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Aliases for LCMT1 Gene

Aliases for LCMT1 Gene

  • Leucine Carboxyl Methyltransferase 1 2 3 3 5
  • [Phosphatase 2A Protein]-Leucine-Carboxy Methyltransferase 1 3 4
  • Protein Phosphatase Methyltransferase 1 2 3
  • Protein-Leucine O-Methyltransferase 3 4
  • LCMT 3 4
  • [Phosphatase 2A Protein]-Leucine-Carboxy Methyltransferase 2
  • EC 4
  • CGI-68 3
  • PPMT1 3

External Ids for LCMT1 Gene

Previous GeneCards Identifiers for LCMT1 Gene

  • GC16P025222
  • GC16P025050
  • GC16P025089
  • GC16P025030
  • GC16P025123
  • GC16P023216
  • GC16P025226
  • GC16P025412
  • GC16P025542
  • GC16P025607
  • GC16P025674
  • GC16P025738
  • GC16P025801
  • GC16P025864

Summaries for LCMT1 Gene

Entrez Gene Summary for LCMT1 Gene

  • LCMT1 catalyzes the methylation of the carboxyl group of the C-terminal leucine residue (leu309) of the catalytic subunit of protein phosphatase-2A (PPP2CA; MIM 176915) (De Baere et al., 1999 [PubMed 10600115]).[supplied by OMIM, Mar 2008]

GeneCards Summary for LCMT1 Gene

LCMT1 (Leucine Carboxyl Methyltransferase 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include methyltransferase activity and S-adenosylmethionine-dependent methyltransferase activity. An important paralog of this gene is LCMT2.

UniProtKB/Swiss-Prot for LCMT1 Gene

  • Methylates the carboxyl group of the C-terminal leucine residue of protein phosphatase 2A catalytic subunits to form alpha-leucine ester residues.

Gene Wiki entry for LCMT1 Gene

Additional gene information for LCMT1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCMT1 Gene

Genomics for LCMT1 Gene

GeneHancer (GH) Regulatory Elements for LCMT1 Gene

Promoters and enhancers for LCMT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J025108 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 657.1 -0.9 -895 3.7 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 FOS KLF13 SP3 LCMT1 LCMT1-AS1 RBBP6 ARHGAP17 LINC02191 LINC2194 LOC100420641 LCMT1-AS2 HMGN2P3 LOC100421173
GH16J025029 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 650.2 -80.5 -80492 3 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 YY1 POLR2B ZNF766 LOC554206 LCMT1 RBBP6 PIR61012
GH16J025177 Promoter/Enhancer 1.5 EPDnew ENCODE 18.4 +66.7 66654 2.3 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 ETS1 TCF12 SLC30A9 ATF7 AQP8 LCMT1 GC16P026017 LCMT1-AS2
GH16J025059 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 12.6 -47.7 -47745 8 HDGF PKNOX1 ARID4B SIN3A YY1 POLR2B SP3 SP5 ZHX2 REST ARHGAP17 LCMT1 RBBP6 LINC02175 LOC100421173 LCMT1-AS1 SLC5A11 PIR44920 PIR51348 PIR59706
GH16J025256 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 12.4 +146.1 146097 2.8 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 ZNF416 ZNF143 ZNF548 ZKSCAN2 ENSG00000274925 GC16P026016 RBBP6 LOC554206 HMGN2P3 ARHGAP17 ENSG00000261669 SCML2P2 LCMT1-AS2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCMT1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LCMT1 gene promoter:
  • Lmo2
  • Egr-2
  • Spz1
  • deltaCREB
  • CREB
  • Nkx2-2
  • GR
  • GR-alpha
  • CBF(2)
  • CBF-A

Genomic Locations for LCMT1 Gene

Genomic Locations for LCMT1 Gene
66,506 bases
Plus strand
66,506 bases
Plus strand

Genomic View for LCMT1 Gene

Genes around LCMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCMT1 Gene

Proteins for LCMT1 Gene

  • Protein details for LCMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Leucine carboxyl methyltransferase 1
    Protein Accession:
    Secondary Accessions:
    • A6NL89
    • A8K770
    • Q53FC5
    • Q96CI5
    • Q9H6I9
    • Q9NTG4
    • Q9Y378

    Protein attributes for LCMT1 Gene

    334 amino acids
    Molecular mass:
    38379 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for LCMT1 Gene

    Alternative splice isoforms for LCMT1 Gene


neXtProt entry for LCMT1 Gene

Post-translational modifications for LCMT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LCMT1 Gene

Domains & Families for LCMT1 Gene

Protein Domains for LCMT1 Gene

Suggested Antigen Peptide Sequences for LCMT1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the methyltransferase superfamily. LCMT family.
  • Belongs to the methyltransferase superfamily. LCMT family.
genes like me logo Genes that share domains with LCMT1: view

Function for LCMT1 Gene

Molecular function for LCMT1 Gene

UniProtKB/Swiss-Prot Function:
Methylates the carboxyl group of the C-terminal leucine residue of protein phosphatase 2A catalytic subunits to form alpha-leucine ester residues.
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + [phosphatase 2A protein]-leucine = S-adenosyl-L-homocysteine + [phosphatase 2A protein]-leucine methyl ester.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=0.1 uM for PP2AD {ECO:0000269 PubMed:10600115}; KM=1.3 uM for AdoMet {ECO:0000269 PubMed:10600115};

Enzyme Numbers (IUBMB) for LCMT1 Gene

Phenotypes From GWAS Catalog for LCMT1 Gene

Gene Ontology (GO) - Molecular Function for LCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003880 protein C-terminal carboxyl O-methyltransferase activity IDA 10600115
GO:0005515 protein binding IPI 16189514
GO:0008168 methyltransferase activity IEA --
GO:0008276 protein methyltransferase activity IEA --
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity TAS 10600115
genes like me logo Genes that share ontologies with LCMT1: view
genes like me logo Genes that share phenotypes with LCMT1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LCMT1

