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    LCT lactase [ Homo sapiens (human) ]

    Gene ID: 3938, updated on 5-Mar-2024

    Summary

    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
    NEW
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    Genomic context

    Location:
    2q21.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (135787850..135837184, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (136228325..136281636, complement)
    105.20220307 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

    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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 glycosylceramidase activity IEA
    Inferred from Electronic Annotation
    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

    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)

    NEW Try the new Transcript table

    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_002299.4NP_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:8991364
      Glyco_hydro_1; Glycosyl hydrolase family 1
      cl23725
      Location:84221
      Glyco_hydro_1; Glycosyl hydrolase family 1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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_017004088.3XP_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_054342009.1XP_054197984.1  lactase/phlorizin hydrolase isoform X1