GENE REFERENCE / HGNC:9143

PHOX2B

paired like homeobox 2B

protein-coding gene4p13Gene information

What does this gene do?

The PHOX2B gene provides instructions for making a protein that is important during development before birth. The PHOX2B protein helps support the formation of nerve cells (neurons) and regulates the process by which the neurons mature to carry out specific functions (differentiation). During neuron development, the protein is active in the neural crest, which is a group of cells in the early embryo that give rise to many tissues and organs. Neural crest cells migrate to form parts of the autonomic nervous system, which controls body functions such as breathing, blood pressure, heart rate, and digestion. Neural crest cells also give rise to many tissues in the face and skull, and other tissue and cell types.

The protein produced from the PHOX2B gene contains two areas where a protein building block (amino acid) called alanine is repeated multiple times. These stretches of alanines are known as polyalanine tracts or poly(A) tracts.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-05-08. Source review: 2012-08.

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
Haddad syndromeMONDO:0020493 · Evaluated 2021-06-15	Autosomal dominant	DefinitiveHereditary Cancer Gene Curation Expert Panel
central hypoventilation syndrome, congenital, 1, with or without Hirschsprung diseaseMONDO:0800026 · Evaluated 2022-12-30	Autosomal dominant	DefinitiveHereditary Cancer 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: 1,319
Submissions for variants in or overlapping this gene: 2,324
Submissions explicitly reporting this gene: 2,296
Alleles reported pathogenic / likely pathogenic: 89
VariationIDs with uncertain significance: 695
VariationIDs with conflicting classifications: 43

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 PHOX2B?

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 89 alleles in PHOX2B 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 PHOX2B.

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

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