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Aliases for LCT Gene

Aliases for LCT Gene

  • Lactase 2 3
  • LPH 3 4 6
  • Lactase-Glycosylceramidase 3 4
  • LAC 3 6
  • Lactase-Phlorizin Hydrolase-1 3
  • Lactase-Phlorizin Hydrolase 3
  • EC 3.2.1 63
  • LPH1 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 family 1 of glycosyl hydrolases. The protein is integral to plasma membrane and has both phlorizin hydrolase activity and lactase activity. [provided by RefSeq, Jul 2008]

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 Metabolism and Metabolism. GO annotations related to this gene include glycosylceramidase activity and lactase activity. An important paralog of this gene is GBA3.

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

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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:
Reactome Protein details:
REFSEQ proteins:

Domains for LCT Gene

Suggested Antigen Peptide Sequences for LCT Gene

Graphical View of Domain Structure for InterPro Entry



  • P09848
  • 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 --
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds --
GO:0017042 glycosylceramidase activity IEA --
genes like me logo Genes that share ontologies with LCT: view

Animal Model Products

miRNA for LCT Gene

miRTarBase miRNAs that target LCT

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LCT

In Situ Assay Products

Flow Cytometry Products

No data available for Phenotypes , Animal Models , Transcription Factor Targeting 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
golgi apparatus 2
cytosol 1
endoplasmic reticulum 1
extracellular 1
lysosome 1
mitochondrion 1
nucleus 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for LCT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 2460343
GO:0016020 membrane TAS 2460343
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with LCT: view

Pathways 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:0005975 carbohydrate metabolic process TAS --
GO:0044245 polysaccharide digestion TAS --
GO:0044281 small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with LCT: view

Compounds for LCT Gene

(84) HMDB Compounds for LCT Gene

Compound Synonyms Cas Number PubMed IDs
  • 3-dehydro-beta-D-galactose
Not Available
  • 3'-dehydro-beta-D-galactosyl-beta-D-glucopyranoside
  • Hexopyranose
  • (+)-lactose
  • b-D-Glucopyranose

(15) Novoseek inferred chemical compound relationships for LCT Gene

Compound -log(P) Hits PubMed IDs
lactose 87.3 48
pyridoxine-5-beta-d-glucoside 86.1 4
phlorizin 84.4 23
iptg 45.6 2
galactose 43.5 6
genes like me logo Genes that share compounds with LCT: view

Transcripts for LCT Gene

mRNA/cDNA for LCT Gene

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

Unigene Clusters for LCT Gene

Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LCT

Primer Products

Flow Cytometry Products

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 (33.1).

Protein differential expression in normal tissues for LCT Gene

This gene is overexpressed in Pancreatic juice (68.0).

Integrated Proteomics: protein expression 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 expressions with LCT: view

Expression partners for LCT Gene

In Situ Assay 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

Selected 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 MAF
rs730005 -- 135,825,124(+) GCTGT(C/T)TGACT intron-variant
rs745500 -- 135,825,622(-) TTCTG(C/T)AGGAG intron-variant
rs746857 -- 135,797,320(+) TGTTG(A/G)GAATT intron-variant
rs748841 -- 135,800,587(+) ACAAG(C/T)GCCCA intron-variant
rs872151 -- 135,799,235(+) GTTTC(C/T)CCCGA intron-variant

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

Relevant External Links for LCT Gene

HapMap Linkage Disequilibrium report
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

MalaCards: The human disease database.

Search for LCT Gene in MalaCards »

(4) Diseases for LCT Gene including...

(1) OMIM Diseases for LCT Gene (603202)


  • 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.

(8) Novoseek inferred disease relationships for LCT Gene

Disease -log(P) Hits PubMed IDs
lactase deficiency, congenital 96.5 5
hypolactasia, adult type 90.2 2
lactose intolerance 89.9 12
lactase deficiency 77.2 2
malabsorption 26.4 1

Relevant External Links for LCT

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
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
  2. The C/C(-13910) and G/G(-22018) genotypes for adult-type hypolactasia are not associated with inflammatory bowel disease. (PMID: 12795467) BA1ning C. … Schmidt H. (Scand. J. Gastroenterol. 2003) 3 23 48
  3. The T allele of a single-nucleotide polymorphism 13.9 kb upstream of the lactase gene (LCT) (C-13.9kbT) does not predict or cause the lactase-persistence phenotype in Africans. (PMID: 15106124) Mulcare C.A. … Thomas M.G. (Am. J. Hum. Genet. 2004) 3 23 48
  4. Genotyping of the lactase-phlorizin hydrolase -13910 polymorphism by LightCycler PCR and implications for the diagnosis of lactose intolerance. (PMID: 16391332) Bodlaj G. … Berg J. (Clin. Chem. 2006) 3 23 48
  5. Mutations in the translated region of the lactase gene (LCT) underlie congenital lactase deficiency. (PMID: 16400612) Kuokkanen M. … Jaervelae I. (Am. J. Hum. Genet. 2006) 3 4 23

Products for LCT Gene

Sources for LCT Gene

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