GENE REFERENCE / HGNC:2076

CLN5

CLN5 lysosomal BMP synthase

protein-coding gene13q22.3Gene information

What does this gene do?

The CLN5 gene provides instructions for making a protein whose function is not well understood. Cells produce a CLN5 protein that is inactive and contains extra protein segments. This inactive protein is called a preprotein. For the CLN5 preprotein to become active, the additional segments must be removed, followed by additional processing steps. The active CLN5 protein is then transported to cell compartments called lysosomes, which digest and recycle different types of molecules. Research suggests that the CLN5 protein may play a role in the process by which lysosomes break down or recycle damaged or unneeded proteins within cells.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-06-02. Source review: 2016-11.

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 2021-09-08	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: 868
Submissions for variants in or overlapping this gene: 1,710
Submissions explicitly reporting this gene: 1,625
Alleles reported pathogenic / likely pathogenic: 167
VariationIDs with uncertain significance: 277
VariationIDs with conflicting classifications: 43

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 CLN5?

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 167 alleles in CLN5 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 CLN5.

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

Buy BioDecode See a sample report →Check file compatibility →