FMO4

gene
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Summary

FMO4 (flavin containing dimethylaniline monoxygenase 4, HGNC:3772) is a protein-coding gene on chromosome 1q24.3, encoding Dimethylaniline monooxygenase [N-oxide-forming] 4 (P31512). This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides.

Metabolic N-oxidation of diet-derived amino-trimethylamine (TMA) is mediated by flavin-containing monooxygenase and is subject to an inherited FMO3 polymorphism in man. This results in a small subpopulation with reduced TMA N-oxidation capacity and causes fish odor syndrome (Trimethylaminuria). Three forms of the enzyme are encoded by genes clustered in the 1q23-q25 region. Flavin-containing monooxygenases are NADPH-dependent flavoenzymes that catalyzes the oxidation of soft nucleophilic heteroatom centers in drugs, pesticides, and xenobiotics.

Source: NCBI Gene 2329 — RefSeq curated summary.

At a glance

  • GWAS associations: 10
  • Clinical variants (ClinVar): 98 total
  • Phenotypes (HPO): 1
  • Druggable target: yes
  • Dosage sensitivity (ClinGen): haploinsufficiency dosage sensitivity unlikely, triplosensitivity no evidence
  • MANE Select transcript: NM_002022

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3772
Approved symbolFMO4
Nameflavin containing dimethylaniline monoxygenase 4
Location1q24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000076258
Ensembl biotypeprotein_coding
OMIM136131
Entrez2329

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 12 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000367749, ENST00000462992, ENST00000475780, ENST00000480136, ENST00000497228, ENST00000853709, ENST00000853710, ENST00000853711, ENST00000853712, ENST00000853713, ENST00000853714, ENST00000853715, ENST00000853716, ENST00000919758, ENST00000959333, ENST00000959334

RefSeq mRNA: 1 — MANE Select: NM_002022 NM_002022

CCDS: CCDS1295

Canonical transcript exons

ENST00000367749 — 10 exons

ExonStartEnd
ENSE00000789750171332709171332908
ENSE00000789751171334411171334763
ENSE00001022028171316186171316327
ENSE00001445542171341413171342084
ENSE00003548928171323004171323192
ENSE00003587017171319818171319957
ENSE00003679873171331640171331782
ENSE00003680340171324138171324300
ENSE00003681912171337356171337425
ENSE00003842448171314183171314413

Expression profiles

Bgee: expression breadth ubiquitous, 202 present calls, max score 89.40.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 1.4208 / max 161.6560, expressed in 177 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
66051.7960864
66061.4397704
65961.4208177
66040.6397377
65940.070936
65950.069533

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
nephron tubuleUBERON:000123189.40gold quality
right lobe of liverUBERON:000111488.07gold quality
ileal mucosaUBERON:000033187.88gold quality
liverUBERON:000210786.99gold quality
kidney epitheliumUBERON:000481986.92gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.46gold quality
adult mammalian kidneyUBERON:000008285.37gold quality
kidneyUBERON:000211384.71gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.55gold quality
renal glomerulusUBERON:000007483.25gold quality
cortex of kidneyUBERON:000122582.67gold quality
metanephric glomerulusUBERON:000473682.47gold quality
ascending aortaUBERON:000149681.41gold quality
thoracic aortaUBERON:000151581.29gold quality
descending thoracic aortaUBERON:000234581.24gold quality
hair follicleUBERON:000207381.00gold quality
calcaneal tendonUBERON:000370180.72gold quality
palpebral conjunctivaUBERON:000181279.81gold quality
apex of heartUBERON:000209879.71gold quality
mucosa of transverse colonUBERON:000499179.63gold quality
mucosa of paranasal sinusUBERON:000503079.53silver quality
aortaUBERON:000094779.22gold quality
left coronary arteryUBERON:000162679.06gold quality
pancreatic ductal cellCL:000207979.00silver quality
germinal epithelium of ovaryUBERON:000130478.45gold quality
right uterine tubeUBERON:000130278.17gold quality
coronary arteryUBERON:000162178.13gold quality
popliteal arteryUBERON:000225077.80gold quality
tibial arteryUBERON:000761077.77gold quality
duodenumUBERON:000211477.66gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no4.63

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOS

miRNA regulators (miRDB)

42 targeting FMO4, 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-5011-5P100.0083.465820
HSA-MIR-318599.9968.121959
HSA-MIR-450099.9972.722367
HSA-MIR-453499.9966.581907
HSA-MIR-453199.9969.703181
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-570-3P99.9672.414910
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-808299.9567.271170
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-10395-5P99.8667.35676
HSA-MIR-374C-5P99.8072.062910
HSA-MIR-655-3P99.8072.192909
HSA-MIR-430699.7270.503630
HSA-MIR-154-3P99.5070.05831
HSA-MIR-487A-3P99.5069.95840
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-6797-3P99.1766.94668
HSA-MIR-892C-5P99.1670.562116
HSA-MIR-6510-5P99.1466.591081

