The protein encoded by this gene belongs to the glycosyl hydrolase 1 family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme is integral to the plasma membrane and has both phlorizin hydrolase activity and lactase activity. Mutations in this gene are associated with congenital lactase deficiency. Polymorphisms in thi... See more...

Aliases for LCT Gene

Aliases for LCT Gene

  • Lactase 2 3 5
  • Lactase-Phlorizin Hydrolase 3 4
  • Lactase-Glycosylceramidase 3 4
  • LPH 3 4
  • Lactase-Phlorizin Hydrolase-1 3
  • EC 3.2.1 50
  • LPH1 3
  • LAC 3
  • LCT 5

External Ids for LCT Gene

Previous GeneCards Identifiers for LCT Gene

  • GC02M134200
  • GC02M134843
  • GC02M136567
  • GC02M136756
  • GC02M136379
  • GC02M136261
  • GC02M128538

Summaries for LCT Gene

Entrez Gene Summary for LCT Gene

  • The protein encoded by this gene belongs to the glycosyl hydrolase 1 family of proteins. The encoded preproprotein is proteolytically processed to generate the mature enzyme. This enzyme is integral to the plasma membrane and has both phlorizin hydrolase activity and lactase activity. Mutations in this gene are associated with congenital lactase deficiency. Polymorphisms in this gene are associated with lactase persistence, in which intestinal lactase activity persists at childhood levels into adulthood. [provided by RefSeq, Jan 2016]

GeneCards Summary for LCT Gene

LCT (Lactase) is a Protein Coding gene. Diseases associated with LCT include Lactase Deficiency, Congenital and Lactose Intolerance. Among its related pathways are Galactose metabolism and Glycosaminoglycan metabolism. Gene Ontology (GO) annotations related to this gene include hydrolase activity, hydrolyzing O-glycosyl compounds and lactase activity. An important paralog of this gene is KL.

UniProtKB/Swiss-Prot Summary for LCT Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LCT Gene

Genomics for LCT Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LCT Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J135836 Promoter/Enhancer 0.5 EPDnew ENCODE 250.7 +0.5 486 1.2 LCT DARS1 MCM6 RF00017-2996 UBXN4
GH02J135835 Enhancer 0.2 Ensembl 250.7 +1.5 1494 0.2 LCT RF00017-2996 UBXN4
GH02J135797 Enhancer 0.9 Ensembl ENCODE 12.8 +39.2 39194 1.6 ZNF654 MYC CEBPA ATF3 REST CTCF CEBPB TRIM22 BHLHE40 MNT DARS1 LCT-AS1 LCT MCM6 MAP3K19 RAB3GAP1 UBXN4 HSALNG0019075 HSALNG0019076
GH02J135791 Enhancer 0.8 Ensembl ENCODE 12.7 +45.0 44966 1.6 YY1 MAFF ZNF316 EBF1 MAFK BATF MAFG IKZF1 HNF4A RFX5 LCT-AS1 LCT RAB3GAP1 MAP3K19 UBXN4 HSALNG0019075 HSALNG0019074
GH02J135894 Enhancer 0.9 FANTOM5 Ensembl 11 -55.1 -55105 5.4 CTCF MNT ARNT ELF1 ZNF316 NFE2 SPI1 ETV1 EP400 FOXK2 DARS1 LCT LCT-AS1 ENSG00000200664 MCM6 MANEALP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCT on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LCT

Top Transcription factor binding sites by QIAGEN in the LCT gene promoter:
  • C/EBPalpha
  • COMP1
  • Evi-1
  • NF-kappaB
  • NF-kappaB1
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • PPAR-alpha
  • STAT5A

Genomic Locations for LCT Gene

Latest Assembly
49,346 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
49,335 bases
Minus strand

(GRCh37/hg19 by Ensembl)
49,341 bases
Minus strand

Genomic View for LCT Gene

Genes around LCT on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCT Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCT Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCT Gene

Proteins for LCT Gene

  • Protein details for LCT Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Lactase-phlorizin hydrolase
    Protein Accession:
    Secondary Accessions:
    • Q4ZG58

