Gene
LCT
lactase
- HGNC 6530(opens in a new tab)
- Ensembl gene ENSG00000115850(opens in a new tab)
- NCBI Gene 3938(opens in a new tab)
Summary
- Cytogenetic location
- 2q21.3
- Coordinates
- Chromosome 2: 135,787,850–135,837,184 (GRCh38)
- Exons
- 17 exons across 49.3 kb
- Protein
- 1,927 amino acids
- Inheritance
- Autosomal recessive
- MANE Select transcript
- ENST00000264162.7NM_002299.4
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Congenital Disaccharidase Deficiencies
- Congenital lactase deficiencyAutosomal recessive
A severe deficiency of the lactase enzyme from birth, caused by LCT variants, that causes watery diarrhoea once milk feeding begins.
- 2 GenCC submitters rate it definitive or strong
What knowing changes
A lactose-free diet resolves symptoms and prevents dehydration and poor growth in infancy.
Inheritance
- Autosomal recessive
- It takes a changed copy from each parent. With one, you are a carrier and usually unaffected; when both parents are carriers, each child has a one-in-four chance of inheriting two.
How LCT is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 6.3 kb of the gene's 49.3 kb; 5,784 of those bases code for the protein.
How a genome test reads LCT
7
positions in LCT where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 49.3 kb of LCT, introns included, not only the 6.3 kb of exons.
Traits linked to LCT
The Human Phenotype Ontology lists these as features of the rare conditions LCT can cause. Each trait's page lists the other genes linked to it.
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). LCT gene: lactase. Retrieved 16 October 2026, from https://dantelabs.com/genes/lct
Dante Labs. LCT gene: lactase [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/lct
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