GENE REFERENCE / HGNC:6530

LCT

lactase

protein-coding gene2q21.3Gene information

What does this gene do?

The LCT gene provides instructions for making an enzyme called lactase. This enzyme helps to digest lactose, a sugar found in milk and several other dairy products.

Lactase is produced by some of the cells that line the walls of the small intestine. These cells, called intestinal epithelial cells, have small, finger-like projections called microvilli. As food passes through the intestine, the microvilli collect nutrients so they can be absorbed into the bloodstream. Groups of these microvilli are known collectively as the brush border. Lactase functions at the brush border to break down lactose into smaller sugars called glucose and galactose for absorption.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-03-24. Source review: 2023-03.

ClinGen reviews

We found no matching ClinGen review in the data used here. This does not rule out a link between the gene and a condition.

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: 1,024
Submissions for variants in or overlapping this gene: 1,380
Submissions explicitly reporting this gene: 1,344
Alleles reported pathogenic / likely pathogenic: 54
VariationIDs with uncertain significance: 424
VariationIDs with conflicting classifications: 38

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 LCT?

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 54 alleles in LCT 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 LCT.

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

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