GENE REFERENCE / HGNC:4122

GALNS

galactosamine (N-acetyl)-6-sulfatase

protein-coding gene16q24.3Gene information

What does this gene do?

The GALNS gene provides instructions for producing an enzyme called N-acetylgalactosamine 6-sulfatase. This enzyme is located in lysosomes, which are compartments within cells that break down and recycle different types of molecules. N-acetylgalactosamine 6-sulfatase is involved in the breakdown of large sugar molecules called glycosaminoglycans (GAGs) or mucopolysaccharides. Specifically, this enzyme removes a chemical group known as a sulfate from a GAG called keratan sulfate. Keratan sulfate is particularly abundant in cartilage and the clear covering of the eye (cornea).

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2010-06.

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
mucopolysaccharidosis type 4AMONDO:0009659 · Evaluated 2022-06-16	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: 1,553
Submissions for variants in or overlapping this gene: 2,813
Submissions explicitly reporting this gene: 2,689
Alleles reported pathogenic / likely pathogenic: 355
VariationIDs with uncertain significance: 381
VariationIDs with conflicting classifications: 153

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 GALNS?

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 355 alleles in GALNS 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 GALNS.

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

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