Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
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

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
rs386833835	C>A,T	Likely-pathogenic	Coding sequence variant, missense variant, stop gained
rs386833836	ACTC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs386833837	T>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs386833838	AG>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1553436217	CTTTTCTGTGGGCATCACTGAG>-	Likely-pathogenic	Frameshift variant, coding sequence variant

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
MIRT2029366	hsa-miR-4801	CLIP-seq
MIRT2029367	hsa-miR-516b	CLIP-seq
MIRT2029368	hsa-miR-570	CLIP-seq
MIRT2029369	hsa-miR-875-3p	CLIP-seq

Show/Hide all (4)

Transcription factor	Regulation	Reference
CDX2	Activation	9148757
HNF1A	Activation	9582375
HOXC11	Unknown	9582375
POU2F1	Activation	20960210

Show/Hide all (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
GO:0004336	Function	Galactosylceramidase activity	ISS
GO:0004348	Function	Glucosylceramidase activity	ISS
GO:0004553	Function	Hydrolase activity, hydrolyzing O-glycosyl compounds	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS	2460343
GO:0005975	Process	Carbohydrate metabolic process	IEA
GO:0005990	Process	Lactose catabolic process	IBA
GO:0005990	Process	Lactose catabolic process	IDA	3929764, 9762914, 12594539
GO:0008422	Function	Beta-glucosidase activity	IBA
GO:0008422	Function	Beta-glucosidase activity	IDA	3929764, 12594539
GO:0008422	Function	Beta-glucosidase activity	IEA
GO:0008422	Function	Beta-glucosidase activity	ISS
GO:0016020	Component	Membrane	IEA
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016798	Function	Hydrolase activity, acting on glycosyl bonds	IEA
GO:0042803	Function	Protein homodimerization activity	IDA	9593732
GO:0046477	Process	Glycosylceramide catabolic process	ISS
GO:0080079	Function	Cellobiose glucosidase activity	IEA
GO:0098591	Component	External side of apical plasma membrane	IBA
GO:0098591	Component	External side of apical plasma membrane	IDA	9593732
GO:0140749	Function	Phlorizin hydrolase activity	IDA	3929764, 9762914, 12594539
GO:0140749	Function	Phlorizin hydrolase activity	IEA
GO:1901733	Process	Quercetin catabolic process	IDA	12594539
GO:2000892	Process	Cellobiose catabolic process	IBA
GO:2000892	Process	Cellobiose catabolic process	IDA	3929764

MIM	HGNC	e!Ensembl
603202	6530	ENSG00000115850

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

	KEGG		Reactome
	Galactose metabolism Metabolic pathways Carbohydrate digestion and absorption		Digestion of dietary carbohydrate Intestinal saccharidase deficiencies

274

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Congenital lactase deficiency	Likely pathogenic; Pathogenic	rs749118441, rs121908936, rs121908937, rs1276818330, rs386833832, rs386833833, rs386833834, rs386833835, rs386833836, rs386833837, rs386833838, rs1312031160, rs763006562	RCV002506946 RCV000006964 RCV000006966 RCV003335938 RCV000049800 RCV000049801 RCV000049802 RCV000049803 RCV000049804 RCV000049805 RCV000049806 RCV003222281 RCV003222282
LCT-related disorder	Pathogenic; Likely pathogenic	rs2077596325, rs2467240516, rs2467223826	RCV003983884 RCV003414172 RCV003414182

