FMO2

gene
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Summary

FMO2 (flavin containing dimethylaniline monoxygenase 2, HGNC:3770) is a protein-coding gene on chromosome 1q24.3, encoding Flavin-containing monooxygenase 2 (Q99518). Catalyzes the oxidative metabolism of numerous xenobiotics, including mainly therapeutic drugs and insecticides that contain a soft nucleophile, most commonly nitrogen and sulfur and participates to their bioactivation.

This gene encodes a flavin-containing monooxygenase family member. It is an NADPH-dependent enzyme that catalyzes the N-oxidation of some primary alkylamines through an N-hydroxylamine intermediate. However, some human populations contain an allele (FMO2*2A) with a premature stop codon, resulting in a protein that is C-terminally-truncated, has no catalytic activity, and is likely degraded rapidly. This gene is found in a cluster with other related family members on chromosome 1. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 2327 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 4 total
  • Druggable target: yes
  • MANE Select transcript: NM_001460

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:3770
Approved symbolFMO2
Nameflavin containing dimethylaniline monoxygenase 2
Location1q24.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000094963
Ensembl biotypeprotein_coding
OMIM603955
Entrez2327

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000209929, ENST00000462643, ENST00000483192, ENST00000488431, ENST00000489354, ENST00000493513, ENST00000529935, ENST00000895513, ENST00000895514, ENST00000945245

RefSeq mRNA: 3 — MANE Select: NM_001460 NM_001301347, NM_001365900, NM_001460

CCDS: CCDS1293

Canonical transcript exons

ENST00000209929 — 9 exons

ExonStartEnd
ENSE00001321274171208794171212686
ENSE00001823058171185300171185359
ENSE00003536750171207718171207790
ENSE00003541886171193335171193523
ENSE00003549156171199346171199488
ENSE00003580370171196649171196811
ENSE00003604976171205279171205634
ENSE00003610243171185708171185845
ENSE00003642194171203865171204064

Expression profiles

Bgee: expression breadth ubiquitous, 244 present calls, max score 99.08.

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

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
65961.4208177

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
pericardiumUBERON:000240799.08gold quality
right lungUBERON:000216798.93gold quality
lower lobe of lungUBERON:000894998.69gold quality
descending thoracic aortaUBERON:000234597.95gold quality
mammary ductUBERON:000176597.82gold quality
thoracic aortaUBERON:000151597.66gold quality
ascending aortaUBERON:000149697.58gold quality
epithelium of mammary glandUBERON:000324496.50gold quality
vena cavaUBERON:000408796.48gold quality
esophagus squamous epitheliumUBERON:000692096.41gold quality
epithelium of esophagusUBERON:000197696.19gold quality
upper lobe of lungUBERON:000894895.70gold quality
upper lobe of left lungUBERON:000895295.59gold quality
lungUBERON:000204895.40gold quality
mammary glandUBERON:000191195.29gold quality
thoracic mammary glandUBERON:000520095.28gold quality
adipose tissue of abdominal regionUBERON:000780894.66gold quality
omental fat padUBERON:001041494.59gold quality
peritoneumUBERON:000235894.58gold quality
cardiac muscle of right atriumUBERON:000337994.43gold quality
adipose tissueUBERON:000101394.26gold quality
esophagus mucosaUBERON:000246994.18gold quality
coronary arteryUBERON:000162194.03gold quality
left coronary arteryUBERON:000162694.03gold quality
cardiac atriumUBERON:000208194.00gold quality
right atrium auricular regionUBERON:000663193.82gold quality
myocardiumUBERON:000234993.67gold quality
aortaUBERON:000094793.65gold quality
superficial temporal arteryUBERON:000161493.43gold quality
tongueUBERON:000172393.43gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-CURD-126yes1881.07
E-GEOD-130148yes794.02
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

144 targeting FMO2, 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-3646100.0073.565283
HSA-MIR-5692A100.0074.406850
HSA-MIR-4510100.0066.602050
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-126-5P100.0072.713180
HSA-MIR-574-5P100.0066.01989
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-3163100.0077.238605
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-186-5P99.9970.833707
HSA-MIR-428299.9975.366408
HSA-MIR-150-5P99.9966.691976
HSA-MIR-548N99.9871.944170
HSA-MIR-477599.9875.006394
HSA-MIR-60799.9773.625593
HSA-MIR-548AN99.9770.912817
HSA-MIR-590-3P99.9674.346478

Literature-anchored findings (GeneRIF, showing 8)

