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LCT lactase [ Homo sapiens (human) ]

Gene ID: 3938, updated on 2-Nov-2024

Summary

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Official Symbol
LCTprovided by HGNC
Official Full Name
lactaseprovided by HGNC
Primary source
HGNC:HGNC:6530
See related
Ensembl:ENSG00000115850 MIM:603202; AllianceGenome:HGNC:6530
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LAC; LPH; LPH1
Summary
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]
Expression
Biased expression in duodenum (RPKM 121.7) and small intestine (RPKM 73.8) See more
Orthologs
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Genomic context

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See LCT in Genome Data Viewer
Location:
2q21.3
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135787850..135837184, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (136228325..136281636, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (136545420..136594754, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene R3H domain containing 1 Neighboring gene uncharacterized LOC124907893 Neighboring gene microRNA 128-1 Neighboring gene uncharacterized LOC107985946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16577 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:136499891-136500666 Neighboring gene UBX domain protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:136554979-136555500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:136555501-136556024 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:136574960-136576159 Neighboring gene LCT antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:136633103-136633638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16579 Neighboring gene minichromosome maintenance complex component 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:136656467-136656966 Neighboring gene MANEAL pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Evaluation of a novel reverse-hybridization StripAssay for typing DNA variants useful in diagnosis of adult-type hypolactasia. Tag CG, et al. Clin Chim Acta, 2008 Jun. PMID 18396155
  2. Impact of molecularly defined hypolactasia, self-perceived milk intolerance and milk consumption on bone mineral density in a population sample in Northern Europe. Kull M, et al. Scand J Gastroenterol, 2009. PMID 19039706
  3. Lactose digestion and the evolutionary genetics of lactase persistence. Ingram CJ, et al. Hum Genet, 2009 Jan. PMID 19034520
  4. Genetic test for lactase non-persistence and hydrogen breath test: is genotype better than phenotype to diagnose lactose malabsorption? Di Stefano M, et al. Dig Liver Dis, 2009 Jul. PMID 19010095
  5. [Diagnosing lactose intolerance in adults]. Jørgensen MK, et al. Ugeskr Laeger, 2008 Oct 13. PMID 18940163

See all (167) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Variant of the lactase LCT gene explains association between milk intake and incident type 2 diabetes.
    Title: Variant of the lactase LCT gene explains association between milk intake and incident type 2 diabetes.
  2. Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.
    Title: Association of Estimated Daily Lactose Consumption, Lactase Persistence Genotype (rs4988235), and Gut Microbiota in Healthy Adults in the United States.
  3. DNA polymorphisms associated with lactase persistence, self-perceived symptoms of lactose intolerance, milk and dairy consumption, and ancestry, in the Uruguayan population.
    Title: DNA polymorphisms associated with lactase persistence, self-perceived symptoms of lactose intolerance, milk and dairy consumption, and ancestry, in the Uruguayan population.
  4. Milk intake, lactase persistence genotype, plasma proteins and risks of cardiovascular events in the Swedish general population.
    Title: Milk intake, lactase persistence genotype, plasma proteins and risks of cardiovascular events in the Swedish general population.
  5. Very low frequency of the lactase persistence allele LCT-13910T in the Armenian population.
    Title: Very low frequency of the lactase persistence allele LCT-13910T in the Armenian population.
  6. Lactase persistence phenotype and genotype in Iranian Mazani-Shahmirzadi and Afghan Hazara ethnicities.
    Title: Lactase persistence phenotype and genotype in Iranian Mazani-Shahmirzadi and Afghan Hazara ethnicities.
  7. Hypomorphic variants of lactase-phlorizin hydrolase in congenital lactase deficiency are trafficking incompetent and functionally inactive.
    Title: Hypomorphic variants of lactase-phlorizin hydrolase in congenital lactase deficiency are trafficking incompetent and functionally inactive.
  8. Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.
    Title: Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project.
  9. Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.
    Title: Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort.
  10. Development of a novel SNP assay to detect lactase persistence associated genetic variants.
    Title: Development of a novel SNP assay to detect lactase persistence associated genetic variants.
Submit: New GeneRIF Correction See all GeneRIFs (118)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Congenital lactase deficiency
MedGen: C0268179 OMIM: 223000 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables beta-glucosidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables beta-glucosidase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables cellobiose glucosidase activity IEA
Inferred from Electronic Annotation
more info
  
enables galactosylceramidase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables glucosylceramidase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables lactase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables lactase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables lactase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables phlorizin hydrolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in cellobiose catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glycosylceramide catabolic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lactose catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in quercetin catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in external side of apical plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
lactase/phlorizin hydrolase
Names
lactase-glycosylceramidase
lactase-phlorizin hydrolase-1
NP_002290.2
XP_016859577.1
XP_054197984.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008104.2 RefSeqGene

    Range
    22990..72325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_338

mRNA and Protein(s)

  1. NM_002299.4 → NP_002290.2  lactase/phlorizin hydrolase preproprotein

    See identical proteins and their annotated locations for NP_002290.2

    Status: REVIEWED

    Source sequence(s)
    AC011893, BX642122, X07994
    Consensus CDS
    CCDS2178.1
    UniProtKB/Swiss-Prot
    P09848, Q4ZG58
    Related
    ENSP00000264162.2, ENST00000264162.7
    Conserved Domains (2) summary
    pfam00232
    Location:899 → 1364
    Glyco_hydro_1; Glycosyl hydrolase family 1
    cl23725
    Location:84 → 221
    Glyco_hydro_1; Glycosyl hydrolase family 1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    135787850..135837184 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004088.3 → XP_016859577.1  lactase/phlorizin hydrolase isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    136228325..136281636 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342009.1 → XP_054197984.1  lactase/phlorizin hydrolase isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P09848.3 GenPept UniProtKB/Swiss-Prot:P09848

Gene LinkOut

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