Functional genomics

ClinGen dosage: haploinsufficiency 40 (dosage sensitivity unlikely), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 1)

  • Data show a compelling visual demonstration of the isoform-specific localization patterns of FMO1, -3, and -4 in the rat liver and kidney and the first evidence for expression of FMO4 at the protein level in mouse and human liver and kidney microsomes. (PMID:19307449)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
mus_musculusFmo4ENSMUSG00000026692
rattus_norvegicusFmo4ENSRNOG00000003400
caenorhabditis_elegansWBGENE00001476
caenorhabditis_elegansWBGENE00001478
caenorhabditis_elegansWBGENE00001480
caenorhabditis_elegansC01H6.4WBGENE00007254
caenorhabditis_elegansC46H11.2WBGENE00016728

Paralogs (5): FMO3 (ENSG00000007933), FMO1 (ENSG00000010932), FMO2 (ENSG00000094963), FOXRED2 (ENSG00000100350), FMO5 (ENSG00000131781)

Protein

Protein identifiers

Dimethylaniline monooxygenase [N-oxide-forming] 4P31512 (reviewed: P31512)

Alternative names: Dimethylaniline oxidase 4, Hepatic flavin-containing monooxygenase 4

All UniProt accessions (1): P31512

UniProt curated annotations — full annotation on UniProt →

Function. This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides.

Subcellular location. Microsome membrane. Endoplasmic reticulum membrane.

Tissue specificity. Liver.

Similarity. Belongs to the FMO family.

RefSeq proteins (1): NP_002013* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000960Flavin_mOaseFamily
IPR002256Flavin_mOase_4Family
IPR020946Flavin_mOase-likeFamily
IPR036188FAD/NAD-bd_sfHomologous_superfamily
IPR050346FMO-likeFamily

Pfam: PF00743

Enzyme classification (BRENDA):

  • EC 1.14.13.8 — flavin-containing monooxygenase (BRENDA: 30 organisms, 458 substrates, 77 inhibitors, 260 Km, 123 kcat entries)

Substrate kinetics (BRENDA)

72 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
METHIMAZOLE0.007–0.575818
TAMOXIFEN0.0013–0.12115
INDOLE0.005–0.913
BENZYDAMINE0.0186–0.065911
ETHIONAMIDE0.104–2.13110
METHYL P-TOLYL SULFIDE0.0048–10.210
FENTHION0.145–0.3519
MERCAPTOIMIDAZOLE0.018–0.05279
NADPH0.0031–0.1329
TRIMETHYLAMINE0.0015–0.589
SULINDAC SULFIDE0.0101–0.01638
CHLORPROMAZINE0.022–0.087
IMIPRAMINE0.0047–0.027
L-METHIONINE2.8–486
10-[(N,N-DIMETHYLAMINOOCTYL)-2-(TRIFLUOROMETHYL)15–385

Catalyzed reactions (Rhea), 1 shown:

  • N,N-dimethylaniline + NADPH + O2 + H(+) = N,N-dimethylaniline N-oxide + NADP(+) + H2O (RHEA:24468)

UniProt features (15 total): sequence variant 8, binding site 5, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P31512-F191.520.81

Functional residue map

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

Ligand- & substrate-binding residues (5): 9–13; 32; 40–41; 60–61; 195–198

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 226 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_LIPID_MODIFICATION, E2F_Q4, MODULE_93, E2F_Q4_01, REACTOME_BIOLOGICAL_OXIDATIONS, E2F4DP1_01, GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOBP_NADPPLUS_METABOLIC_PROCESS, XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN, KYNG_DNA_DAMAGE_DN, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_KETONE_METABOLIC_PROCESS

GO Biological Process (4): xenobiotic metabolic process (GO:0006805), xenobiotic catabolic process (GO:0042178), negative regulation of fatty acid oxidation (GO:0046322), energy homeostasis (GO:0097009)

GO Molecular Function (6): N,N-dimethylaniline monooxygenase activity (GO:0004499), flavin adenine dinucleotide binding (GO:0050660), NADP binding (GO:0050661), monooxygenase activity (GO:0004497), protein binding (GO:0005515), oxidoreductase activity (GO:0016491)

GO Cellular Component (3): endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
metabolic process1
cellular response to xenobiotic stimulus1
xenobiotic metabolic process1
catabolic process1
fatty acid oxidation1
negative regulation of fatty acid metabolic process1
regulation of fatty acid oxidation1
multicellular organismal-level homeostasis1
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen1
nucleotide binding1
anion binding1
adenyl nucleotide binding1
oxidoreductase activity1
binding1
catalytic activity1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
cellular anatomical structure1

