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Aliases for LCT Gene

Aliases for LCT Gene

  • Lactase 5 2 3
  • Lactase-Glycosylceramidase 3 4
  • LPH 3 4
  • Lactase-Phlorizin Hydrolase-1 3
  • EC 3.2.1 63
  • LPH1 3
  • LAC 3

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 Glycosaminoglycan metabolism and Galactose metabolism. 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 for LCT Gene

  • LPH splits lactose in the small intestine.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCT Gene

Genomics for LCT Gene

Regulatory Elements for LCT Gene

Enhancers for LCT Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around LCT on UCSC Golden Path with GeneCards custom track

Genomic Location for LCT Gene

135,787,840 bp from pter
135,837,180 bp from pter
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

Proteomics data for LCT Gene at MOPED

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

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for LCT Gene

Suggested Antigen Peptide Sequences for LCT Gene

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

No data available for Gene Families for LCT Gene

Function for LCT Gene

Molecular function for LCT Gene

GENATLAS Biochemistry:
lactase/phlorizin hydrolase,beta-galactosidase from intestinal mucosa
UniProtKB/Swiss-Prot CatalyticActivity:
Lactose + H(2)O = D-galactose + D-glucose.
UniProtKB/Swiss-Prot CatalyticActivity:
Glycosyl-N-acylsphingosine + H(2)O = N-acylsphingosine + a sugar.
UniProtKB/Swiss-Prot Function:
LPH splits lactose in the small intestine.

Enzyme Numbers (IUBMB) for LCT Gene

Gene Ontology (GO) - Molecular Function for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000016 lactase activity TAS --
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

Animal Model Products

miRNA for LCT Gene

miRTarBase miRNAs that target 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

Jensen Localization Image for LCT Gene COMPARTMENTS Subcellular localization image for LCT gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
extracellular 2
golgi apparatus 2
cytosol 1
lysosome 1
nucleus 1
peroxisome 1
vacuole 1

Gene Ontology (GO) - Cellular Components for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with LCT: view

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

Gene Ontology (GO) - Biological Process for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IEA --
GO:0005975 carbohydrate metabolic process IEA --
GO:0009744 response to sucrose IEA --
GO:0010033 response to organic substance IEA --
GO:0010045 response to nickel cation IEA --
genes like me logo Genes that share ontologies with LCT: view

No data available for SIGNOR curated interactions for LCT Gene

Drugs & Compounds for LCT Gene

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vitamin C Approved Nutra Target 471,471
lactose Experimental Pharma 0
2-Deoxy-2fluoro-Glucose Experimental Pharma Target 0

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

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'-Dehydro-beta-D-galactosyl-beta-D-glucopyranoside
  • 3'-Dehydro-beta-delta-galactosyl-beta-delta-glucopyranoside
  • 3'-Ketolactose
  • a-D-Glucopyranose
  • a-D-Glucose
  • a-Dextrose
  • a-Glucose
  • alpha-D-Glucopyranose
  • b-D-Galactose
  • b-Galactose
  • beta D-Galactose
  • beta-D-Galactopyranose
  • beta-D-Galactose
  • beta-D-Galactopyranosyl-(1->4)-beta-D-glucopyranose
  • beta-D-Galactopyranosyl-(1->4)-beta-D-glucose
  • beta-Lactose
genes like me logo Genes that share compounds with LCT: view

Transcripts for LCT Gene

mRNA/cDNA for LCT Gene

(1) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(16) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for LCT Gene

Representative Sequences:

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

No ASD Table

Relevant External Links for LCT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LCT Gene

mRNA expression in normal human tissues 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, PaxDb, and MOPED for LCT Gene

SOURCE GeneReport for Unigene cluster for LCT Gene Hs.551506

mRNA Expression by UniProt/SwissProt for LCT Gene

Tissue specificity: Intestine.
genes like me logo Genes that share expression patterns with LCT: view

