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Aliases for CSKMT Gene

Aliases for CSKMT Gene

  • Citrate Synthase Lysine Methyltransferase 2 3 5
  • Methyltransferase-Like Protein 12, Mitochondrial 3 4
  • Methyltransferase Like 12 2 3
  • METTL12 3 4
  • CS-KMT 3 4
  • Citrate Synthase-Lysine N-Methyltransferase CSKMT, Mitochondrial 3
  • Putative Methyltransferase LOC751071, Mitochondrial 3
  • EC 2.1.1.- 4
  • U99HG 3

External Ids for CSKMT Gene

Previous HGNC Symbols for CSKMT Gene

  • METTL12

Previous GeneCards Identifiers for CSKMT Gene

  • GC11P062668

Summaries for CSKMT Gene

GeneCards Summary for CSKMT Gene

CSKMT (Citrate Synthase Lysine Methyltransferase) is a Protein Coding gene.

UniProtKB/Swiss-Prot 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).

Additional gene information for CSKMT Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CSKMT Gene

Genomics for CSKMT Gene

GeneHancer (GH) Regulatory Elements for CSKMT Gene

Promoters and enhancers for CSKMT 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
GH11J062664 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 698.4 +0.8 779 4.1 HDGF HNRNPUL1 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 YBX1 YY1 CSKMT SNORA57 GC11P062673 ENSG00000255432 C11orf98 LBHD1 EML3 NXF1 SNHG1 GANAB
GH11J062838 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 123.3 +175.6 175583 4.8 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 WDR74 RNU2-2P GC11M062842 NXF1 CSKMT INTS5 SNHG1 UBXN1 MTA2 GANAB
GH11J062852 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 84.7 +190.6 190574 5.9 MLX FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NXF1 SNHG1 SLC3A2 GC11M062919 GC11M062934 GC11M062939 GC11M062942 SNORD29 SNORD28 SNORD27
GH11J062041 Enhancer 1.3 ENCODE dbSUPER 86.8 -619.8 -619835 8.1 PKNOX1 SMAD1 ARNT ZFP64 FEZF1 ZNF766 ZNF213 E2F8 FOS SP3 CSKMT CPSF7 SNHG1 GANAB NXF1 LOC105369332 TUT1 TMEM138 INTS5 MTA2
GH11J062669 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 52.2 +6.2 6226 4.2 HDGF HNRNPUL1 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 LBHD1 UQCC3 GC11M062588 EML3 LOC105369332 MTA2 GANAB WDR74 STX5 CSKMT
- 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 UCSC Golden Path with GeneCards custom track

Genomic Locations for CSKMT Gene

Genomic Locations for CSKMT Gene
3,234 bases
Plus strand
3,190 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

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CSKMT Gene

Suggested Antigen Peptide Sequences for CSKMT Gene

GenScript: Design optimal peptide antigens:

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:
S-adenosyl-L-methionine + [citrate synthase]-L-lysine = S-adenosyl-L-homocysteine + [citrate synthase]-N(6)-methyl-L-lysine.
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + [citrate synthase]-N6-methyl-L-lysine = S-adenosyl-L-homocysteine + [citrate synthase]-N(6),N(6)-dimethyl-L-lysine.
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + [citrate synthase]-N(6),N(6)-dimethyl-L-lysine = S-adenosyl-L-homocysteine + [citrate synthase]-N(6),N(6),N(6)-trimethyl-L-lysine.
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: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

Clone Products

No data available for Human Phenotype Ontology , Animal Models , miRNA , 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 3
extracellular 1

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

SuperPathways for CSKMT Gene

No Data Available

Interacting Proteins for CSKMT Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: ENSP00000431287 for CSKMT Gene via STRING

Symbol External ID(s) Details

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

(2) REFSEQ mRNAs :
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Clone Products

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

No ASD Table

Relevant External Links for CSKMT Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CSKMT Gene

NURSA nuclear receptor signaling pathways regulating expression of CSKMT Gene:


Evidence on tissue expression from TISSUES for CSKMT Gene

  • Nervous system(4.1)
No Expression Related Data Available

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 34 33
  • 99.17 (n)
(Bos Taurus)
Mammalia METTL12 34 33
  • 83.54 (n)
(Canis familiaris)
Mammalia METTL12 34 33
  • 81.39 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia mettl12 33
  • 48.67 (n)
(Danio rerio)
Actinopterygii zgc:113305 33
  • 50.57 (n)
METTL12 34
  • 37 (a)
Species where no ortholog for CSKMT was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

No data available for Paralogs for CSKMT Gene

Variants for CSKMT Gene

Sequence variations from dbSNP and Humsavar for CSKMT Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs1000900240 -- 62,667,298(+) A/G 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs1001255103 -- 62,667,674(+) G/T downstream_transcript_variant
rs1003009191 -- 62,665,794(+) C/T 5_prime_UTR_variant, coding_sequence_variant, missense_variant
rs1003195972 -- 62,664,525(+) T/C upstream_transcript_variant
rs1003659267 -- 62,664,236(+) T/C upstream_transcript_variant

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

Additional Disease Information for CSKMT

No disorders were found for CSKMT Gene.

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

Publications for CSKMT Gene

  1. Human METTL12 is a mitochondrial methyltransferase that modifies citrate synthase. (PMID: 28391595) Rhein VF … Walker JE (FEBS letters 2017) 2 3 4 58
  2. 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 58
  3. Human chromosome 11 DNA sequence and analysis including novel gene identification. (PMID: 16554811) Taylor TD … Sakaki Y (Nature 2006) 3 4 58
  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 58
  5. Human METTL20 methylates lysine residues adjacent to the recognition loop of the electron transfer flavoprotein in mitochondria. (PMID: 25023281) Rhein VF … Walker JE (The Journal of biological chemistry 2014) 4 58

Products for CSKMT Gene

Sources for CSKMT Gene

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