Aliases for CSKMT Gene

Aliases for CSKMT Gene

  • Citrate Synthase Lysine Methyltransferase 2 3 5
  • CS-KMT 2 3 4
  • Citrate Synthase-Lysine N-Methyltransferase CSKMT, Mitochondrial 3 4
  • Methyltransferase-Like Protein 12, Mitochondrial 3 4
  • Methyltransferase Like 12 2 3
  • METTL12 3 4
  • U99HG 2 3
  • EC 2.1.1.- 4
  • CSKMT 5

External Ids for CSKMT Gene

Previous HGNC Symbols for CSKMT Gene

  • METTL12

Previous GeneCards Identifiers for CSKMT Gene

  • GC11P062678
  • GC11P062680
  • GC11P062684
  • GC11P062687
  • GC11P062668
  • GC11P062671
  • GC11P062674
  • GC11P062692

Summaries for CSKMT Gene

GeneCards Summary for CSKMT Gene

CSKMT (Citrate Synthase Lysine Methyltransferase) is a Protein Coding gene. Diseases associated with CSKMT include Diarrhea 2, With Microvillus Atrophy. An important paralog of this gene is EEF1AKNMT.

UniProtKB/Swiss-Prot Summary for CSKMT Gene

  • Protein-lysine methyltransferase that selectively trimethylates citrate synthase (CS) in mitochondria (PubMed:28391595, PubMed:28887308). Seems to conduct trimethylation in a highly distributive manner rather than in a processive manner, and thus introduces a single methly group per binding event (PubMed:28887308).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CSKMT Gene

Genomics for CSKMT Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CSKMT Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CSKMT on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CSKMT

Genomic Locations for CSKMT Gene

Latest Assembly
3,244 bases
Plus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
2,797 bases
Plus strand

(GRCh37/hg19 by Ensembl)
3,188 bases
Plus strand

Genomic View for CSKMT Gene

Genes around CSKMT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CSKMT Gene

Proteins for CSKMT Gene

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

    Protein Symbol:
    Recommended name:
    Citrate synthase-lysine N-methyltransferase CSKMT, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B7Z4C1

    Protein attributes for CSKMT Gene

    240 amino acids
    Molecular mass:
    25910 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CSKMT Gene

Post-translational modifications for CSKMT Gene

No Post-translational modifications

Other Protein References for CSKMT Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CSKMT Gene

Domains & Families for CSKMT Gene

Gene Families for CSKMT Gene

Protein Domains for CSKMT Gene

Suggested Antigen Peptide Sequences for CSKMT Gene

GenScript: Design optimal peptide antigens:
  • Methyltransferase-like protein 12, mitochondrial (MTL12_HUMAN)

Graphical View of Domain Structure for InterPro Entry



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

Function for CSKMT Gene

Molecular function for CSKMT Gene

UniProtKB/Swiss-Prot Function:
Protein-lysine methyltransferase that selectively trimethylates citrate synthase (CS) in mitochondria (PubMed:28391595, PubMed:28887308). Seems to conduct trimethylation in a highly distributive manner rather than in a processive manner, and thus introduces a single methly group per binding event (PubMed:28887308).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[citrate synthase] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[citrate synthase] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:55544, Rhea:RHEA-COMP:14212, Rhea:RHEA-COMP:14213, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; Evidence={ECO:0000269|PubMed:28887308};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=N(6)-methyl-L-lysyl-[citrate synthase] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl-[citrate synthase] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:55548, Rhea:RHEA-COMP:14213, Rhea:RHEA-COMP:14214, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929, ChEBI:CHEBI:61976; Evidence={ECO:0000269|PubMed:28887308};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=N(6),N(6)-dimethyl-L-lysyl-[citrate synthase] + S-adenosyl-L-methionine = H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl-[citrate synthase] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:55552, Rhea:RHEA-COMP:14214, Rhea:RHEA-COMP:14215, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961, ChEBI:CHEBI:61976; Evidence={ECO:0000269|PubMed:28887308};.
UniProtKB/Swiss-Prot EnzymeRegulation:
Citrate synthase-lysine methyltransferase activity is inhibited by S-adenosylhomocysteine (AdoHcy) and oxaloacetate (OAA) (PubMed:28887308).

