CHDH

gene
On this page

Summary

CHDH (choline dehydrogenase, HGNC:24288) is a protein-coding gene on chromosome 3p21.1, encoding Choline dehydrogenase, mitochondrial (Q8NE62).

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.

Source: NCBI Gene 55349 — RefSeq curated summary.

At a glance

  • GWAS associations: 6
  • Clinical variants (ClinVar): 121 total
  • MANE Select transcript: NM_018397

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24288
Approved symbolCHDH
Namecholine dehydrogenase
Location3p21.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000016391
Ensembl biotypeprotein_coding
Entrez55349

Gene structure

Transcript identifiers

Ensembl transcripts: 36 — 36 protein_coding

ENST00000315251, ENST00000467802, ENST00000481668, ENST00000875878, ENST00000875879, ENST00000875880, ENST00000875881, ENST00000875882, ENST00000875883, ENST00000875884, ENST00000875885, ENST00000875886, ENST00000875887, ENST00000875888, ENST00000875889, ENST00000875890, ENST00000875891, ENST00000875892, ENST00000875893, ENST00000875894, ENST00000875895, ENST00000911850, ENST00000911851, ENST00000959581, ENST00000959582, ENST00000959583, ENST00000959584, ENST00000959585, ENST00000959586, ENST00000959587, ENST00000959588, ENST00000959589, ENST00000959590, ENST00000959591, ENST00000959592, ENST00000959593

RefSeq mRNA: 1 — MANE Select: NM_018397 NM_018397

CCDS: CCDS2873

Canonical transcript exons

ENST00000315251 — 9 exons

ExonStartEnd
ENSE000007718205382249153822642
ENSE000007718215382164753821776
ENSE000007718225382047453820608
ENSE000007718235381953253819674
ENSE000007718245381893853819040
ENSE000010798775381233553818195
ENSE000012152345382330653824067
ENSE000013438245384092953840999
ENSE000013438375384608353846419

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 98.41.

FANTOM5 (CAGE): breadth broad, TPM avg 1.9550 / max 50.8453, expressed in 648 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
425181.3193553
425170.4416210
425190.154475
425150.034112
425160.00553

Top tissues by expression

252 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
kidney epitheliumUBERON:000481998.41gold quality
renal medullaUBERON:000036293.94gold quality
pylorusUBERON:000116690.80gold quality
epithelial cell of pancreasCL:000008390.37gold quality
cerebellar vermisUBERON:000472090.23gold quality
adult mammalian kidneyUBERON:000008289.40gold quality
right lobe of liverUBERON:000111488.94gold quality
liverUBERON:000210788.19gold quality
cardia of stomachUBERON:000116288.11gold quality
cardiac muscle of right atriumUBERON:000337987.56gold quality
left ventricle myocardiumUBERON:000656687.47gold quality
kidneyUBERON:000211387.17gold quality
ileal mucosaUBERON:000033186.76gold quality
middle temporal gyrusUBERON:000277186.34gold quality
pancreatic ductal cellCL:000207986.03silver quality
parotid glandUBERON:000183185.46gold quality
ventral tegmental areaUBERON:000269185.32gold quality
tracheaUBERON:000312685.22gold quality
medial globus pallidusUBERON:000247785.03gold quality
globus pallidusUBERON:000187585.01gold quality
epithelium of mammary glandUBERON:000324484.99gold quality
mammary ductUBERON:000176584.88gold quality
vena cavaUBERON:000408784.71silver quality
subthalamic nucleusUBERON:000190684.39gold quality
dorsal plus ventral thalamusUBERON:000189783.92gold quality
body of pancreasUBERON:000115083.52gold quality
inferior vagus X ganglionUBERON:000536383.40gold quality
nippleUBERON:000203083.34gold quality
upper arm skinUBERON:000426383.00gold quality
medulla oblongataUBERON:000189682.78gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

