GENE REFERENCE / HGNC:4125

GALNT3

polypeptide N-acetylgalactosaminyltransferase 3

protein-coding gene2q24.3Gene information

What does this gene do?

The GALNT3 gene provides instructions for making a protein called ppGalNacT3, which is found in many types of cells. This protein plays a major role in regulating phosphate levels within the body (phosphate homeostasis). Among its many functions, phosphate plays a critical role in the formation and growth of bones in childhood and helps maintain bone strength in adults. Phosphate levels are controlled in large part by the kidneys. The kidneys normally rid the body of excess phosphate by excreting it in urine, and they reabsorb this mineral into the bloodstream when more is needed.

The ppGalNacT3 protein regulates the activity of a protein called fibroblast growth factor 23, which is produced in bone cells and whose function is to signal the body to decrease phosphate reabsorption by the kidneys. The ppGalNacT3 protein attaches sugar molecules to particular regions of fibroblast growth factor 23 through a process called glycosylation. These sugar molecules are required for the protein's transport out of cells and to protect the protein from being broken down. When phosphate levels are increased, ppGalNacT3 glycosylates fibroblast growth factor 23 so it will not be broken down. Signaling from fibroblast growth factor 23 leads to a decrease in phosphate reabsorption, which helps to maintain normal phosphate levels in the body.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. 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
tumoral calcinosis, hyperphosphatemic, familial, 1MONDO:0100252 · Evaluated 2024-02-06	Autosomal recessive	DefinitiveCongenital Disorders of Glycosylation 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: 612
Submissions for variants in or overlapping this gene: 819
Submissions explicitly reporting this gene: 738
Alleles reported pathogenic / likely pathogenic: 80
VariationIDs with uncertain significance: 217
VariationIDs with conflicting classifications: 17

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 GALNT3?

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 80 alleles in GALNT3 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 GALNT3.

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

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