    Protein attributes for LCT Gene

    1927 amino acids
    Molecular mass:
    218587 Da
    Quaternary structure:
    No Data Available

neXtProt entry for LCT Gene

Selected DME Specific Peptides for LCT Gene


Post-translational modifications for LCT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LCT Gene

Domains & Families for LCT Gene

Gene Families for LCT Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins

Protein Domains for LCT Gene

  • Glycoside hydrolase, family 1
  • 6-phospho-beta-galactosidase, eukaryotic

Suggested Antigen Peptide Sequences for LCT Gene

GenScript: Design optimal peptide antigens:
  • Lactase-glycosylceramidase (LPH_HUMAN)
  • LCT (Q45V77_HUMAN)
  • Lactase-phlorizin hydrolase-1 (Q6Y1I9_HUMAN)

Graphical View of Domain Structure for InterPro Entry



  • The sequence exhibits 4 regions (I-IV) of internal homology; therefore LPH might have evolved by two cycles of partial gene duplication.
  • Belongs to the glycosyl hydrolase 1 family.
  • The sequence exhibits 4 regions (I-IV) of internal homology; therefore LPH might have evolved by two cycles of partial gene duplication.
  • Belongs to the glycosyl hydrolase 1 family.
genes like me logo Genes that share domains with LCT: view

Function for LCT Gene

Molecular function for LCT Gene

UniProtKB/Swiss-Prot Function:
LPH splits lactose in the small intestine.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + lactose = D-galactose + D-glucose; Xref=Rhea:RHEA:10076, ChEBI:CHEBI:4139, ChEBI:CHEBI:4167, ChEBI:CHEBI:15377, ChEBI:CHEBI:17716; EC=;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Glycosyl-N-acylsphingosine + H(2)O = N-acylsphingosine + a sugar.; EC=;.
GENATLAS Biochemistry:
lactase/phlorizin hydrolase,beta-galactosidase from intestinal mucosa

Enzyme Numbers (IUBMB) for LCT Gene

Phenotypes From GWAS Catalog for LCT Gene

Gene Ontology (GO) - Molecular Function for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000016 lactase activity TAS,IBA 21873635
GO:0003824 catalytic activity IEA --
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds IEA --
GO:0008422 beta-glucosidase activity IBA 21873635
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with LCT: view
genes like me logo Genes that share phenotypes with LCT: view

Human Phenotype Ontology for LCT Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for LCT Gene

miRTarBase miRNAs that target LCT

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCT

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for LCT Gene

Localization for LCT Gene

Subcellular locations from UniProtKB/Swiss-Prot for LCT Gene

Apical cell membrane. Single-pass type I membrane protein. Note=Brush border.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCT gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 4
extracellular 2
mitochondrion 2
nucleus 2
cytosol 2
lysosome 2
golgi apparatus 2
cytoskeleton 1
peroxisome 1
endosome 1

Gene Ontology (GO) - Cellular Components for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IBA 21873635
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 2460343
GO:0016020 membrane TAS 2460343
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with LCT: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LCT Gene

Pathways & Interactions for LCT Gene

genes like me logo Genes that share pathways with LCT: view

Pathways by source for LCT Gene

1 GeneGo (Thomson Reuters) pathway for LCT Gene
  • Galactose metabolism

SIGNOR curated interactions for LCT Gene

Is activated by:

Gene Ontology (GO) - Biological Process for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IEA --
GO:0008152 metabolic process IEA --
GO:0044245 polysaccharide digestion TAS --
genes like me logo Genes that share ontologies with LCT: view

Drugs & Compounds for LCT Gene

(23) Drugs for LCT Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
lactose Approved, Experimental, Investigational Pharma 0
Gluconolactone Approved, Experimental Pharma Target 0
D-glucose Approved, Experimental, Investigational, Vet_approved Pharma 0
Glycerol Approved, Investigational Pharma 207
Water Approved Pharma 0

