GENE REFERENCE / HGNC:8616

PAX2

paired box 2

protein-coding gene10q24.31Gene information

What does this gene do?

The PAX2 gene belongs to a family of genes that plays a critical role in the formation of tissues and organs during embryonic development. The members of the PAX gene family are also important for maintaining the normal function of certain cells after birth. To carry out these roles, the PAX genes provide instructions for making proteins that attach to specific areas of DNA and help control the activity (expression) of particular genes. On the basis of this action, PAX proteins are called transcription factors.

During embryonic development, the PAX2 gene provides instructions for producing a protein that is involved in the formation of the eyes, ears, brain and spinal cord (central nervous system), kidneys, urinary tract, and genital tract. After birth, the PAX2 protein is thought to protect against cell death during periods of cellular stress.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-04-18. Source review: 2022-08.

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
focal segmental glomerulosclerosis 7MONDO:0014451 · Evaluated 2021-09-13	Autosomal dominant	DefinitiveGlomerulopathy 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: 723
Submissions for variants in or overlapping this gene: 1,127
Submissions explicitly reporting this gene: 1,047
Alleles reported pathogenic / likely pathogenic: 169
VariationIDs with uncertain significance: 271
VariationIDs with conflicting classifications: 24

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 PAX2?

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 169 alleles in PAX2 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 PAX2.

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

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