GENE REFERENCE / HGNC:2074

CLN3

CLN3 lysosomal/endosomal transmembrane protein, battenin

protein-coding gene16p12.1Gene information

What does this gene do?

The CLN3 gene provides instructions for making a protein that is found in tissues throughout the body, yet its function is unclear. The CLN3 protein is found in many compartments within cells, but its role in lysosomes is most well-studied. Lysosomes are cellular compartments that digest and recycle different types of molecules. The CLN3 protein spans the membrane surrounding lysosomes, helping to facilitate communication between it and the rest of the cell.

Studies have associated the CLN3 protein with many cellular processes, including recycling of worn-out cell parts and unneeded proteins (autophagy), maintenance of the relative acidity (pH) of lysosomes, the movement of molecules from the cell surface into the cell (endocytosis), transportation (trafficking) of proteins to where they are needed in the cell, self-destruction of cells (apoptosis), cell growth and division (proliferation), and maintenance of the body's water balance (osmoregulation). It is uncertain which of these varied functions is the primary role of the CLN3 protein, or if these processes instead represent downstream effects.

Source: MedlinePlus, National Library of Medicine. Source publication: 2022-06-28. Source review: 2020-02.

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
neuronal ceroid lipofuscinosisMONDO:0016295 · Evaluated 2023-04-04	Autosomal recessive	DefinitiveEpilepsy 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: 1,374
Submissions for variants in or overlapping this gene: 2,413
Submissions explicitly reporting this gene: 2,298
Alleles reported pathogenic / likely pathogenic: 276
VariationIDs with uncertain significance: 387
VariationIDs with conflicting classifications: 52

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 CLN3?

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 276 alleles in CLN3 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 CLN3.

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

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