(84) Additional Compounds for LCT Gene - From: HMDB and Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 3-Dehydro-beta-D-galactose
  • 3-Dehydro-beta-delta-galactose
  • 3-Keto-beta-D-galactose
  • 3-Keto-beta-delta-galactose
  • 3-Keto-b-D-galactose
  • 3'-Dehydro-beta-D-galactosyl-beta-D-glucopyranoside
  • 3'-Dehydro-beta-delta-galactosyl-beta-delta-glucopyranoside
  • 4-O-(beta-D-Xylo-hexopyranosyl-3-ulose)-D-glucopyranose
  • 4-O-beta-D-Xylo-hexopyranos-3-ulos-1-yl-D-glucose
  • alpha-D-GLC
  • alpha-Dextrose
  • a-D-GLC
  • Α-D-GLC
  • a-Dextrose
  • beta-D-Gal
  • Gal-beta
  • b-D-Gal
  • β-D-Gal
  • b-D-Galactose
  • 4-O-beta-D-Galactopyranosyl-beta-D-glucopyranose
  • beta-D-Galactopyranosyl-(1->4)-beta-D-glucose
  • beta-D-Galp-(1->4)-beta-D-GLCP
  • beta-D-Lactose
  • Galb1-4GLCB
genes like me logo Genes that share compounds with LCT: view

Transcripts for LCT Gene

mRNA/cDNA for LCT Gene

2 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCT

Alternative Splicing Database (ASD) splice patterns (SP) for LCT Gene

No ASD Table

Relevant External Links for LCT Gene

GeneLoc Exon Structure for

Expression for LCT Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LCT Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LCT Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x33.1).

Protein differential expression in normal tissues from HIPED for LCT Gene

This gene is overexpressed in Pancreatic juice (68.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LCT Gene

Protein tissue co-expression partners for LCT Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LCT

SOURCE GeneReport for Unigene cluster for LCT Gene:


mRNA Expression by UniProt/SwissProt for LCT Gene:

Tissue specificity: Intestine.

Evidence on tissue expression from TISSUES for LCT Gene

  • Intestine(3.6)
  • Stomach(2.5)
  • Nervous system(2.3)
  • Muscle(2.2)
  • Lung(2.2)
  • Blood(2.2)
  • Heart(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for LCT Gene

Germ Layers:
  • endoderm
  • digestive
  • duodenum
  • intestine
  • large intestine
  • small intestine
genes like me logo Genes that share expression patterns with LCT: view

Primer products for research

Orthologs for LCT Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LCT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LCT 29 30
  • 99.01 (n)
(Canis familiaris)
Mammalia LCT 29 30
  • 86.92 (n)
(Bos Taurus)
Mammalia LCT 29 30
  • 85.28 (n)
(Mus musculus)
Mammalia Lct 29 16 30
  • 80.23 (n)
(Rattus norvegicus)
Mammalia Lct 29
  • 79.68 (n)
(Monodelphis domestica)
Mammalia LCT 30
  • 72 (a)
(Ornithorhynchus anatinus)
Mammalia LCT 30
  • 67 (a)
(Gallus gallus)
Aves LCT 29 30
  • 65.14 (n)
(Anolis carolinensis)
Reptilia LCT 30
  • 61 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia lct.2 29
  • 63.75 (n)
(Danio rerio)
Actinopterygii lct 29 30
  • 58.75 (n)
SI:DKEY-79P17.2 30
  • 54 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta CG9701 30 31
  • 43 (a)
(Caenorhabditis elegans)
Secernentea E02H9.5 31
  • 35 (a)
klo-2 30
  • 34 (a)
klo-1 30
  • 34 (a)
C50F7.10 31
  • 33 (a)
(Glycine max)
eudicotyledons Gma.16515 29
(Oryza sativa)
Liliopsida Os.35044 29
(Triticum aestivum)
Liliopsida Ta.4035 29
(Zea mays)
Liliopsida Zm.418 29
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 53 (a)
-- 30
  • 51 (a)
-- 30
  • 45 (a)
Species where no ortholog for LCT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for LCT Gene

