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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]
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. 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.
GeneHancer (GH) Identifier | GH Type | GH Score |
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 RF00017-3320 UBXN4 | ||
GH02J135835 | Enhancer | 0.2 | Ensembl | 250.7 | +1.5 | 1494 | 0.2 | LCT RF00017-3320 UBXN4 | ||
GH02J135797 | Enhancer | 0.9 | Ensembl ENCODE | 12.8 | +39.2 | 39194 | 1.6 | CEBPA MNT CTCF BHLHE40 ELF1 CEBPB SIN3A REST MAX TRIM22 | DARS1 LCT-AS1 LCT MCM6 MAP3K19 RAB3GAP1 UBXN4 HSALNG0019075 HSALNG0019076 | |
GH02J135791 | Enhancer | 0.8 | Ensembl ENCODE | 12.7 | +45.0 | 44966 | 1.6 | MAFF EBF1 ZNF316 BATF MAFK MAFG IKZF1 HNF4A RFX5 NBN | LCT-AS1 LCT RAB3GAP1 MAP3K19 UBXN4 HSALNG0019075 NONHSAG029370.2 | |
GH02J135894 | Enhancer | 0.9 | FANTOM5 Ensembl | 11 | -55.1 | -55105 | 5.4 | MNT ARNT CTCF ELF1 ZNF316 SPI1 NFE2 FOXK2 EP400 MAFG | DARS1 LCT LCT-AS1 ENSG00000200664 MCM6 MANEALP1 |
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 | -- |
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 | -- |
SuperPathway | Contained pathways | ||
---|---|---|---|
1 | Galactose metabolism |
Galactose metabolism
.38
|
|
2 | Metabolism |
.40
|
|
3 | Carbohydrate digestion and absorption | ||
4 | Digestion of dietary carbohydrate | ||
5 | Glycosaminoglycan metabolism |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0005975 | carbohydrate metabolic process | IEA | -- |
GO:0008152 | metabolic process | IEA | -- |
GO:0044245 | polysaccharide digestion | TAS | -- |
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 | 205 | |||
Water | Approved | Pharma | 0 |
Name | Synonyms | Role | CAS Number | PubChem IDs | PubMed IDs | |
---|---|---|---|---|---|---|
3-Keto-b-D-galactose |
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3'-Ketolactose |
|
15990-62-2 |
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alpha-D-Glucose |
|
492-62-6 |
|
|||
beta-D-Galactose |
|
7296-64-2 |
|
|||
beta-Lactose |
|
5965-66-2 |
|
This gene was present in the common ancestor of eukaryotes.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | LCT 30 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | LCT 30 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | LCT 30 31 |
|
OneToOne | |
Mouse (Mus musculus) |
Mammalia | Lct 30 17 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Lct 30 |
|
||
Oppossum (Monodelphis domestica) |
Mammalia | LCT 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | LCT 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | LCT 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | LCT 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | lct.2 30 |
|
||
Zebrafish (Danio rerio) |
Actinopterygii | lct 30 31 |
|
OneToMany | |
SI:DKEY-79P17.2 31 |
|
OneToMany | |||
Fruit Fly (Drosophila melanogaster) |
Insecta | CG9701 31 32 |
|
OneToMany | |
Worm (Caenorhabditis elegans) |
Secernentea | E02H9.5 32 |
|
|
|
klo-2 31 |
|
ManyToMany | |||
klo-1 31 |
|
ManyToMany | |||
C50F7.10 32 |
|
|
|||
Soybean (Glycine max) |
eudicotyledons | Gma.16515 30 |
|
||
Rice (Oryza sativa) |
Liliopsida | Os.35044 30 |
|
||
Wheat (Triticum aestivum) |
Liliopsida | Ta.4035 30 |
|
||
Corn (Zea mays) |
Liliopsida | Zm.418 30 |
|
||
Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
ManyToMany | |
-- 31 |
|
ManyToMany | |||
-- 31 |
|
ManyToMany |
SNP ID | Clinical significance and condition | Chr 02 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
892984 | Uncertain Significance: Congenital lactase deficiency | 135,789,743(-) |
A/G NM_002299.4(LCT):c.5391T>C (p.Asn1797=) |
SYNONYMOUS | |
892985 | Uncertain Significance: Congenital lactase deficiency | 135,790,653(-) |
C/T NM_002299.4(LCT):c.5335+5G>A |
INTRON | |
892986 | Likely Benign: Congenital lactase deficiency | 135,800,595(-) |
G/A NM_002299.4(LCT):c.4866+12C>T |
INTRON | |
892987 | Uncertain Significance: Congenital lactase deficiency | 135,800,697(-) |
G/A NM_002299.4(LCT):c.4776C>T (p.Gly1592=) |
SYNONYMOUS | |
893033 | Uncertain Significance: Congenital lactase deficiency | 135,808,692(-) |
G/C NM_002299.4(LCT):c.3655C>G (p.Pro1219Ala) |
MISSENSE |
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 |
Disorder | Aliases | PubMed IDs |
---|---|---|
lactase deficiency, congenital |
|
|
lactose intolerance |
|
|
osmotic diarrhea |
|
|
sucrase-isomaltase deficiency, congenital |
|
|
outlet dysfunction constipation |
|
|