Enzyme Numbers (IUBMB) for CSKMT Gene

Phenotypes From GWAS Catalog for CSKMT Gene

Gene Ontology (GO) - Molecular Function for CSKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
GO:0008168 methyltransferase activity IEA --
GO:0016278 lysine N-methyltransferase activity IDA 28391595
GO:0016279 protein-lysine N-methyltransferase activity IDA 28887308
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with CSKMT: view

Phenotypes for CSKMT Gene

genes like me logo Genes that share phenotypes with CSKMT: view

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

Localization for CSKMT Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSKMT 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 CSKMT gene
Compartment Confidence
mitochondrion 4
nucleus 3
cytosol 2
extracellular 0

Gene Ontology (GO) - Cellular Components for CSKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
genes like me logo Genes that share ontologies with CSKMT: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CSKMT Gene

Pathways & Interactions for CSKMT Gene

PathCards logo

SuperPathways for CSKMT Gene

No Data Available

Gene Ontology (GO) - Biological Process for CSKMT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006479 protein methylation IDA 28887308
GO:0018023 peptidyl-lysine trimethylation IDA 28391595
GO:0018026 peptidyl-lysine monomethylation IDA 28391595
GO:0018027 peptidyl-lysine dimethylation IDA 28391595
GO:0032259 methylation IEA --
genes like me logo Genes that share ontologies with CSKMT: view

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

Drugs & Compounds for CSKMT Gene

No Compound Related Data Available

Transcripts for CSKMT Gene

mRNA/cDNA for CSKMT Gene

8 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

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

No ASD Table

Relevant External Links for CSKMT Gene

GeneLoc Exon Structure for

Expression for CSKMT Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CSKMT

Evidence on tissue expression from TISSUES for CSKMT Gene

  • Nervous system(4.1)
No Expression Related Data Available

Primer products for research

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

Orthologs for CSKMT Gene

This gene was present in the common ancestor of chordates.

Orthologs for CSKMT Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia METTL12 30 31
  • 99.17 (n)
(Bos Taurus)
Mammalia METTL12 30 31
  • 83.54 (n)
(Canis familiaris)
Mammalia METTL12 30 31
  • 81.39 (n)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia mettl12 30
  • 48.67 (n)
(Danio rerio)
Actinopterygii zgc:113305 30
  • 50.57 (n)
METTL12 31
  • 37 (a)
Species where no ortholog for CSKMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Mouse (Mus musculus)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rat (Rattus norvegicus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CSKMT Gene

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

Paralogs for CSKMT Gene

Paralogs for CSKMT Gene

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

Variants for CSKMT Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CSKMT Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
rs372150390 Benign: not provided 62,666,509(+) C/T
NM_001043229.2(CSKMT):c.181C>T (p.Gln61Ter)
rs11231181 - p.Gly125Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CSKMT Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
nsv555174 CNV gain 21841781
nsv832182 CNV gain+loss 17160897

Variation tolerance for CSKMT Gene

Residual Variation Intolerance Score: 85.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.54; 72.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CSKMT Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for CSKMT Gene

MalaCards: The human disease database

(1) MalaCards diseases for CSKMT Gene - From: COP

Disorder Aliases PubMed IDs
diarrhea 2, with microvillus atrophy
  • diar2
- elite association - COSMIC cancer census association via MalaCards
Search CSKMT in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CSKMT

genes like me logo Genes that share disorders with CSKMT: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CSKMT Gene

Publications for CSKMT Gene

  1. Uncovering human METTL12 as a mitochondrial methyltransferase that modulates citrate synthase activity through metabolite-sensitive lysine methylation. (PMID: 28887308) Małecki J … Falnes PØ (The Journal of biological chemistry 2017) 2 3 4
  2. Human METTL12 is a mitochondrial methyltransferase that modifies citrate synthase. (PMID: 28391595) Rhein VF … Walker JE (FEBS letters 2017) 2 3 4
  3. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PMID: 16554811) Taylor TD … Sakaki Y (Nature 2006) 3 4
  4. 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
  5. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3

Products for CSKMT Gene

Sources for CSKMT Gene