Gene Tree for LCT (if available)
Gene Tree for LCT (if available)
Evolutionary constrained regions (ECRs) for LCT: view image
Alliance of Genome Resources:
Additional Orthologs for LCT

Paralogs for LCT Gene

Paralogs for LCT Gene

(4) SIMAP similar genes for LCT Gene using alignment to 4 proteins:

  • H0Y4E4_HUMAN
  • Q45V77_HUMAN
  • Q6Y1I9_HUMAN
genes like me logo Genes that share paralogs with LCT: view

Variants for LCT Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LCT Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
1002395 Uncertain Significance: not provided 135,836,746(-) G/A
NM_002299.4(LCT):c.424C>T (p.Arg142Trp)
1016272 Uncertain Significance: not provided 135,804,097(-) G/A
NM_002299.4(LCT):c.4496C>T (p.Thr1499Met)
1025930 Uncertain Significance: not provided 135,788,386(-) G/A
NM_002299.4(LCT):c.5722C>T (p.Arg1908Cys)
1032814 Uncertain Significance: Congenital lactase deficiency 135,788,385(-) C/T
NM_002299.4(LCT):c.5723G>A (p.Arg1908His)
1036577 Uncertain Significance: not provided 135,800,723(-) C/T
NM_002299.4(LCT):c.4750G>A (p.Asp1584Asn)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LCT Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LCT Gene

Variant ID Type Subtype PubMed ID
esv3592582 CNV gain 21293372
nsv1116797 CNV deletion 24896259
nsv1123397 CNV deletion 24896259
nsv2942 CNV insertion 18451855
nsv471870 CNV novel sequence insertion 20440878
nsv480348 CNV novel sequence insertion 20440878
nsv819525 CNV gain 19587683

Variation tolerance for LCT Gene

Residual Variation Intolerance Score: 7.97% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.69; 93.22% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCT Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for
Leiden Open Variation Database (LOVD)

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCT Gene

Disorders for LCT Gene

MalaCards: The human disease database

(23) MalaCards diseases for LCT Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search LCT in MalaCards View complete list of genes associated with diseases


  • Congenital lactase deficiency (COLACD) [MIM:223000]: Autosomal recessive, rare and severe gastrointestinal disorder. It is characterized by watery diarrhea in infants fed with breast milk or other lactose-containing formulas. An almost total lack of LCT activity is found in jejunal biopsy material of patients with congenital lactase deficiency. Opposite to congenital lactase deficiency, also known as lactose intolerance, is the most common enzyme deficiency worldwide. It is caused by developmental down-regulation of lactase activity during childhood or early adulthood. The decline of lactase activity is a normal physiological phenomenon; however, the majority of Northern Europeans have the ability to maintain lactase activity and digest lactose throughout life (lactase persistence). The down-regulation of lactase activity operates at the transcriptional level and it is associated with a noncoding variation in the MCM6 gene, located in the upstream vicinity of LCT. {ECO:0000269 PubMed:16400612}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for LCT

Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LCT: view

No data available for Genatlas for LCT Gene

Publications for LCT Gene

  1. Mutations in the translated region of the lactase gene (LCT) underlie congenital lactase deficiency. (PMID: 16400612) Kuokkanen M … Jarvela I (American journal of human genetics 2006) 3 4 22 72
  2. Identification of a variant associated with adult-type hypolactasia. (PMID: 11788828) Enattah NS … Järvelä I (Nature genetics 2002) 3 4 22 40
  3. Genes related to the metabolism of nutrients in the Kola Sami population. (PMID: 18468259) Kozlov A … Yankovsky N (International journal of circumpolar health 2008) 3 22 40
  4. Genetic testing for adult-type hypolactasia in Italian families. (PMID: 18605960) Mottes M … Borgna-Pignatti C (Clinical chemistry and laboratory medicine 2008) 3 22 40
  5. Effects of the lactase 13910 C/T and calcium-sensor receptor A986S G/T gene polymorphisms on the incidence and recurrence of colorectal cancer in Hungarian population. (PMID: 18980667) Bácsi K … Speer G (BMC cancer 2008) 3 22 40

Products for LCT Gene

Sources for LCT Gene