GENE REFERENCE / HGNC:23026

GNPTG

N-acetylglucosamine-1-phosphate transferase subunit gamma

protein-coding gene16p13.3Gene information

What does this gene do?

The GNPTG gene provides instructions for making one part, the gamma subunit, of an enzyme called GlcNAc-1-phosphotransferase. This enzyme is made up of two alpha (α), two beta (β), and two gamma (γ) subunits. The alpha and beta subunits are produced from a different gene, called GNPTAB. GlcNAc-1-phosphotransferase helps prepare certain newly made enzymes for transport to lysosomes. Lysosomes are compartments within the cell that use digestive enzymes called hydrolases to break down large molecules into smaller ones that can be reused by cells.

GlcNAc-1-phosphotransferase is involved in the first step of making a molecule called mannose-6-phosphate (M6P). M6P acts as a tag that indicates a hydrolase should be transported to the lysosome. Specifically, GlcNAc-1-phosphotransferase transfers a molecule called GlcNac-1-phosphate to a newly produced hydrolase. In the next step, a molecule is removed to reveal an M6P attached to the hydrolase. Once a hydrolase has an M6P tag, it can be transported to a lysosome.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2009-08.

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
GNPTG-mucolipidosisMONDO:0009652 · Evaluated 2022-12-28	Autosomal recessive	DefinitiveLysosomal Diseases 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: 1,097
Submissions for variants in or overlapping this gene: 1,672
Submissions explicitly reporting this gene: 1,593
Alleles reported pathogenic / likely pathogenic: 175
VariationIDs with uncertain significance: 303
VariationIDs with conflicting classifications: 41

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 GNPTG?

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 175 alleles in GNPTG 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 GNPTG.

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

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