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LCT (lactase)

Identity

Other namesLAC
LPH
LPH1
HGNC (Hugo) LCT
LocusID (NCBI) 3938
Atlas_Id 49871
Location 2q21.3  [Link to chromosome band 2q21]
Location_base_pair Starts at 136545410 and ends at 136594750 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
LCT (2q21.3) / MBTPS1 (16q23.3)SSH2 (17q11.2) / LCT (2q21.3)ZDHHC5 (11q12.1) / LCT (2q21.3)
ZDHHC5 11q12.1 / LCT 2q21.3

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)LCT   6530
Cards
Entrez_Gene (NCBI)LCT  3938  lactase
AliasesLAC; LPH; LPH1
GeneCards (Weizmann)LCT
Ensembl hg19 (Hinxton)ENSG00000115850 [Gene_View]  chr2:136545410-136594750 [Contig_View]  LCT [Vega]
Ensembl hg38 (Hinxton)ENSG00000115850 [Gene_View]  chr2:136545410-136594750 [Contig_View]  LCT [Vega]
ICGC DataPortalENSG00000115850
TCGA cBioPortalLCT
AceView (NCBI)LCT
Genatlas (Paris)LCT
WikiGenes3938
SOURCE (Princeton)LCT
Genomic and cartography
GoldenPath hg19 (UCSC)LCT  -     chr2:136545410-136594750 -  2q21.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LCT  -     2q21.3   [Description]    (hg38-Dec_2013)
EnsemblLCT - 2q21.3 [CytoView hg19]  LCT - 2q21.3 [CytoView hg38]
Mapping of homologs : NCBILCT [Mapview hg19]  LCT [Mapview hg38]
OMIM223000   603202   
Gene and transcription
Genbank (Entrez)BC156075 BC156950 BX642122 X07994
RefSeq transcript (Entrez)NM_002299
RefSeq genomic (Entrez)NC_000002 NC_018913 NG_008104 NT_005403 NW_004929304
Consensus coding sequences : CCDS (NCBI)LCT
Cluster EST : UnigeneHs.551506 [ NCBI ]
CGAP (NCI)Hs.551506
Alternative Splicing GalleryENSG00000115850
Gene ExpressionLCT [ NCBI-GEO ]   LCT [ EBI - ARRAY_EXPRESS ]   LCT [ SEEK ]   LCT [ MEM ]
Gene Expression Viewer (FireBrowse)LCT [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3938
GTEX Portal (Tissue expression)LCT
Protein : pattern, domain, 3D structure
UniProt/SwissProtP09848 (Uniprot)
NextProtP09848  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP09848
Splice isoforms : SwissVarP09848 (Swissvar)
Catalytic activity : Enzyme3.2.1.108 [ Enzyme-Expasy ]   3.2.1.1083.2.1.108 [ IntEnz-EBI ]   3.2.1.108 [ BRENDA ]   3.2.1.108 [ KEGG ]   
PhosPhoSitePlusP09848
Domaine pattern : Prosite (Expaxy)GLYCOSYL_HYDROL_F1_1 (PS00572)    GLYCOSYL_HYDROL_F1_2 (PS00653)   
Domains : Interpro (EBI)Glyco_hydro_1    Glyco_hydro_1_AS    Glyco_hydro_1_N_CS    Glyco_hydro_catalytic_dom    Glycoside_hydrolase_SF   
Domain families : Pfam (Sanger)Glyco_hydro_1 (PF00232)   
Domain families : Pfam (NCBI)pfam00232   
DMDM Disease mutations3938
Blocks (Seattle)LCT
SuperfamilyP09848
Human Protein AtlasENSG00000115850
Peptide AtlasP09848
HPRD04437
IPIIPI00017648   IPI00930743   IPI00916950   
Protein Interaction databases
DIP (DOE-UCLA)P09848
IntAct (EBI)P09848
FunCoupENSG00000115850
BioGRIDLCT
STRING (EMBL)LCT
ZODIACLCT
Ontologies - Pathways
QuickGOP09848
Ontology : AmiGOlactase activity  response to hypoxia  plasma membrane  integral component of plasma membrane  brush border  carbohydrate metabolic process  response to nutrient  beta-glucosidase activity  response to sucrose  response to iron(II) ion  response to nickel cation  response to lead ion  membrane  apical plasma membrane  transferase activity  glycosylceramidase activity  response to drug  response to starvation  response to estrogen  polysaccharide digestion  response to ethanol  glycosyl compound metabolic process  
Ontology : EGO-EBIlactase activity  response to hypoxia  plasma membrane  integral component of plasma membrane  brush border  carbohydrate metabolic process  response to nutrient  beta-glucosidase activity  response to sucrose  response to iron(II) ion  response to nickel cation  response to lead ion  membrane  apical plasma membrane  transferase activity  glycosylceramidase activity  response to drug  response to starvation  response to estrogen  polysaccharide digestion  response to ethanol  glycosyl compound metabolic process  
Pathways : KEGGGalactose metabolism    Carbohydrate digestion and absorption   
NDEx Network
Atlas of Cancer Signalling NetworkLCT
Wikipedia pathwaysLCT
Orthology - Evolution
OrthoDB3938
GeneTree (enSembl)ENSG00000115850
Phylogenetic Trees/Animal Genes : TreeFamLCT
Homologs : HomoloGeneLCT
Homology/Alignments : Family Browser (UCSC)LCT
Gene fusions - Rearrangements
Fusion: TCGAZDHHC5 11q12.1 LCT 2q21.3 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerLCT [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LCT
dbVarLCT
ClinVarLCT
1000_GenomesLCT 
Exome Variant ServerLCT
ExAC (Exome Aggregation Consortium)LCT (select the gene name)
Genetic variants : HAPMAP3938
Genomic Variants (DGV)LCT [DGVbeta]
Mutations
ICGC Data PortalLCT 
TCGA Data PortalLCT 
Broad Tumor PortalLCT
OASIS PortalLCT [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLCT 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LCT
DgiDB (Drug Gene Interaction Database)LCT
DoCM (Curated mutations)LCT (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LCT (select a term)
intoGenLCT
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)2:136545410-136594750  ENSG00000115850
CONAN: Copy Number AnalysisLCT 
Mutations and Diseases : HGMDLCT
OMIM223000    603202   
MedgenLCT
Genetic Testing Registry LCT
NextProtP09848 [Medical]
TSGene3938
GENETestsLCT
Huge Navigator LCT [HugePedia]
snp3D : Map Gene to Disease3938
BioCentury BCIQLCT
ClinGenLCT
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3938
Chemical/Pharm GKB GenePA30315
Clinical trialLCT
Miscellaneous
canSAR (ICR)LCT (select the gene name)
Probes
Litterature
PubMed125 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLCT
EVEXLCT
GoPubMedLCT
iHOPLCT
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 9 19:05:06 CEST 2016

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