Protein interactions and networks

STRING

1682 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FMO4LINC03043A4D0Y5380
FMO4CYP2S1Q96SQ9375
FMO4ADH1BP00325354
FMO4SLC10A1Q14973350
FMO4CYP2F1P24903350
FMO4CCSO14618346
FMO4CYP2C8P10632345
FMO4ABCC2Q92887320
FMO4CYP4B1P13584319
FMO4TMEM212A6NML5306
FMO4SLCO5A1Q9H2Y9303
FMO4SLCO2A1Q92959303
FMO4SLCO3A1Q9UIG8303
FMO4SLCO6A1Q86UG4303
FMO4CTXN2P0C2S0301

IntAct

5 interactions, top by confidence:

ABTypeScore
FMO4RHBDD2psi-mi:“MI:0915”(physical association)0.560
FMO1LDHCpsi-mi:“MI:0914”(association)0.350
FMO4RHBDD2psi-mi:“MI:0915”(physical association)0.000

BioGRID (4): FMO4 (Two-hybrid), FMO4 (Affinity Capture-MS), FMO4 (Affinity Capture-MS), FMO4 (Proximity Label-MS)

ESM2 similar proteins: A4IFM3, O14756, O54753, O54909, O55240, O60774, O75452, O75828, O88451, P16549, P17636, P31512, P32417, P36365, P36367, P49109, P50170, P50285, P55006, P97501, P97872, Q01740, Q0IH28, Q0VFE7, Q27979, Q3T001, Q3T0R4, Q566S6, Q58NB6, Q5R6U1, Q5R7A2, Q6IAN0, Q6IRI9, Q8HYJ9, Q8HYR6, Q8K2I3, Q8K3P0, Q8K4C0, Q8L9C4, Q8N5I4

Diamond homologs: A8MRX0, P31512, P63534, P9WN18, P9WN19, P9WQ14, P9WQ15, Q03460, Q05756, Q0DG35, Q0JKD0, Q28505, Q93Y23, Q94BV5, Q94K43, Q9C8T8, Q9C8U0, Q9FF12, Q9FLK4, Q9FWW3, Q9FWW6, Q9FWW9, Q9HFE4, Q9LV03, Q9RKB5, Q9SH25, Q9SS04, Q9SXD5, Q9SXD9, Q9SXE1, A0A0B5RNJ4, A3SLM3, A3VVZ4, B6BQB2, B8ANW0, B8EIZ7, P38866, Q10RE2, Q1V023, Q5LT63

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance76
Likely benign6
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

1758 predictions. Top by Δscore:

VariantEffectΔscore
1:171319923:G:GTdonor_gain1.0000
1:171319948:G:GTdonor_gain1.0000
1:171332855:G:GTdonor_gain1.0000
1:171341412:GGGGA:Gacceptor_gain1.0000
1:171314410:CAAGG:Cdonor_loss0.9900
1:171314411:AAGG:Adonor_loss0.9900
1:171319929:A:AGdonor_gain0.9900
1:171319958:G:GGdonor_gain0.9900
1:171324136:A:AGacceptor_gain0.9900
1:171324137:G:GGacceptor_gain0.9900
1:171324298:CTGGT:Cdonor_loss0.9900
1:171324299:TGGTG:Tdonor_loss0.9900
1:171324301:G:GAdonor_loss0.9900
1:171324302:TGA:Tdonor_loss0.9900
1:171324303:GAGT:Gdonor_loss0.9900
1:171324304:AGT:Adonor_loss0.9900
1:171332890:GAT:Gdonor_gain0.9900
1:171332892:T:TGdonor_gain0.9900
1:171337350:CCACA:Cacceptor_loss0.9900
1:171337351:CACAG:Cacceptor_loss0.9900
1:171337352:ACAGG:Aacceptor_loss0.9900
1:171337353:CAG:Cacceptor_loss0.9900
1:171337354:AGGAC:Aacceptor_loss0.9900
1:171337355:G:Tacceptor_loss0.9900
1:171337421:AAAAG:Adonor_loss0.9900
1:171337422:AAAG:Adonor_loss0.9900
1:171337423:AAG:Adonor_loss0.9900
1:171337425:GGTAT:Gdonor_loss0.9900
1:171337427:T:Adonor_loss0.9900
1:171341407:TCTCA:Tacceptor_loss0.9900