40 targeting CHDH, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-612499.8769.783551
HSA-MIR-127699.3668.181642
HSA-MIR-520A-5P99.3566.721632
HSA-MIR-525-5P99.3566.851615
HSA-MIR-6808-5P99.3166.232150
HSA-MIR-504-3P99.3067.181745
HSA-MIR-324-3P99.2666.311034
HSA-MIR-797499.2465.481137
HSA-MIR-6734-3P99.1566.271627
HSA-MIR-939-3P98.9765.072347
HSA-MIR-480198.9669.422096
HSA-MIR-6756-3P98.9466.791104
HSA-MIR-3127-3P98.9467.341055
HSA-MIR-181A-2-3P98.9167.601168
HSA-MIR-29B-1-5P98.8668.351364
HSA-MIR-64898.6466.13553
HSA-MIR-4731-3P98.5668.601860
HSA-MIR-4722-5P98.4666.341611
HSA-MIR-4691-5P98.4166.771343
HSA-MIR-6792-3P98.4166.861359
HSA-MIR-4691-3P98.1166.831204
HSA-MIR-6742-3P97.9564.501490
HSA-MIR-6765-3P97.8364.591165
HSA-MIR-392197.8167.451431
HSA-MIR-466097.7967.441328
HSA-MIR-6747-3P97.7364.841596
HSA-MIR-4667-5P97.6166.671683
HSA-MIR-4653-5P97.2267.721429
HSA-MIR-1233-3P96.8165.44573

Literature-anchored findings (GeneRIF, showing 10)

  • HOXB13, IL17BR, and CHDH are regulated by estrogen in breast cancer (PMID:17975144)
  • single nucleotide polymorphisms of choline-metabolizing genes, PEMT -774G>C (rs12325817) and CHDH +432G>T (rs12676), were found be related to breast cancer risk (PMID:18230680)
  • CHDH A119C and MTHFR C677T play an important role in modulating the homocysteine levels in Indian population. (PMID:20031640)
  • CHDH and PLD2 as novel candidate genes, the nucleotide variants of which could be associated with the risk of tooth agenesis. (PMID:21308979)
  • the PEMT -774G>C and CHDH +432G>T polymorphisms were associated with sperm concentration. This finding suggests a possible influence of these genes on sperm quality (PMID:22387881)
  • The rs12676 single nucleotide polymorphism is associated with altered sperm motility patterns and dysmorphic mitochondrial structure in sperm. (PMID:22558321)
  • CHDH is not a substrate of PARK2 but interacts with SQSTM1 independently of PARK2 to recruit SQSTM1 into depolarized mitochondria (PMID:25483962)
  • CHDH gene is located at chromosome 3p21.1, a risk region implicated in previous brains of bipolar disorder genome-wide association studies (PMID:27562178)
  • In genotypic combination analysis considering PEMT -744GG/CHDH +432GG/BHMT +742GG as the reference combination, PEMT -744GC/CHDH +432GG/BHMT +742GG genotypic combination was significantly higher in mothers of a down syndrome child compared with that in control mothers with an odds ratio of 2.061 (95% CI: 1.10-3.86, P=0.0342). (PMID:27677362)
  • There is no correlation between single CHDH rs893363 and CHDH rs2289205 polymorphisms and the incidence of intrauterine fetal death. (PMID:28509322)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriochdhENSDARG00000100304
mus_musculusChdhENSMUSG00000015970
rattus_norvegicusChdhENSRNOG00000015859
drosophila_melanogasterninaGFBGN0037896
caenorhabditis_elegansWBGENE00007917

Protein

Protein identifiers

Choline dehydrogenase, mitochondrialQ8NE62 (reviewed: Q8NE62)

All UniProt accessions (3): Q8NE62, C9J7D8, C9JYW4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Mitochondrion inner membrane.

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

Similarity. Belongs to the GMC oxidoreductase family.

