LCT (lactase)

Gene
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
3938
Gene name Gene Name - the full gene name approved by the HGNC.
Lactase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
LCT
Synonyms (NCBI Gene) Gene synonyms aliases
LAC, LPH, LPH1
Chromosome Chromosome number
2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
2q21.3
Summary Summary of gene provided in NCBI Entrez Gene.
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
SNPs SNP information provided by dbSNP.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(10)
SNP ID Visualize variation Clinical significance Consequence
rs121908936 A>T Pathogenic Stop gained, coding sequence variant
rs121908937 C>G Pathogenic Coding sequence variant, missense variant
rs386833832 ACTCC>- Likely-pathogenic Coding sequence variant, frameshift variant
rs386833833 C>T Likely-pathogenic Coding sequence variant, missense variant
rs386833834 G>A,C Likely-pathogenic Coding sequence variant, synonymous variant, stop gained
miRNA miRNA information provided by mirtarbase database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(9)
miRTarBase ID miRNA Experiments Reference
MIRT039283 hsa-miR-671-5p CLASH 23622248
MIRT2029362 hsa-miR-1299 CLIP-seq
MIRT2029363 hsa-miR-3148 CLIP-seq
MIRT2029364 hsa-miR-4731-3p CLIP-seq
MIRT2029365 hsa-miR-4782-5p CLIP-seq
Transcription factors
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all(4)
Transcription factor Regulation Reference
CDX2 Activation 9148757
HNF1A Activation 9582375
HOXC11 Unknown 9582375
POU2F1 Activation 20960210
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
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GO ID Ontology Definition Evidence Reference
GO:0000016 Function Lactase activity IBA 21873635
GO:0005783 Component Endoplasmic reticulum IBA 21873635
GO:0005886 Component Plasma membrane TAS
GO:0005887 Component Integral component of plasma membrane TAS 2460343
GO:0005975 Process Carbohydrate metabolic process IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
603202 6530 ENSG00000115850
Protein
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID P09848
Protein name Lactase/phlorizin hydrolase (Lactase/glycosylceramidase) [Includes: Lactase (EC 3.2.1.108); Glycosylceramidase (EC 3.2.1.62) (Phlorizin hydrolase)]
Protein function Broad specificity glycosidase of the intestinal brush border membrane that hydrolyzes lactose, the main sugar in mammalian milk, to produce D-glucose and D-galactose (PubMed:12594539, PubMed:16400612, PubMed:3929764, PubMed:9762914). The mature
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00232 Glyco_hydro_1 74 → 225 Glycosyl hydrolase family 1 Domain
PF00232 Glyco_hydro_1 378 → 847 Glycosyl hydrolase family 1 Domain
PF00232 Glyco_hydro_1 899 → 1364 Glycosyl hydrolase family 1 Domain
PF00232 Glyco_hydro_1 1373 → 1840 Glycosyl hydrolase family 1 Domain
Tissue specificity TISSUE SPECIFICITY: Specifically expressed in small intestine. {ECO:0000269|PubMed:2460343}.
Sequence 