AlphaMissense

3682 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:171319946:T:AW41R0.993
1:171319946:T:CW41R0.993
1:171324254:C:GC146W0.992
1:171323063:G:CK64N0.991
1:171323063:G:TK64N0.991
1:171324189:T:AW125R0.989
1:171324189:T:CW125R0.989
1:171319948:G:CW41C0.986
1:171319948:G:TW41C0.986
1:171334740:G:CR386P0.986
1:171331672:A:CS173R0.983
1:171331674:T:AS173R0.983
1:171331674:T:GS173R0.983
1:171332718:A:CS213R0.983
1:171332720:T:AS213R0.983
1:171332720:T:GS213R0.983
1:171334742:T:AW387R0.983
1:171334742:T:CW387R0.983
1:171319915:C:GC30W0.982
1:171319862:A:CS13R0.981
1:171319864:T:AS13R0.981
1:171319864:T:GS13R0.981
1:171323079:A:CS70R0.981
1:171323081:T:AS70R0.981
1:171323081:T:GS70R0.981
1:171341577:G:CR472P0.981
1:171323143:T:CL91P0.979
1:171319947:G:CW41S0.978
1:171331651:T:CF166L0.977
1:171331653:T:AF166L0.977

dbSNP variants (sampled 300 via entrez): RS1000319188 (1:171338499 C>T), RS1000427504 (1:171317792 T>A,C), RS1000600894 (1:171327271 A>G), RS1000653502 (1:171326902 A>T), RS1000733598 (1:171329860 C>A,T), RS1000811787 (1:171332447 G>A), RS1000844981 (1:171314842 C>A), RS1000904062 (1:171315442 T>TG), RS1001482246 (1:171317130 C>G), RS1001534684 (1:171317319 A>C), RS1001549024 (1:171326342 A>T), RS1001605807 (1:171320128 A>G), RS1001797717 (1:171323192 G>A,T), RS1001942871 (1:171321527 C>G), RS1002123412 (1:171336039 G>C)

Disease associations

OMIM: gene MIM:136131 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): trimethylaminuria (MONDO:0011182)

Orphanet (1): NON RARE IN EUROPE: Trimethylaminuria (Orphanet:35056)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0003614Trimethylaminuria

GWAS associations

10 associations (top):

StudyTraitp-value
GCST003075_1Cognitive decline rate in late mild cognitive impairment1.000000e-06
GCST003075_100Cognitive decline rate in late mild cognitive impairment9.000000e-07
GCST003075_101Cognitive decline rate in late mild cognitive impairment2.000000e-10
GCST003075_9Cognitive decline rate in late mild cognitive impairment2.000000e-10
GCST004125_11Type 2 diabetes (age of onset)4.000000e-06
GCST006586_46Urinary albumin excretion1.000000e-08
GCST007354_22Intracranial aneurysm2.000000e-10
GCST009733_124Urinary metabolite levels in chronic kidney disease2.000000e-15
GCST009733_176Urinary metabolite levels in chronic kidney disease2.000000e-16
GCST009733_209Urinary metabolite levels in chronic kidney disease1.000000e-17

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0007710cognitive decline measurement
EFO:0004285albuminuria
EFO:0005116urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3542432 (PROTEIN FAMILY)

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

PharmGKB variants

4 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2020870FMO20.000
rs2076322FMO40.000
rs7512785FMO20.000
rs7515157FMO20.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects methylation, increases expression2
Acetaminophendecreases expression2
Benzo(a)pyreneaffects methylation, decreases expression2
Nickeldecreases expression2
Cyclosporinedecreases expression2
Aflatoxin B1decreases expression2
GSK-J4decreases expression1
lasiocarpinedecreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
bisphenol Aincreases expression, affects cotreatment1
chlortolurondecreases expression1
senecioninedecreases expression1
senkirkinedecreases expression1
heliotrinedecreases expression1
ethyl-p-hydroxybenzoateincreases expression1
perfluoro-n-nonanoic aciddecreases expression1
entinostatincreases expression1
NCX 4040increases expression1
bisphenol Saffects cotreatment, increases expression1
incobotulinumtoxinAincreases expression1
Sunitinibdecreases expression1
Air Pollutantsaffects expression, increases abundance1
Calcitriolincreases expression, affects cotreatment1
Cisplatindecreases expression1
Cytarabinedecreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Doxorubicindecreases expression1
Indomethacinaffects cotreatment, increases expression1
Ozoneaffects expression, increases abundance1

ChEMBL screening assays

1 unique, capped per target: 1 admet

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4153816ADMETDrug metabolism in human hepatocytes assessed as formation of FMO-mediated N,N-Dimethyl-3-[[5-(3-methyl-2-oxo-1-tetrahydropyran-4-yl-imidazo[4,5c]quinolin-8-yl)-2-pyridyl]oxy]propan-1-amine oxideThe Identification of Potent, Selective, and Orally Available Inhibitors of Ataxia Telangiectasia Mutated (ATM) Kinase: The Discovery of AZD0156 (8-{6-[3-(Dimethylamino)propoxy]pyridin-3-yl}-3-methyl-1-(tetrahydro-2 H-pyran-4-yl)-1,3-dihydro-2 H-imidazo[4,5- c]quinolin-2-one). — J Med Chem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): brain aneurysm, trimethylaminuria