RefSeq proteins (1): NP_060867* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000172GMC_OxRdtase_NDomain
IPR007867GMC_OxRtase_CDomain
IPR012132GMC_OxRdtaseFamily
IPR036188FAD/NAD-bd_sfHomologous_superfamily

Pfam: PF00732, PF05199

Enzyme classification (BRENDA):

  • EC 1.1.99.1 — choline dehydrogenase (BRENDA: 9 organisms, 61 substrates, 27 inhibitors, 10 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
CHOLINE1.7–74
PHENAZINE METHOSULFATE0.14–1.13
2,6-DICHLOROPHENOLINDOPHENOL11
BETAINE ALDEHYDE3.11
P-BENZOQUINONE0.831

Catalyzed reactions (Rhea), 1 shown:

  • choline + A = betaine aldehyde + AH2 (RHEA:17433)

UniProt features (14 total): modified residue 6, sequence variant 3, transit peptide 1, chain 1, sequence conflict 1, active site 1, binding site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NE62-F192.840.90

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 511 (proton acceptor)

Ligand- & substrate-binding residues (1): 42–71

Post-translational modifications (6): 436, 484, 484, 496, 496, 580

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-6798163Choline catabolism

MSigDB gene sets: 119 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, BENPORATH_ES_WITH_H3K27ME3, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOCC_MITOCHONDRIAL_ENVELOPE, GOBP_AMINO_ACID_BETAINE_METABOLIC_PROCESS, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, WONG_MITOCHONDRIA_GENE_MODULE, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_CH_OH_GROUP_OF_DONORS, GOBP_MODIFIED_AMINO_ACID_METABOLIC_PROCESS, MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6, TGGAAA_NFAT_Q4_01, GOCC_ORGANELLE_INNER_MEMBRANE, GAVIN_FOXP3_TARGETS_CLUSTER_P6, LINDGREN_BLADDER_CANCER_CLUSTER_1_DN

GO Biological Process (2): obsolete glycine betaine biosynthetic process from choline (GO:0019285), choline catabolic process (GO:0042426)

GO Molecular Function (5): choline dehydrogenase activity (GO:0008812), flavin adenine dinucleotide binding (GO:0050660), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), oxidoreductase activity, acting on CH-OH group of donors (GO:0016614)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial inner membrane (GO:0005743), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Metabolism of amino acids and derivatives1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
choline metabolic process1
biogenic amine catabolic process1
oxidoreductase activity, acting on CH-OH group of donors1
nucleotide binding1
anion binding1
binding1
catalytic activity1
oxidoreductase activity1
cytoplasm1
intracellular membrane-bounded organelle1
organelle inner membrane1
mitochondrial membrane1
cellular anatomical structure1

Protein interactions and networks

STRING

2634 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CHDHBHMTQ93088744
CHDHSQSTM1Q13501699
CHDHPEMTQ9UBM1636
CHDHMTRQ99707623
CHDHSARDHQ9UL12623
CHDHDMGDHQ9UI17580
CHDHMTHFRP42898565
CHDHALDH7A1P49419556
CHDHMTHFD1P11586555
CHDHCHKAP35790544
CHDHDHODHQ02127540
CHDHAHCYP23526528
CHDHSQORQ9Y6N5521
CHDHMTRRQ9UBK8519
CHDHH7C2H4H7C2H4513

IntAct

40 interactions, top by confidence:

ABTypeScore
COQ8ACOQ9psi-mi:“MI:0914”(association)0.670
NDUFS7NDUFS8psi-mi:“MI:0914”(association)0.640
NOTCH2NLACHDHpsi-mi:“MI:0915”(physical association)0.560
CHDHNOTCH2NLApsi-mi:“MI:0915”(physical association)0.560
CHDHKLK6psi-mi:“MI:0915”(physical association)0.560
BPNT1GTPBP10psi-mi:“MI:0914”(association)0.530
YBEYNME4psi-mi:“MI:0914”(association)0.530
CHDHRPL8psi-mi:“MI:0915”(physical association)0.370
CHDHSEZ6psi-mi:“MI:0915”(physical association)0.370
YBEYNUDT19psi-mi:“MI:0914”(association)0.350
NDUFS7psi-mi:“MI:0914”(association)0.350
TRMT1HDAC3psi-mi:“MI:0914”(association)0.350
TMEM70FDXRpsi-mi:“MI:0914”(association)0.350
COQ9NDUFS8psi-mi:“MI:0914”(association)0.350
NMES1COX7A2Lpsi-mi:“MI:0914”(association)0.350
COQ9ACOT7psi-mi:“MI:0914”(association)0.350
FAM136AALDH1L1psi-mi:“MI:0914”(association)0.350
NDUFA4NDUFS8psi-mi:“MI:0914”(association)0.350
COQ8BCOQ9psi-mi:“MI:0914”(association)0.350
NMES1TIMM44psi-mi:“MI:0914”(association)0.350
MAIP1COQ9psi-mi:“MI:0914”(association)0.350
NDUFA4COX7A2Lpsi-mi:“MI:0914”(association)0.350

