LCT Gene (Lactase) - Function, Deficiency, and Clinical Significance
Comprehensive biomedical resource for the LCT gene encoding lactase-phlorizin hydrolase, including genetic variants, expression, and associated disorders.
Gene Information Card
| Symbol | LCT |
|---|---|
| Full Name | Lactase |
| Gene Type | protein-coding |
| Chromosomal Location | 2q21.3 |
| NCBI Gene ID | 3938 ncbi.nlm.nih.gov/gene/3938 |
| Ensembl ID | ENSG00000115850 |
| UniProt ID | P09848 |
| OMIM ID | 603202 |
| HGNC ID | 6530 |
| Aliases | LAC, LPH, lactase-phlorizin hydrolase |
Description
The LCT gene encodes lactase-phlorizin hydrolase, an enzyme expressed primarily in the brush border of the small intestine. It catalyzes the hydrolysis of lactose into glucose and galactose, essential for dairy digestion. Genetic variants in LCT are associated with adult-type hypolactasia (lactose intolerance) and rare congenital lactase deficiency. The gene is located on chromosome 2q21.3 and spans approximately 49 kb with 17 exons.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Lactose intolerance, adult type | Reduced LCT expression due to non-coding variants (e.g., rs4988235) leads to lactase non-persistence, causing malabsorption of lactose. | ClinVar, OMIM |
| Congenital lactase deficiency | Biallelic loss-of-function mutations in LCT (e.g., p.Tyr1390*) result in absent lactase activity from birth, causing severe diarrhea upon lactose ingestion. | ClinVar, OMIM |
| Lactose intolerance, congenital | Same as congenital lactase deficiency; early-onset severe lactose malabsorption due to LCT mutations. | OMIM |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Small intestine | 102.8 | High |
| Kidney | 0.2 | Not detected |
| Liver | 0.1 | Not detected |
| Pancreas | 0.1 | Not detected |
| Colon | 0.1 | Not detected |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| Caco-2 | 0.0 | Colorectal adenocarcinoma cell line; LCT expression not detected in standard RNA-seq. |
| HT-29 | 0.0 | Colorectal adenocarcinoma cell line; LCT expression not detected. |
| HCT 116 | 0.0 | Colorectal carcinoma cell line; LCT expression not detected. |
| SW480 | 0.0 | Colorectal adenocarcinoma cell line; LCT expression not detected. |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| rs4988235 | SNP (intronic) | High (global ~40-80% depending on population) | Associated with lactase non-persistence; reduces LCT expression in adulthood. |
| c.4170T>A (p.Tyr1390*) | Nonsense | Rare | Loss-of-function; causes congenital lactase deficiency. |
| c.300+1G>A | Splice donor | Rare | Loss-of-function; causes congenital lactase deficiency. |
| c.5579C>T (p.Thr1860Met) | Missense | Rare | Likely loss-of-function; reported in congenital lactase deficiency. |
Mutation functional classification
Loss of Function (LOF)
Nonsense, frameshift, and splice-site mutations in LCT (e.g., p.Tyr1390*, c.300+1G>A) result in truncated or absent lactase enzyme, leading to congenital lactase deficiency.
Gain of Function (GOF)
No gain-of-function mutations are reported for LCT.
Dominant Negative (DN)
No dominant-negative mutations are reported for LCT.
View complete mutation data：
Gene Ontology (GO)
| • lactase activity | • phlorizin hydrolase activity |
| • hydrolase activity | • hydrolyzing O-glycosyl compounds |
| • carbohydrate metabolic process | • lactose catabolic process |
| • brush border membrane | • integral component of membrane |
Pathways
• Lactose degradation
• Galactose metabolism
• Carbohydrate digestion and absorption
Protein Summary
Lactase-phlorizin hydrolase (LPH) is a type I transmembrane protein of 1927 amino acids (UniProt P09848). It is synthesized as a single-chain precursor and proteolytically cleaved into mature LPH localized to the intestinal brush border. The enzyme has two active sites: one for lactase activity (hydrolyzing lactose) and one for phlorizin hydrolase activity (hydrolyzing glycosylceramides). LPH is essential for lactose digestion in mammals.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| LCT Knockout HEK293 Cell Line | EDJ-KQ5113 | Human | 3938 | Details Get a Quote |
| B3GLCT Knockout HEK293 Cell Line | EDJ-KQ10430 | Human | 145173 | Details Get a Quote |
| LCTL Knockout HEK293 Cell Line | EDJ-KQ11579 | Human | 197021 | Details Get a Quote |
| B3GLCT Knockout A-549 Cell Line | EDJ-KQ37801 | Human | 145173 | Details Get a Quote |
| B3GLCT Knockout HCT 116 Cell Line | EDJ-KQ37802 | Human | 145173 | Details Get a Quote |
| B3GLCT Knockout HeLa Cell Line | EDJ-KQ37803 | Human | 145173 | Details Get a Quote |
| LCTL Knockout A-549 Cell Line | EDJ-KQ39914 | Human | 197021 | Details Get a Quote |
| LCTL Knockout HeLa Cell Line | EDJ-KQ39915 | Human | 197021 | Details Get a Quote |
| LCT Knockout HeLa Cell Line | EDJ-KQ53784 | Human | 3938 | Details Get a Quote |
| LCT Knockout A-549 Cell Line | EDJ-KQ62262 | Human | 3938 | Details Get a Quote |
| LCT Knockout HCT 116 Cell Line | EDJ-KQ70746 | Human | 3938 | Details Get a Quote |
| LCTL Knockout HCT 116 Cell Line | EDJ-KQ75859 | Human | 197021 | Details Get a Quote |
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