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    LCT lactase [ Homo sapiens (human) ]

    Gene ID: 3938, updated on 10-Dec-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
    mouse all
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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
    • 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
    		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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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