  • analysis of flavin-containing monooxygenase isoform 2 (FMO2) polymorphisms in Hispanics (PMID:15864117)
  • analysis of how the functional variant flavin-containing monooxygenase 2*1 is at high frequency throughout sub-Saharan Africa (PMID:18794725)
  • Characterization of sulfoxygenation and structural implications of human flavin-containing monooxygenase isoform 2 (FMO2.1) variants S195L and N413K. (PMID:19420133)
  • study provides an evidence for the existence of an evolutionary adaptation to an ancient disease based on an ancestral genetic variant acting in a FMO2 haplotypic framework in Ethiopian populations (PMID:28981537)
  • The functional FMO2(427Q) isoform was active against nicotine; the truncated FMO2(Q472stop) isoform exhibited no enzyme activity. (PMID:30381441)
  • Cancer-associated fibroblasts-derived FMO2 as a biomarker of macrophage infiltration and prognosis in epithelial ovarian cancer. (PMID:36114029)
  • Flavin containing monooxygenase 2 regulates renal tubular cell fibrosis and paracrine secretion via SMURF2 in AKI-CKD transformation. (PMID:37800598)
  • Discovery and identification of the prognostic significance and potential mechanism of FMO2 in breast cancer. (PMID:37963835)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
mus_musculusFmo2ENSMUSG00000040170
rattus_norvegicusFmo2ENSRNOG00000003510
caenorhabditis_elegansWBGENE00001476
caenorhabditis_elegansWBGENE00001478
caenorhabditis_elegansWBGENE00001480
caenorhabditis_elegansC01H6.4WBGENE00007254
caenorhabditis_elegansC46H11.2WBGENE00016728

Paralogs (5): FMO3 (ENSG00000007933), FMO1 (ENSG00000010932), FMO4 (ENSG00000076258), FOXRED2 (ENSG00000100350), FMO5 (ENSG00000131781)

Protein

Protein identifiers

Flavin-containing monooxygenase 2Q99518 (reviewed: Q99518)

Alternative names: Dimethylaniline oxidase 2, FMO 1B1, Pulmonary flavin-containing monooxygenase 2

All UniProt accessions (3): Q99518, A0A0D9SFZ0, A0A0D9SG76

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the oxidative metabolism of numerous xenobiotics, including mainly therapeutic drugs and insecticides that contain a soft nucleophile, most commonly nitrogen and sulfur and participates to their bioactivation. Specifically catalyzes S-oxygenation of sulfur derived compounds such as thioureas-derived compounds, thioetherorganophosphates to their sulfenic acid. In vitro, catalyzes S-oxygenation of the second-line antitubercular drugs thiacetazone (TAZ) and ethionamide (ETA), forming a sulfinic acid and a carbodiimide via a postulated sulfenic acid intermediate. Also catalyzes S-oxygenation of the thioether-containing organophosphate insecticides, phorate and disulfoton.

Subcellular location. Microsome membrane. Endoplasmic reticulum membrane.

Tissue specificity. Expressed in lung (at protein level). Expressed predominantly in lung, and at a much lesser extent in kidney. Also expressed in fetal lung, but not in liver, kidney and brain.

Polymorphism. The sequence shown is that of the allele FMO21. FMO22A is the major allele in the human population, however it encodes a truncated and catalytically inactive protein. FMO22A occurs in essentially 100% of Caucasians and Asians. FMO21 is present at a frequency of approximately 4% to 13% in the sample of population of African descent.

Similarity. Belongs to the FMO family.

RefSeq proteins (3): NP_001288276, NP_001352829, NP_001451* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000960Flavin_mOaseFamily
IPR002254Flavin_mOase_2Family
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

UniProt features (23 total): sequence variant 11, binding site 6, initiator methionine 1, chain 1, cross-link 1, transmembrane region 1, sequence conflict 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99518-F195.260.89

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 (6): 9–13; 32; 40–41; 60–61; 61–62; 195–198

Post-translational modifications (2): 492, 2

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-217271FMO oxidises nucleophiles

MSigDB gene sets: 146 (showing top): GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_DN, GOBP_LIPID_MODIFICATION, REACTOME_BIOLOGICAL_OXIDATIONS, 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, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_KETONE_METABOLIC_PROCESS, GOBP_REGULATION_OF_FATTY_ACID_METABOLIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_REGULATION_OF_LIPID_METABOLIC_PROCESS, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_REGULATION_OF_KETONE_METABOLIC_PROCESS, GOBP_TOXIN_METABOLIC_PROCESS