MELSWHVVFIALLSFSCWGSDWESDRNFISTAGPLTNDLLHNLSGLLGDQSSNFVAGDKD
MYVCHQPLPTFLPEYFSSLHASQITHYKVFLSWAQLLPAGSTQNPDEKTVQCYRRLLKAL
KTARLQPMVILHHQTLPASTLRRTEAFADLFADYATFAFHSFGDLVGIWFTFSDLEEVIK
ELPHQESRASQLQTLSDAHRKAYEIYHESYAFQGGKLSVVLRAEDIPELLLEPPISALAQ
DTVDFLSLDLSYECQNEASLRQKLSKLQTIEPKVKVFIFNLKLPDCPSTMKNPASLLFSL
FEAINKDQVLTIGFDINEFLSCSSSSKKSMSCSLTGSLALQPDQQQDHETTDSSPASAYQ
RIWEAFANQSRAERDAFLQDTFPEGFLWGASTGAFNVEGGWAEGGRGVSIWDPRRPLNTT
EGQATLEVASDSYHKVASDVALLCGLRAQVYKFSISWSRIFPMGHGSSPSLPGVAYYNKL
IDRLQDAGIEPMATLFHWDLPQALQDHGGWQNESVVDAFLDYAAFCFSTFGDRVKLWVTF
HEPWVMSYAGYGTGQHPPGISDPGVASFKVAHLVLKAHARTWHHYNSHHRPQQQGHVGIV
LNSDWAEPLSPERPEDLRASERFLHFMLGWFAHPVFVDGDYPATLRTQIQQMNRQCSHPV
AQLPEFTEAEKQLLKGSADFLGLSHYTSRLISNAPQNTCIPSYDTIGGFSQHVNHVWPQT
SSSWIRVVPWGIRRLLQFVSLEYTRGKVPIYLAGNGMPIGESENLFDDSLRVDYFNQYIN
EVLKAIKEDSVDVRSYIARSLIDGFEGPSGYSQRFGLHHVNFSDSSKSRTPRKSAYFFTS
IIEKNGFLTKGAKRLLPPNTVNLPSKVRAFTFPSEVPSKAKVVWEKFSSQPKFERDLFYH
GTFRDDFLWGVSSSAYQIEGAWDADGKGPSIWDNFTHTPGSNVKDNATGDIACDSYHQLD
ADLNMLRALKVKAYRFSISWSRIFPTGRNSSINSHGVDYYNRLINGLVASNIFPMVTLFH
WDLPQALQDIGGWENPALIDLFDSYADFCFQTFGDRVKFWMTFNEPMYLAWLGYGSGEFP
PGVKDPGWAPYRIAHAVIKAHARVYHTYDEKYRQEQKGVISLSLSTHWAEPKSPGVPRDV
EAADRMLQFSLGWFAHPIFRNGDYPDTMKWKVGNRSELQHLATSRLPSFTEEEKRFIRAT
ADVFCLNTYYSRIVQHKTPRLNPPSYEDDQEMAEEEDPSWPSTAMNRAAPWGTRRLLNWI
KEEYGDIPIYITENGVGLTNPNTEDTDRIFYHKTYINEALKAYRLDGIDLRGYVAWSLMD
NFEWLNGYTVKFGLYHVDFNNTNRPRTARASARYYTEVITNNGMPLAREDEFLYGRFPEG
FIWSAASAAYQIEGAWRADGKGLSIWDTFSHTPLRVENDAIGDVACDSYHKIAEDLVTLQ
NLGVSHYRFSISWSRILPDGTTRYINEAGLNYYVRLIDTLLAASIQPQVTIYHWDLPQTL
QDVGGWENETIVQRFKEYADVLFQRLGDKVKFWITLNEPFVIAYQGYGYGTAAPGVSNRP
GTAPYIVGHNLIKAHAEAWHLYNDVYRASQGGVISITISSDWAEPRDPSNQEDVEAARRY
VQFMGGWFAHPIFKNGDYNEVMKTRIRDRSLAAGLNKSRLPEFTESEKRRINGTYDFFGF
NHYTTVLAYNLNYATAISSFDADRGVASIADRSWPDSGSFWLKMTPFGFRRILNWLKEEY
NDPPIYVTENGVSQREETDLNDTARIYYLRTYINEALKAVQDKVDLRGYTVWSAMDNFEW
ATGFSERFGLHFVNYSDPSLPRIPKASAKFYASVVRCNGFPDPATGPHACLHQPDAGPTI
SPVRQEEVQFLGLMLGTTEAQTALYVLFSLVLLGVCGLAFLSYKYCKRSKQGKTQRSQQE
LSPVSSF
Sequence length 1927
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
  KEGG   Reactome
  Galactose metabolism
Metabolic pathways
Carbohydrate digestion and absorption 		  Digestion of dietary carbohydrate
Intestinal saccharidase deficiencies
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide Causal Diseases (1)
Causal
Disease term Disease name dbSNP ID References
Congenital lactase deficiency Congenital lactase deficiency rs121908936, rs121908937, rs386833832, rs386833833, rs386833834, rs386833835, rs386833836, rs386833837, rs386833838
Show/Hide Text Mining Associations (36)
Associations from Text Mining
Disease Name Relationship Type References
Anemia Sickle Cell Associate 23731540
Arthritis Rheumatoid Associate 33462485
Cardiovascular Diseases Associate 23420841
Cataract Age Related Nuclear Associate 34954695
Celiac Disease Associate 39203877, 428824
Colitis Ulcerative Inhibit 25003680
Colitis Ulcerative Associate 33462485
Colorectal Neoplasms Associate 15831909, 18980667, 19686745
Crohn Disease Inhibit 25003680
Cystic Fibrosis Associate 21407263