Gene Gene information from NCBI Gene database.
Entrez ID 3938
Gene name Lactase
Gene symbol LCT
Synonyms (NCBI Gene)
LACLPHLPH1
Chromosome 2
Chromosome location 2q21.3
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
SNPs SNP information provided by dbSNP.
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.
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 Transcription factors information provided by TRRUST V2 database.
4
Transcription factor Regulation Reference
CDX2 Activation 9148757
HNF1A Activation 9582375
HOXC11 Unknown 9582375
POU2F1 Activation 20960210
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
31
GO ID Ontology Definition Evidence Reference
GO:0000016 Function Lactase activity IBA
GO:0000016 Function Lactase activity IDA 3929764, 9762914, 12594539
GO:0000016 Function Lactase activity IEA
GO:0000016 Function Lactase activity IMP 16400612
GO:0003824 Function Catalytic activity IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603202 6530 ENSG00000115850
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
ELPHQESRASQLQTLSDAHRKAYEIYHESYAFQGGKLSVVLRAED
IPELLLEPPISALAQ
DTVDFLSLDLSYECQNEASLRQKLSKLQTIEPKVKVFIFNLKLPDCPSTMKNPASLLFSL
FEAINKDQVLTIGFDINEFLSCSSSSKKSMSCSLTGSLALQPDQQQDHETTDSSPASAYQ
RIWEAFANQSRAERDAFLQDTFPEGFLWGASTGAFNVEGGWAEGGRGVSIWDPRRPLNTT
EGQATLEVASDSYHKVASDVALLCGLRAQVYKFSISWSRIFPMGHGSSPSLPGVAYYNKL
IDRLQDAGIEPMATLFHWDLPQALQDHGGWQNESVVDAFLDYAAFCFSTFGDRVKLWVTF
HEPWVMSYAGYGTGQHPPGISDPGVASFKVAHLVLKAHARTWHHYNSHHRPQQQGHVGIV
LNSDWAEPLSPERPEDLRASERFLHFMLGWFAHPVFVDGDYPATLRTQIQQMNRQCSHPV
AQLPEFTEAEKQLLKGSADFLGLSHYTSRLISNAPQNTCIPSYDTIGGFSQHVNHVWPQT
SSSWIRVVPWGIRRLLQFVSLEYTRGKVPIYLAGNGMPIGESENLFDDSLRVDYFNQYIN
EVLKAIKEDSVDVRSYIARSLIDGFEGPSGYSQRFGLHHVNFSDSSKSRTPRKSAYFFTS
IIEKNGF
LTKGAKRLLPPNTVNLPSKVRAFTFPSEVPSKAKVVWEKFSSQPKFERDLFYH
GTFRDDFLWGVSSSAYQIEGAWDADGKGPSIWDNFTHTPGSNVKDNATGDIACDSYHQLD
ADLNMLRALKVKAYRFSISWSRIFPTGRNSSINSHGVDYYNRLINGLVASNIFPMVTLFH
WDLPQALQDIGGWENPALIDLFDSYADFCFQTFGDRVKFWMTFNEPMYLAWLGYGSGEFP
PGVKDPGWAPYRIAHAVIKAHARVYHTYDEKYRQEQKGVISLSLSTHWAEPKSPGVPRDV
EAADRMLQFSLGWFAHPIFRNGDYPDTMKWKVGNRSELQHLATSRLPSFTEEEKRFIRAT
ADVFCLNTYYSRIVQHKTPRLNPPSYEDDQEMAEEEDPSWPSTAMNRAAPWGTRRLLNWI
KEEYGDIPIYITENGVGLTNPNTEDTDRIFYHKTYINEALKAYRLDGIDLRGYVAWSLMD
NFEWLNGYTVKFGLYHVDFNNTNRPRTARASARYYTEVITNNGM
PLAREDEFLYGRFPEG
FIWSAASAAYQIEGAWRADGKGLSIWDTFSHTPLRVENDAIGDVACDSYHKIAEDLVTLQ
NLGVSHYRFSISWSRILPDGTTRYINEAGLNYYVRLIDTLLAASIQPQVTIYHWDLPQTL
QDVGGWENETIVQRFKEYADVLFQRLGDKVKFWITLNEPFVIAYQGYGYGTAAPGVSNRP
GTAPYIVGHNLIKAHAEAWHLYNDVYRASQGGVISITISSDWAEPRDPSNQEDVEAARRY
VQFMGGWFAHPIFKNGDYNEVMKTRIRDRSLAAGLNKSRLPEFTESEKRRINGTYDFFGF
NHYTTVLAYNLNYATAISSFDADRGVASIADRSWPDSGSFWLKMTPFGFRRILNWLKEEY
NDPPIYVTENGVSQREETDLNDTARIYYLRTYINEALKAVQDKVDLRGYTVWSAMDNFEW
ATGFSERFGLHFVNYSDPSLPRIPKASAKFYASVVRCNGF
PDPATGPHACLHQPDAGPTI
SPVRQEEVQFLGLMLGTTEAQTALYVLFSLVLLGVCGLAFLSYKYCKRSKQGKTQRSQQE
LSPVSSF
Sequence length 1927
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Galactose metabolism
Metabolic pathways
Carbohydrate digestion and absorption
  Digestion of dietary carbohydrate
Intestinal saccharidase deficiencies
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
15
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Congenital lactase deficiency Likely pathogenic; Pathogenic rs749118441, rs121908936, rs121908937, rs1276818330, rs386833832, rs386833833, rs386833834, rs386833835, rs386833836, rs386833837, rs386833838, rs1312031160, rs763006562 RCV002506946
RCV000006964
RCV000006966
RCV003335938
RCV000049800
View all (8 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
LCT-related disorder Pathogenic; Likely pathogenic rs2077596325, rs2467240516, rs2467223826 RCV003983884
RCV003414172
RCV003414182
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Colorectal cancer Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Lactose intolerance Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenomatous Polyposis Coli Multiple polyposis syndrome BEFREE 31137035
★☆☆☆☆
Found in Text Mining only
Adult T-Cell Lymphoma/Leukemia T-Cell Lymphoma/Leukemia BEFREE 2898099
★☆☆☆☆
Found in Text Mining only
AMYLOIDOSIS, HEREDITARY, TRANSTHYRETIN-RELATED Amyloidosis BEFREE 31137035
★☆☆☆☆
Found in Text Mining only
Anemia Sickle Cell Sickle cell anemia Pubtator 23731540 Associate
★☆☆☆☆
Found in Text Mining only
Antiphospholipid Syndrome Antiphospholipid Syndrome BEFREE 30079628
★☆☆☆☆
Found in Text Mining only
Antithrombin III Deficiency Antithrombin Deficiency BEFREE 16953278
★☆☆☆☆
Found in Text Mining only
Arthritis Rheumatoid Rheumatoid arthritis Pubtator 33462485 Associate
★☆☆☆☆
Found in Text Mining only
Asthenozoospermia Asthenozoospermia BEFREE 31160241
★☆☆☆☆
Found in Text Mining only
Asthma Asthma BEFREE 29211546
★☆☆☆☆
Found in Text Mining only
Bronchopulmonary Dysplasia Bronchopulmonary Dysplasia BEFREE 31723236
★☆☆☆☆
Found in Text Mining only