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Aliases for CHDH Gene

Aliases for CHDH Gene

  • Choline Dehydrogenase 2 3 5
  • CDH 3 4
  • CHD 3 4
  • Choline Dehydrogenase, Mitochondrial 3
  • EC 4

External Ids for CHDH Gene

Previous GeneCards Identifiers for CHDH Gene

  • GC03M053019
  • GC03M053706
  • GC03M053808
  • GC03M053826

Summaries for CHDH Gene

Entrez Gene Summary for CHDH Gene

  • The protein encoded by this gene is a choline dehydrogenase that localizes to the mitochondrion. Variations in this gene can affect susceptibility to choline deficiency. A few transcript variants have been found for this gene, but the full-length nature of only one has been characterized to date. [provided by RefSeq, Dec 2010]

GeneCards Summary for CHDH Gene

CHDH (Choline Dehydrogenase) is a Protein Coding gene. Diseases associated with CHDH include Choline Deficiency Disease and Tooth Agenesis. Among its related pathways are Glycine, serine and threonine metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen and oxidoreductase activity, acting on CH-OH group of donors.

Additional gene information for CHDH Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CHDH Gene

Genomics for CHDH Gene

GeneHancer (GH) Regulatory Elements for CHDH Gene

Promoters and enhancers for CHDH 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
GH03J053841 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 657 +2.3 2266 6 HDGF CLOCK FOXA2 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 ZNF207 IL17RB CHDH RFT1 STIMATE ENSG00000271916
GH03J053775 Enhancer 0.6 ENCODE 10.6 +70.1 70119 1.2 SCRT1 FOXA2 RXRA YY1 SP1 ATF3 EGR1 SCRT2 HNF4A MAFK IL17RB CHDH GC03P053782 PIR47826 CACNA1D
GH03J053820 Enhancer 0.5 ENCODE dbSUPER 12 +24.7 24721 1.5 EBF1 IL17RB CHDH ENSG00000271916
GH03J053804 Enhancer 1.1 Ensembl ENCODE dbSUPER 5.1 +40.3 40309 3.9 PKNOX1 ESRRA NFXL1 RELA ZFHX2 CTBP1 POLR2A FOSL2 ZNF444 FOS RFT1 STIMATE ENSG00000271916 CHDH CACNA1D
GH03J053794 Enhancer 0.4 dbSUPER 11.3 +51.4 51420 0.6 ZNF335 ATF7 ATF2 CHDH IL17RB ENSG00000271916 GC03P053782 CACNA1D
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CHDH on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CHDH gene promoter:
  • NF-kappaB1
  • NF-kappaB
  • c-Ets-1
  • YY1
  • GATA-2
  • ITF-2
  • Tal-1beta

Genomic Locations for CHDH Gene

Genomic Locations for CHDH Gene
34,059 bases
Minus strand
34,059 bases
Minus strand

Genomic View for CHDH Gene

Genes around CHDH on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CHDH Gene

Proteins for CHDH Gene

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

    Protein Symbol:
    Recommended name:
    Choline dehydrogenase, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • Q9NY17

    Protein attributes for CHDH Gene

    594 amino acids
    Molecular mass:
    65358 Da
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    No Data Available

neXtProt entry for CHDH Gene

Post-translational modifications for CHDH Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CHDH Gene

Domains & Families for CHDH Gene

Gene Families for CHDH Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for CHDH Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the GMC oxidoreductase family.
  • Belongs to the GMC oxidoreductase family.
genes like me logo Genes that share domains with CHDH: view

Function for CHDH Gene

Molecular function for CHDH Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Choline + acceptor = betaine aldehyde + reduced acceptor.

Enzyme Numbers (IUBMB) for CHDH Gene

Phenotypes From GWAS Catalog for CHDH Gene

Gene Ontology (GO) - Molecular Function for CHDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0008812 choline dehydrogenase activity TAS --
GO:0016491 oxidoreductase activity IEA --
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors IEA --
GO:0050660 flavin adenine dinucleotide binding IEA --
genes like me logo Genes that share ontologies with CHDH: view
genes like me logo Genes that share phenotypes with CHDH: view

Animal Models for CHDH Gene

MGI Knock Outs for CHDH:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CHDH Gene

Localization for CHDH Gene

Subcellular locations from UniProtKB/Swiss-Prot for CHDH Gene

Mitochondrion inner membrane.

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 CHDH gene
Compartment Confidence
mitochondrion 5
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CHDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005743 mitochondrial inner membrane TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CHDH: view

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

Pathways & Interactions for CHDH Gene

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

UniProtKB/Swiss-Prot Q8NE62-CHDH_HUMAN

  • Pathway: Amine and polyamine biosynthesis; betaine biosynthesis via choline pathway; betaine aldehyde from choline (cytochrome c reductase route): step 1/1.

