping this gene: 64
Submissions explicitly reporting this gene: 47
Alleles reported pathogenic / likely pathogenic: 2
VariationIDs with uncertain significance: 36
VariationIDs with conflicting classifications: 0

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 PHOX2A?

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 2 alleles in PHOX2A 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 PHOX2A.

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

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