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Aliases for CARNMT1 Gene

Aliases for CARNMT1 Gene

  • Carnosine N-Methyltransferase 1 2 3 5
  • C9orf41 3 4
  • Chromosome 9 Open Reading Frame 41 2
  • Carnosine N-Methyltransferase 3
  • UPF0586 Protein C9orf41 3
  • EC 4
  • UPF0586 3

External Ids for CARNMT1 Gene

Previous HGNC Symbols for CARNMT1 Gene

  • C9orf41

Summaries for CARNMT1 Gene

Entrez Gene Summary for CARNMT1 Gene

  • The protein encoded by this gene is a methyltransferase that converts carnosine to anserine, a dipeptide found abundantly in skeletal muscle. The encoded protein can methylate other dipeptides as well. Three transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]

GeneCards Summary for CARNMT1 Gene

CARNMT1 (Carnosine N-Methyltransferase 1) is a Protein Coding gene. Among its related pathways are Metabolism and Histidine metabolism.

UniProtKB/Swiss-Prot for CARNMT1 Gene

  • N-methyltransferase that mediates the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. Also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His).

Additional gene information for CARNMT1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CARNMT1 Gene

Genomics for CARNMT1 Gene

GeneHancer (GH) Regulatory Elements for CARNMT1 Gene

Promoters and enhancers for CARNMT1 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
GH09J075026 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.8 804 3.1 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 YY1 POLR2B ZNF207 ZNF143 CARNMT1 C9orf40 ENSG00000278040 GC09P074993
GH09J074951 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 10.8 +75.6 75643 3.3 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 E2F8 ZNF143 C9orf41-AS1 C9orf40 NMRK1 OSTF1 CARNMT1 TRPM6 RNU6-445P LOC100133316
GH09J075100 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.9 -72.8 -72767 1.2 NCOA3 ESRRA NEUROD1 SIN3A NFXL1 YBX1 ZKSCAN1 CTBP1 GATA3 RCOR1 CARNMT1 NMRK1 TRPM6 RNU6-1228P OSTF1 LOC105376090
GH09J075000 Enhancer 0.9 ENCODE 11.9 +27.0 27033 2.1 FOXA2 MLX ARID4B DMAP1 ETS1 YY1 SLC30A9 ZNF143 RUNX3 NFKBIZ CARNMT1 NMRK1 OSTF1 C9orf40 GC09P074993 ENSG00000229587
GH09J075106 Enhancer 1 Ensembl ENCODE dbSUPER 10.3 -79.7 -79725 3.1 SMAD1 NFIB JUN GABPA NR2F2 NFIC GATA3 GABPB1 CREB1 MYC NMRK1 CARNMT1 RNU6-445P TRPM6 OSTF1 LOC105376090
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CARNMT1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CARNMT1 Gene

Genomic Locations for CARNMT1 Gene
47,467 bases
Minus strand

Genomic View for CARNMT1 Gene

Genes around CARNMT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CARNMT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CARNMT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CARNMT1 Gene

Proteins for CARNMT1 Gene

  • Protein details for CARNMT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Carnosine N-methyltransferase
    Protein Accession:
    Secondary Accessions:
    • Q7Z383
    • Q8N7C5

    Protein attributes for CARNMT1 Gene

    409 amino acids
    Molecular mass:
    47186 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC05369.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

neXtProt entry for CARNMT1 Gene

Post-translational modifications for CARNMT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CARNMT1 Gene

Domains & Families for CARNMT1 Gene

Gene Families for CARNMT1 Gene

Protein Domains for CARNMT1 Gene


Suggested Antigen Peptide Sequences for CARNMT1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the carnosine N-methyltransferase family.
  • Belongs to the carnosine N-methyltransferase family.
genes like me logo Genes that share domains with CARNMT1: view

Function for CARNMT1 Gene

Molecular function for CARNMT1 Gene

UniProtKB/Swiss-Prot Function:
N-methyltransferase that mediates the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. Also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His).
UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + carnosine = S-adenosyl-L-homocysteine + anserine.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=4.959 mM for carnosine {ECO:0000269 PubMed:26001783}; KM=0.053 mM for S-adenosyl-L-methionine {ECO:0000269 PubMed:26001783}; Vmax=1.77 nmol/min/mg enzyme with carnosine as substrate {ECO:0000269 PubMed:26001783}; Note=kcat is 0.09 min(-1) for carnosine. kcat is 3.57 min(-1) for S-adenosyl-L-methionine. {ECO:0000269 PubMed:26001783}; pH dependence: Optimum pH is 7.0-7.5. {ECO:0000269 PubMed:26001783}; Temperature dependence: Optimum temperature is 50 degrees Celsius. {ECO:0000269 PubMed:26001783};

Enzyme Numbers (IUBMB) for CARNMT1 Gene

Phenotypes From GWAS Catalog for CARNMT1 Gene

Gene Ontology (GO) - Molecular Function for CARNMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008168 methyltransferase activity IEA --
GO:0008757 S-adenosylmethionine-dependent methyltransferase activity IBA --
GO:0016740 transferase activity IEA --
GO:0030735 carnosine N-methyltransferase activity TAS --
genes like me logo Genes that share ontologies with CARNMT1: view
genes like me logo Genes that share phenotypes with CARNMT1: view

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CARNMT1 Gene

Localization for CARNMT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CARNMT1 Gene

Cytoplasm, cytosol. Nucleus.

