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LCT lactase [ Homo sapiens (human) ]

Gene ID: 3938, updated on 12-Aug-2018

Summary

Official Symbol
LCTprovided by HGNC
Official Full Name
lactaseprovided by HGNC
Primary source
HGNC:HGNC:6530
See related
Ensembl:ENSG00000115850 MIM:603202; Vega:OTTHUMG00000131738
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

Genomic context

See LCT in Genome Data Viewer
Location:
2q21.3
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (135787840..135837195, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (136545415..136594750, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene R3H domain containing 1 Neighboring gene microRNA 128-1 Neighboring gene uncharacterized LOC107985946 Neighboring gene UBX domain protein 4 Neighboring gene uncharacterized LOC100507600 Neighboring gene minichromosome maintenance complex component 6 Neighboring gene mannosidase endo-alpha like pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Congenital lactase deficiency
MedGen: C0268179 OMIM: 223000 GeneReviews: Not available
Compare labs

NHGRI 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.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
beta-glucosidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
glycosylceramidase activity IEA
Inferred from Electronic Annotation
more info
 
lactase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lactase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
carbohydrate metabolic process IEA
Inferred from Electronic Annotation
more info
 
polysaccharide digestion TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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_002299.3NP_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
    Related
    ENSP00000264162.2, OTTHUMP00000162531, ENST00000264162.6, OTTHUMT00000254657
    Conserved Domains (2) summary
    pfam00232
    Location:8991364
    Glyco_hydro_1; Glycosyl hydrolase family 1
    cl23725
    Location:84221
    Glyco_hydro_1; Glycosyl hydrolase family 1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    135787840..135837195 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004088.2XP_016859577.1  lactase-phlorizin hydrolase isoform X1

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