LCT lactase [Homo sapiens (human)] - Gene

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: mouse all
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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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
Relation of the C/T-13910 LCT Polymorphism with Body Composition Measures and Their Modulation by Dairy Products in a Caucasian Men.
Title: Relation of the C/T-13910 LCT Polymorphism with Body Composition Measures and Their Modulation by Dairy Products in a Caucasian Men.

Submit: New GeneRIF Correction See all GeneRIFs (117)

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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D2S2819 (e-PCR)
- UniSTS:36176

STS-X07994 (e-PCR)
- UniSTS:32892

AFMa338ye5 (e-PCR)
- UniSTS:68230

RH70816 (e-PCR)
- UniSTS:67062

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

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Preferred Names: lactase/phlorizin hydrolase

Names: lactase-glycosylceramidase; lactase-phlorizin hydrolase-1

NP_002290.2

EC 3.2.1.108

EC 3.2.1.62

XP_016859577.1

EC 3.2.1.108

EC 3.2.1.62

XP_054197984.1

EC 3.2.1.108

EC 3.2.1.62

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

NG_008104.2 RefSeqGene

Range

22990..72325

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_338

mRNA and Protein(s)

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