BioGRID (30): NOTCH2NL (Two-hybrid), SQSTM1 (Affinity Capture-Western), CHDH (Affinity Capture-Western), MAP1LC3A (Affinity Capture-Western), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS), CHDH (Affinity Capture-MS)

ESM2 similar proteins: A0A142PTM2, A0A161CEV4, A0A1L9WN49, A0A248QE08, A0A2V5GRB0, A0A3B1EFP9, A0A5C1RDA6, A4UHS8, A4XPI5, A5WA97, A6VEI3, A8GBX9, A8JHB7, B0KN19, B0RNU9, B2JS89, B3PTE0, B5ZUG2, B7V5R3, C3K3D3, C6DKY4, C8VDT4, M2Y151, M5EAX2, P18172, P18173, P9WEH2, Q02DZ0, Q0B711, Q12062, Q1IG70, Q1MJU4, Q2KB43, Q3K5H3, Q48CM7, Q4K4K7, Q4UYN5, Q4ZM63, Q5GMY3, Q5HL11

Diamond homologs: A0A075TRK9, A0A142PTM2, A0A161CEV4, A0A1U8QYA8, A0A2V5GRB0, A0A5C1RDA6, A0B2F7, A1CFL2, A4JJG6, A4TNP2, A4UHS8, A4XPI5, A5IW37, A5VPA6, A5WA97, A6QK99, A6U4Z2, A6U6Y8, A6VEI3, A6X2G7, A7FKL6, A7MFA8, A7X6Z3, A8AJN0, A8GBX9, A8Z5A4, A9AMZ9, A9M9H8, B0CKN4, B0KN19, B1JSR0, B1K707, B1Z034, B2FQ89, B2JS89, B2K8U4, B2TCJ8, B3PTE0, B4EHJ2, B4SHV9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

121 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance97
Likely benign9
Benign4

Top pathogenic / likely-pathogenic (0)

SpliceAI

2168 predictions. Top by Δscore:

VariantEffectΔscore
3:53817749:C:Adonor_gain1.0000
3:53818933:AGTAC:Adonor_loss1.0000
3:53818934:GTA:Gdonor_loss1.0000
3:53818935:TACC:Tdonor_loss1.0000
3:53818936:A:Cdonor_loss1.0000
3:53820470:TCA:Tdonor_loss1.0000
3:53820471:CAC:Cdonor_loss1.0000
3:53820472:A:ATdonor_loss1.0000
3:53820604:AACCC:Aacceptor_gain1.0000
3:53820605:ACCC:Aacceptor_gain1.0000
3:53820606:CCC:Cacceptor_gain1.0000
3:53820606:CCCC:Cacceptor_gain1.0000
3:53820607:CC:Cacceptor_gain1.0000
3:53820607:CCC:Cacceptor_gain1.0000
3:53820608:CC:Cacceptor_gain1.0000
3:53820609:C:CCacceptor_gain1.0000
3:53820609:C:Tacceptor_gain1.0000
3:53820612:A:ACacceptor_gain1.0000
3:53820612:A:Cacceptor_gain1.0000
3:53821640:GACT:Gdonor_loss1.0000
3:53821641:ACTC:Adonor_loss1.0000
3:53821642:CTCAC:Cdonor_loss1.0000
3:53821643:TCA:Tdonor_loss1.0000
3:53821644:C:CGdonor_loss1.0000
3:53821645:A:ACdonor_gain1.0000
3:53821645:ACCA:Adonor_loss1.0000
3:53821646:C:CCdonor_gain1.0000
3:53821772:TAAGC:Tacceptor_gain1.0000
3:53821776:CCTGG:Cacceptor_loss1.0000
3:53821777:C:CAacceptor_loss1.0000