Protein tissue co-expression partners for LCT Gene

- Elite partner

Primer Products

Orthologs for LCT Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LCT Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia LCT 35
  • 85.28 (n)
  • 83.69 (a)
LCT 36
  • 84 (a)
(Canis familiaris)
Mammalia LCT 35
  • 86.92 (n)
  • 86.01 (a)
LCT 36
  • 88 (a)
(Mus musculus)
Mammalia Lct 35
  • 80.23 (n)
  • 80.15 (a)
Lct 16
Lct 36
  • 80 (a)
(Pan troglodytes)
Mammalia LCT 35
  • 99.01 (n)
  • 98.3 (a)
LCT 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Lct 35
  • 79.68 (n)
  • 79.37 (a)
(Monodelphis domestica)
Mammalia LCT 36
  • 72 (a)
(Ornithorhynchus anatinus)
Mammalia LCT 36
  • 67 (a)
(Gallus gallus)
Aves LCT 35
  • 65.14 (n)
  • 63.99 (a)
LCT 36
  • 63 (a)
(Anolis carolinensis)
Reptilia LCT 36
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lct.2 35
  • 63.75 (n)
  • 62.26 (a)
(Danio rerio)
Actinopterygii lct 35
  • 58.75 (n)
  • 55.93 (a)
lct 36
  • 53 (a)
SI:DKEY-79P17.2 36
  • 54 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG9701 37
  • 46 (a)
CG9701 36
  • 43 (a)
(Caenorhabditis elegans)
Secernentea C50F7.10 37
  • 33 (a)
E02H9.5 37
  • 35 (a)
klo-1 36
  • 34 (a)
klo-2 36
  • 34 (a)
(Glycine max)
eudicotyledons Gma.16515 35
(Oryza sativa)
Liliopsida Os.35044 35
(Triticum aestivum)
Liliopsida Ta.4035 35
(Zea mays)
Liliopsida Zm.418 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 45 (a)
-- 36
  • 53 (a)
-- 36
  • 51 (a)
Species with no ortholog for LCT:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for LCT Gene

Paralogs for LCT Gene

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

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

Variants for LCT Gene

Sequence variations from dbSNP and Humsavar for LCT Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs3754689 - 135,833,176(-) TCTCT(A/G/T)TTGTC reference, missense
VAR_026706 Congenital lactase deficiency (COLACD)
rs4954449 - 135,817,964(+) CCAGA(C/T)TCTCT reference, missense
VAR_026708 Congenital lactase deficiency (COLACD)
rs2322659 - 135,798,089(+) CCTCA(C/T)TGTAA reference, missense

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

Variant ID Type Subtype PubMed ID
nsv819525 CNV Gain 19587683
nsv2942 CNV Insertion 18451855

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)

Relevant External Links for LCT Gene

Human Gene Mutation Database (HGMD)

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

Disorders for LCT Gene

MalaCards: The human disease database

(9) MalaCards diseases for LCT Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
lactase deficiency, congenital
  • congenital lactase deficiency
lactose intolerance
  • lm - lactose malabsorption
lactase persistence/nonpersistence
  • lactose intolerance, adult type
neonatal thyrotoxicosis
osmotic diarrhea
- 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 mutations affecting the gene represented in this entry.

Relevant External Links for LCT

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with LCT: view

No data available for Genatlas for LCT Gene

Publications for LCT Gene

  1. Identification of a variant associated with adult-type hypolactasia. (PMID: 11788828) Enattah N.S. … Jaervelae I. (Nat. Genet. 2002) 3 4 23 48 67
  2. Structural hierarchy of regulatory elements in the folding and transport of an intestinal multidomain protein. (PMID: 19955176) Behrendt M. … Naim H.Y. (J. Biol. Chem. 2010) 3 23
  3. Four novel mutations in the lactase gene (LCT) underlying congenital lactase deficiency (CLD). (PMID: 19161632) Torniainen S. … JAorvelAo I. (BMC Gastroenterol 2009) 3 23
  4. Independent introduction of two lactase-persistence alleles into human populations reflects different history of adaptation to milk culture. (PMID: 18179885) Enattah N.S. … Peltonen L. (Am. J. Hum. Genet. 2008) 3 23
  5. Evaluation of a novel reverse-hybridization StripAssay for typing DNA variants useful in diagnosis of adult-type hypolactasia. (PMID: 18396155) Tag C.G. … Weiskirchen R. (Clin. Chim. Acta 2008) 3 23

Products for LCT Gene

Sources for LCT Gene