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs3816088	RCV005895933
Cervical cancer	Benign; Likely benign	rs3816088	RCV005895936
Colorectal cancer	Benign; Likely benign	rs35093754, rs3816088	RCV005895927 RCV005895937
Lactose intolerance	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs140433552, rs1042712, rs761696901, rs557029000, rs35891837, rs886054862, rs2304371, rs17699796, rs375300532, rs146467199, rs372534937, rs114815229, rs140994860, rs116951780, rs146206234 View all (46 more)	RCV000382836 RCV000315325 RCV000371800 RCV000292131 RCV000310179 RCV000304192 RCV000357102 RCV000387278 RCV000341400 RCV000350754 RCV000392208 RCV000368031 RCV000309819 RCV000270319 RCV000406168 RCV000288474 RCV000383655 RCV000304642 RCV000379568 RCV000337708 RCV000326698 RCV000392923 RCV000317377 RCV000277663 RCV000371150 RCV000374209 RCV000295201 RCV000352385 RCV000262636 RCV000386407 RCV000284490 RCV000336547 RCV000378034 RCV000361273 RCV000347971 RCV000301657 RCV000403255 RCV000331835 RCV000384035 RCV000392216 RCV000346697 RCV000310026 RCV000301721 RCV000403725 RCV000301253 RCV000311055 RCV000279167 RCV000309257 RCV000269250 RCV000321074 RCV000279373 RCV000381588 RCV000353910 RCV000325589 RCV000343179 RCV000376775 RCV000264499 RCV000282064 RCV000316915 RCV000333068 RCV000275730
Lymphoma	Benign; Likely benign	rs35093754	RCV005895929
Malignant lymphoma, large B-cell, diffuse	Benign	rs3739022	RCV005895925
Malignant tumor of esophagus	Benign; Likely benign	rs3816088	RCV005895934
Melanoma	Benign; Likely benign	rs35093754, rs3816088	RCV005895932 RCV005895939
Nonpapillary renal cell carcinoma	Likely benign; Benign	rs6719488, rs35093754, rs3816088	RCV005926819 RCV005895926 RCV005895935
Sarcoma	Benign; Likely benign	rs35093754, rs3816088	RCV005895928 RCV005895938
Thymoma	Benign; Likely benign	rs35093754	RCV005895931
Uterine carcinosarcoma	Benign; Likely benign	rs35093754	RCV005895930

Show/Hide Text Mining Associations (36)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
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
Diabetes Mellitus	Associate	11804845, 33577048
Diabetes Mellitus Type 2	Associate	33577048
Disease	Associate	25495501
Fibrosarcoma	Associate	27812865
Fructose Intolerance	Associate	39203877
Hyperglycemia	Associate	33577048
Inflammatory Bowel Diseases	Associate	25003680
Insulin Resistance	Associate	32036847
Irritable Bowel Syndrome	Associate	19943975, 29912753
Lactase Deficiency Congenital	Associate	16400612, 1702075, 19161632, 22688420, 23029545, 23327608, 26215149, 28132945, 29063188, 30689919, 9758622
Lactase Deficiency Congenital	Inhibit	28132945
Lactose Intolerance	Associate	12692047, 16400612, 1702075, 17934640, 18568133, 18980667, 1902057, 19799794, 20225268, 20353605, 22481679, 22564469, 23381829, 28132945, 29912753 View all (17 more)
Lactose Intolerance Adult Type	Associate	12692047, 16400612, 16610034, 17659699, 17911653, 17934640, 19799794, 21407263, 22481679, 24361938, 25495501, 26334798, 31137035, 9758622
Mental Disorders	Associate	22363459
Milk Hypersensitivity	Associate	16610034
Neoplasms	Associate	31964840
Neural Tube Defects	Associate	30689919
Obesity	Associate	20015952, 21193851, 32036847, 33577048
Obesity Abdominal	Associate	23252911
Osteoporosis	Associate	23985982
Pigmentation Disorders	Associate	23731540
Polypoidal Choroidal Vasculopathy	Associate	32509858
Polyradiculoneuropathy Chronic Inflammatory Demyelinating	Associate	32036847
Pre Eclampsia	Associate	23420841
Rhinitis Allergic Seasonal	Associate	34978666
Signs and Symptoms Digestive	Associate	18568133, 19943975, 23327608, 33019743

LCT (lactase)