Gene Ontology (GO) - Biological Process for CHDH Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0019285 glycine betaine biosynthetic process from choline IEA --
GO:0042426 choline catabolic process TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with CHDH: view

No data available for SIGNOR curated interactions for CHDH Gene

Drugs & Compounds for CHDH Gene

(7) Drugs for CHDH Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Enzyme, substrate 176
Betaine Approved Nutra 36
Choline salicylate Approved Nutra Enzyme, substrate 0
FAD Approved Pharma 0
spermine Approved Nutra Full agonist, Agonist, Antagonist, Pore Blocker, Channel blocker 0

(3) Additional Compounds for CHDH Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Betaine aldehyde
  • Glycine betaine aldehyde
  • (Formylmethyl)trimethyl-ammonium
  • (Formylmethyl)trimethylammonium
  • BTL
  • N,N,N-Trimethyl-2-oxo ethanaminium
  • N'-acetylspermine
  • N'-monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-acetamide
  • N-Acetylspermine
  • 1,7-diamino-4-Azaheptane
  • 3,3'-Iminobis(propylamine)
  • 3,3'-Iminobispropylamine
  • 3,3'-Iminodi(propylamine)
  • 3,3-Diaminodipropylamine
genes like me logo Genes that share compounds with CHDH: view

Transcripts for CHDH Gene

mRNA/cDNA for CHDH Gene

Unigene Clusters for CHDH Gene

Choline dehydrogenase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c · 5d ^ 6 ^ 7a · 7b ^ 8 ^ 9
SP1: -
SP2: -

Relevant External Links for CHDH Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CHDH Gene

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

mRNA differential expression in normal tissues according to GTEx for CHDH Gene

This gene is overexpressed in Liver (x7.0) and Kidney - Cortex (x5.9).

Protein differential expression in normal tissues from HIPED for CHDH Gene

This gene is overexpressed in Salivary gland (22.4), Kidney (19.1), and Liver (6.5).

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

Protein tissue co-expression partners for CHDH Gene

NURSA nuclear receptor signaling pathways regulating expression of CHDH Gene:


SOURCE GeneReport for Unigene cluster for CHDH Gene:


Evidence on tissue expression from TISSUES for CHDH Gene

  • Liver(4.5)
  • Kidney(4.3)
genes like me logo Genes that share expression patterns with CHDH: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CHDH Gene

Orthologs for CHDH Gene

This gene was present in the common ancestor of animals.

Orthologs for CHDH Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CHDH 34 33
  • 99.49 (n)
(Canis familiaris)
Mammalia CHDH 34 33
  • 88.59 (n)
(Bos Taurus)
Mammalia CHDH 34 33
  • 87.69 (n)
(Mus musculus)
Mammalia Chdh 16 34 33
  • 83.14 (n)
(Ornithorhynchus anatinus)
Mammalia CHDH 34
  • 83 (a)
(Rattus norvegicus)
Mammalia Chdh 33
  • 83 (n)
(Monodelphis domestica)
Mammalia CHDH 34
  • 77 (a)
(Gallus gallus)
Aves CHDH 34 33
  • 67.35 (n)
(Anolis carolinensis)
Reptilia CHDH 34
  • 70 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.31969 33
(Danio rerio)
Actinopterygii chdh 34 33
  • 70.39 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG12398 34 35
  • 32 (a)
CG9503 34 35
  • 32 (a)
CG6142 34 35
  • 32 (a)
CG9522 34 35
  • 31 (a)
CG9518 34 35
  • 31 (a)
CG9519 34 35
  • 31 (a)
CG9521 34 35
  • 31 (a)
Gld 34 35
  • 30 (a)
CG9512 34 35
  • 30 (a)
CG12539 34 35
  • 29 (a)
CG9514 34 35
  • 28 (a)
CG9509 34 35
  • 27 (a)
ninaG 34 35
  • 26 (a)
Eo 34
  • 25 (a)
CG9517 34 35
  • 24 (a)
(Caenorhabditis elegans)
Secernentea C34C6.4 34 35 33
  • 52.98 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5658 34
  • 67 (a)
Species where no ortholog for CHDH was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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 (Oryza sativa)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for CHDH Gene

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

Paralogs for CHDH Gene

No data available for Paralogs for CHDH Gene

Variants for CHDH Gene

Sequence variations from dbSNP and Humsavar for CHDH Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000090787 -- 53,815,509(-) T/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000124129 -- 53,833,552(-) GG/G intron_variant
rs1000177999 -- 53,830,334(-) T/C intron_variant
rs1000234981 -- 53,839,936(-) G/A intron_variant
rs1000283119 -- 53,833,956(-) T/C intron_variant

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

Variant ID Type Subtype PubMed ID
dgv283n21 CNV loss 19592680
dgv4746n100 CNV gain 25217958
dgv4747n100 CNV gain 25217958
esv3575570 CNV gain 25503493
nsv1003621 CNV loss 25217958
nsv1006990 CNV gain 25217958
nsv1013783 CNV gain 25217958
nsv954867 CNV deletion 24416366

Variation tolerance for CHDH Gene

Residual Variation Intolerance Score: 12% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.41; 88.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CHDH Gene

Human Gene Mutation Database (HGMD)
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 CHDH Gene

Disorders for CHDH Gene

MalaCards: The human disease database

(2) MalaCards diseases for CHDH Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
choline deficiency disease
  • choline deficiency
tooth agenesis
  • familial tooth agenesis
- elite association - COSMIC cancer census association via MalaCards
Search CHDH in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CHDH

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CHDH: view

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

Publications for CHDH Gene

  1. Common genetic polymorphisms affect the human requirement for the nutrient choline. (PMID: 16816108) da Costa KA … Zeisel SH (FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2006) 3 22 44 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. Cystathionine beta-synthase 844Ins68 polymorphism is not associated with the levels of homocysteine and cysteine in an Indian population. (PMID: 20175737) Kumar J … Sengupta S (Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals 2010) 3 22 58
  4. Associations of folate and choline metabolism gene polymorphisms with orofacial clefts. (PMID: 19737740) Mostowska A … Jagodzinski PP (Journal of medical genetics 2010) 3 44 58
  5. Polymorphisms located in the region containing BHMT and BHMT2 genes as maternal protective factors for orofacial clefts. (PMID: 20662904) Mostowska A … Jagodzinski PP (European journal of oral sciences 2010) 3 44 58

Products for CHDH Gene

Sources for CHDH Gene

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