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 CARNMT1 gene
Compartment Confidence
nucleus 5
cytosol 5
plasma membrane 2
cytoskeleton 2
mitochondrion 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for CARNMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 26001783
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with CARNMT1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CARNMT1 Gene

Pathways & Interactions for CARNMT1 Gene

genes like me logo Genes that share pathways with CARNMT1: view

Gene Ontology (GO) - Biological Process for CARNMT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006548 histidine catabolic process TAS --
GO:0032259 methylation IEA --
GO:0035498 carnosine metabolic process IDA 26001783
genes like me logo Genes that share ontologies with CARNMT1: view

No data available for SIGNOR curated interactions for CARNMT1 Gene

Drugs & Compounds for CARNMT1 Gene

No Compound Related Data Available

Transcripts for CARNMT1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CARNMT1 Gene

No ASD Table

Relevant External Links for CARNMT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CARNMT1 Gene

NURSA nuclear receptor signaling pathways regulating expression of CARNMT1 Gene:


mRNA Expression by UniProt/SwissProt for CARNMT1 Gene:

Tissue specificity: Expressed at higher level in kidney. Expressed at lower level in brain and skeletal musclea.

Evidence on tissue expression from TISSUES for CARNMT1 Gene

  • Nervous system(4.3)

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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for CARNMT1 Gene

Orthologs for CARNMT1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for CARNMT1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia C9orf41 34
  • 100 (a)
C9H9orf41 33
  • 99.92 (n)
(Canis familiaris)
Mammalia C9orf41 34
  • 97 (a)
C1H9orf41 33
  • 95.49 (n)
(Bos Taurus)
Mammalia C9orf41 34
  • 96 (a)
C8H9orf41 33
  • 94.46 (n)
(Rattus norvegicus)
Mammalia RGD1311863 33
  • 92.48 (n)
(Mus musculus)
Mammalia 2410127L17Rik 34 33
  • 92.21 (n)
Carnmt1 16
(Monodelphis domestica)
Mammalia C9orf41 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia C9orf41 34
  • 76 (a)
(Gallus gallus)
Aves CZH9ORF41 34 33
  • 84.35 (n)
(Anolis carolinensis)
Reptilia C9orf41 34
  • 74 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia c9orf41 33
  • 75.48 (n)
Str.7522 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5307 33
(Danio rerio)
Actinopterygii C5H9orf41 34
  • 68 (a)
zgc:112985 33
  • 67.75 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP007115 33
  • 52.63 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG11596 34 33
  • 49.81 (n)
(Caenorhabditis elegans)
Secernentea Y48E1C.2 34 33
  • 49.8 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C13750g 33
  • 47.26 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YNL092W 33
  • 46.12 (n)
-- 34
  • 28 (a)
-- 36
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL085C 33
  • 43.66 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G32170 33
  • 54.55 (n)
(Glycine max)
eudicotyledons Gma.12593 33
(Oryza sativa)
Liliopsida Os05g0511300 33
  • 56.13 (n)
Os.17049 33
(Triticum aestivum)
Liliopsida Ta.11407 33
(Hordeum vulgare)
Liliopsida Hv.3236 33
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC1778.07 33
  • 49.1 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU03692 33
  • 46.05 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
Species where no ortholog for CARNMT1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for CARNMT1 Gene

Gene Tree for CARNMT1 (if available)
Gene Tree for CARNMT1 (if available)
Evolutionary constrained regions (ECRs) for CARNMT1: view image

Paralogs for CARNMT1 Gene

No data available for Paralogs for CARNMT1 Gene

Variants for CARNMT1 Gene

Sequence variations from dbSNP and Humsavar for CARNMT1 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs1000179980 -- 75,022,273(-) G/C intron_variant
rs1000238880 -- 75,020,392(-) C/T intron_variant
rs1000257714 -- 75,022,523(-) C/T intron_variant
rs1000341911 -- 74,984,577(-) G/C genic_downstream_transcript_variant, intron_variant
rs1000396034 -- 74,985,116(-) T/C genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CARNMT1 Gene

Variant ID Type Subtype PubMed ID
esv3620712 CNV loss 21293372

Variation tolerance for CARNMT1 Gene

Residual Variation Intolerance Score: 16.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.62; 13.39% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CARNMT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CARNMT1 Gene

Disorders for CARNMT1 Gene

No disorders were found for CARNMT1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CARNMT1 Gene

Publications for CARNMT1 Gene

  1. UPF0586 Protein C9orf41 Homolog Is Anserine-producing Methyltransferase. (PMID: 26001783) Drozak J … de Heer E (The Journal of biological chemistry 2015) 2 3 4 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for CARNMT1 Gene

Sources for CARNMT1 Gene

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