AlphaMissense

3853 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:53817897:G:CN555K0.997
3:53817897:G:TN555K0.997
3:53818031:G:CH511D0.997
3:53820588:C:GD336H0.996
3:53818038:G:CS508R0.995
3:53818038:G:TS508R0.995
3:53818040:T:GS508R0.995
3:53819637:G:CF386L0.995
3:53819637:G:TF386L0.995
3:53819639:A:GF386L0.995
3:53823561:A:GW150R0.995
3:53823561:A:TW150R0.995
3:53823604:A:CN135K0.995
3:53823604:A:TN135K0.995
3:53817925:G:AS546F0.994
3:53817925:G:TS546Y0.994
3:53818014:A:CC516W0.994
3:53820587:T:AD336V0.994
3:53820587:T:GD336A0.994
3:53823573:C:GD146H0.994
3:53817932:C:GD544H0.993
3:53817937:A:TV542D0.993
3:53819641:C:TG385E0.993
3:53823535:C:AW158C0.993
3:53823535:C:GW158C0.993
3:53823537:A:GW158R0.993
3:53823537:A:TW158R0.993
3:53817931:T:AD544V0.992
3:53818031:G:TH511N0.992
3:53822629:G:CS239R0.992

dbSNP variants (sampled 300 via entrez): RS1000090787 (3:53815509 T>C), RS1000124129 (3:53833551 TG>T), RS1000177999 (3:53830334 T>C), RS1000234981 (3:53839936 G>A), RS1000283119 (3:53833956 T>C), RS1000335796 (3:53834212 C>T), RS1000412172 (3:53823229 C>G), RS1000425843 (3:53841999 AG>A), RS1000443254 (3:53815198 A>G), RS1000583248 (3:53827782 G>A), RS1000648905 (3:53846022 C>A,G,T), RS1000701076 (3:53846188 C>T), RS1000709185 (3:53829484 G>C), RS1000799028 (3:53836396 C>G,T), RS1000855623 (3:53826811 T>A,C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

6 associations (top):

StudyTraitp-value
GCST002115_6Axial length8.000000e-06
GCST005951_50Body mass index5.000000e-11
GCST007327_68Smoking status (ever vs never smokers)4.000000e-08
GCST007929_91Medication use (calcium channel blockers)1.000000e-08
GCST009569_1interleukin 17 receptor B levels2.000000e-18
GCST010002_424Refractive error9.000000e-24

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0005318axial length measurement
EFO:0004340body mass index
EFO:0004318smoking behavior
EFO:0009930Calcium channel blocker use measurement
EFO:0008176interleukin 17 receptor B measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs6801605CHDH0.000

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects expression, affects cotreatment, increases methylation2
sodium arsenitedecreases expression2
Leflunomidedecreases expression2
Acetaminophendecreases expression2
Estradiolincreases expression2
Nickeldecreases expression2
Valproic Acidaffects cotreatment, decreases expression2
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
perfluorooctanoic aciddecreases expression1
CGP 52608affects binding, increases reaction1
K 7174decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
teriflunomidedecreases expression1
bisphenol Sdecreases methylation1
NSC 689534decreases expression, affects binding1
Temozolomideincreases expression1
Sunitinibdecreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Arsenicaffects metabolic processing1
Benzo(a)pyreneincreases methylation1
Calcitriolincreases expression1
Carbamazepineaffects expression1
Cholineaffects response to substance1
Cisplatindecreases expression1
Copperaffects binding, decreases expression1
Diclofenacaffects expression1
Dimethyl Sulfoxideincreases expression1
Formaldehydedecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.