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCMT1

Clone Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LCMT1 Gene

Localization for LCMT1 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LCMT1 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IBA --
genes like me logo Genes that share ontologies with LCMT1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LCMT1 Gene

Pathways & Interactions for LCMT1 Gene

SuperPathways for LCMT1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LCMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000086 G2/M transition of mitotic cell cycle TAS --
GO:0006464 cellular protein modification process TAS 10600115
GO:0006479 protein methylation IMP 17724024
GO:0006481 C-terminal protein methylation IDA 10600115
GO:0010906 regulation of glucose metabolic process IEA --
genes like me logo Genes that share ontologies with LCMT1: view

No data available for Pathways by source and SIGNOR curated interactions for LCMT1 Gene

Drugs & Compounds for LCMT1 Gene

(2) Drugs for LCMT1 Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Leucine Approved Nutra Target 0
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for LCMT1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • (3S)-5'-[(3-amino-3-Carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
genes like me logo Genes that share compounds with LCMT1: view

Transcripts for LCMT1 Gene

Unigene Clusters for LCMT1 Gene

Leucine carboxyl methyltransferase 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LCMT1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LCMT1 Gene

No ASD Table

Relevant External Links for LCMT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for LCMT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LCMT1 Gene

Protein differential expression in normal tissues from HIPED for LCMT1 Gene

This gene is overexpressed in Testis (9.8), Skin (6.4), and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LCMT1 Gene

Protein tissue co-expression partners for LCMT1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LCMT1 Gene:


SOURCE GeneReport for Unigene cluster for LCMT1 Gene:


Evidence on tissue expression from TISSUES for LCMT1 Gene

  • Nervous system(4.7)
  • Muscle(4.3)
  • Lung(4.2)
genes like me logo Genes that share expression patterns with LCMT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCMT1 Gene

Orthologs for LCMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LCMT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia LCMT1 34 33
  • 99.9 (n)
(Canis familiaris)
Mammalia LCMT1 34 33
  • 88.53 (n)
(Bos Taurus)
Mammalia LCMT1 34 33
  • 86.45 (n)
(Mus musculus)
Mammalia Lcmt1 16 34 33
  • 86.24 (n)
(Rattus norvegicus)
Mammalia Lcmt1 33
  • 85.61 (n)
(Ornithorhynchus anatinus)
Mammalia LCMT1 34
  • 80 (a)
(Monodelphis domestica)
Mammalia LCMT1 34
  • 78 (a)
(Gallus gallus)
Aves LCMT1 34 33
  • 74.39 (n)
(Anolis carolinensis)
Reptilia LCMT1 34
  • 63 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia lcmt1 33
  • 69.63 (n)
Str.5797 33
(Danio rerio)
Actinopterygii lcmt1 34 33
  • 66.24 (n)
Dr.1860 33
fruit fly
(Drosophila melanogaster)
Insecta CG3793 34 33
  • 54.1 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008768 33
  • 54.1 (n)
(Caenorhabditis elegans)
Secernentea CELE_B0285.4 33
  • 45.78 (n)
B0285.4 34
  • 36 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PPM2 34
  • 11 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G02100 33
  • 48.29 (n)
(Oryza sativa)
Liliopsida Os06g0140100 33
  • 48.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8848 34
  • 49 (a)
Species where no ortholog for LCMT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LCMT1 Gene

Gene Tree for LCMT1 (if available)
Gene Tree for LCMT1 (if available)
Evolutionary constrained regions (ECRs) for LCMT1: view image

Paralogs for LCMT1 Gene

Paralogs for LCMT1 Gene Pseudogenes for LCMT1 Gene

genes like me logo Genes that share paralogs with LCMT1: view

Variants for LCMT1 Gene

Sequence variations from dbSNP and Humsavar for LCMT1 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs1000013234 -- 25,151,616(+) G/A intron_variant, splice_donor_variant
rs1000061360 -- 25,151,841(+) C/T intron_variant
rs1000113500 -- 25,152,147(+) G/T intron_variant
rs1000115938 -- 25,137,827(+) T/G intron_variant
rs1000144007 -- 25,135,527(+) G/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LCMT1 Gene

Variant ID Type Subtype PubMed ID
dgv2827n100 CNV gain 25217958
dgv48e19 CNV loss 19470904
dgv809e212 CNV loss 25503493
esv2660591 CNV deletion 23128226
esv2714121 CNV deletion 23290073
esv2758638 CNV gain+loss 17122850
esv3441 CNV loss 18987735
esv34994 CNV gain 17911159
esv3638267 CNV gain 21293372

Variation tolerance for LCMT1 Gene

Residual Variation Intolerance Score: 29.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.71; 15.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCMT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCMT1 Gene

Disorders for LCMT1 Gene

Additional Disease Information for LCMT1

No disorders were found for LCMT1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LCMT1 Gene

Publications for LCMT1 Gene

  1. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai CH … Lin W (Genome research 2000) 2 3 4 58
  2. The structural basis for tight control of PP2A methylation and function by LCMT-1. (PMID: 21292165) Stanevich V … Xing Y (Molecular cell 2011) 3 4 58
  3. The structure of human leucine carboxyl methyltransferase 1 that regulates protein phosphatase PP2A. (PMID: 21206058) Tsai ML … Djordjevic S (Acta crystallographica. Section D, Biological crystallography 2011) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for LCMT1 Gene

Sources for LCMT1 Gene

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