GO Biological Process (7): obsolete organic acid metabolic process (GO:0006082), NADP+ metabolic process (GO:0006739), xenobiotic metabolic process (GO:0006805), toxin metabolic process (GO:0009404), negative regulation of fatty acid oxidation (GO:0046322), oxygen metabolic process (GO:0072592), energy homeostasis (GO:0097009)

GO Molecular Function (5): N,N-dimethylaniline monooxygenase activity (GO:0004499), flavin adenine dinucleotide binding (GO:0050660), NADP binding (GO:0050661), monooxygenase activity (GO:0004497), oxidoreductase activity (GO:0016491)

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

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Phase I - Functionalization of compounds1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
metabolic process2
purine nucleotide metabolic process1
nicotinamide nucleotide metabolic process1
cellular response to xenobiotic stimulus1
secondary metabolic 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
catalytic activity1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1894 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FMO2ZNF888P0CJ79398
FMO2ABCC2Q92887392
FMO2LINC03043A4D0Y5380
FMO2CYP2F1P24903350
FMO2CCSO14618346
FMO2ADH1BP00325335
FMO2RHBDL2Q9NX52324
FMO2SNTNA6NMZ2320
FMO2CYP2S1Q96SQ9320
FMO2TMEM212A6NML5318
FMO2CYGBQ8WWM9314
FMO2NAT2P11245307
FMO2SVEP1Q4LDE5304
FMO2FAM216BQ8N7L0304
FMO2TSPAN19P0C672303

IntAct

6 interactions, top by confidence:

ABTypeScore
FMO2GNB2psi-mi:“MI:0915”(physical association)0.400
FMO2STK38Lpsi-mi:“MI:0915”(physical association)0.400
FMO2bipApsi-mi:“MI:0915”(physical association)0.370
ilvC2FMO2psi-mi:“MI:0915”(physical association)0.000
FMO2psi-mi:“MI:0915”(physical association)0.000

BioGRID (4): GNB2 (Affinity Capture-MS), STK38L (Affinity Capture-MS), FMO2 (Two-hybrid), FMO2 (Affinity Capture-MS)

ESM2 similar proteins: A4IFM3, F4JJJ3, M1BYJ7, O14756, O49312, O54753, O60774, O64489, O88451, P16549, P17635, P17636, P31512, P31513, P32417, P36365, P36366, P36367, P49109, P49326, P49328, P50170, P50285, P97501, P97872, Q01740, Q04799, Q28505, Q3T001, Q5REK0, Q6IRI9, Q7YS44, Q8HYJ9, Q8HZ69, Q8HZ70, Q8K2I3, Q8K4B7, Q8K4C0, Q8SPQ7, Q8VHG0

Diamond homologs: A0A0B5RNJ4, A3SLM3, A3VVZ4, B6BQB2, B8EIZ7, O23024, O60774, P16549, P17635, P31512, P36365, P36366, P36367, P49326, P50285, P97872, Q01740, Q1V023, Q28505, Q5LT63, Q5REK0, Q6IRI9, Q8HZ69, Q8HZ70, Q8K2I3, Q8K4C0, Q8MP06, Q93Y23, Q99518, Q9C8U0, Q9FWW6, Q9SH25, Q9SS04, Q9SXD5, B8NM63, B8NM73, P32417, Q7YS44, Q8HYJ9, Q8SPQ7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance3
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1160 predictions. Top by Δscore:

VariantEffectΔscore
1:171185356:AAAGG:Adonor_loss1.0000
1:171185357:AAGG:Adonor_loss1.0000
1:171185358:AGGT:Adonor_loss1.0000
1:171185359:GGTAA:Gdonor_loss1.0000
1:171185360:G:Cdonor_loss1.0000
1:171185361:T:Gdonor_loss1.0000
1:171185840:TTCA:Tdonor_gain1.0000
1:171185844:AAG:Adonor_loss1.0000
1:171185845:AG:Adonor_loss1.0000
1:171185846:G:GGdonor_gain1.0000
1:171185846:G:Tdonor_loss1.0000
1:171188966:G:GTdonor_gain1.0000
1:171188969:G:GGdonor_gain1.0000
1:171193329:CTTCA:Cacceptor_loss1.0000
1:171193330:TTCAG:Tacceptor_loss1.0000
1:171193331:TCA:Tacceptor_loss1.0000
1:171193332:CAGGA:Cacceptor_loss1.0000
1:171193333:A:AGacceptor_gain1.0000
1:171193333:A:Tacceptor_loss1.0000
1:171193334:G:GGacceptor_gain1.0000
1:171193334:GGA:Gacceptor_gain1.0000
1:171193334:GGAGA:Gacceptor_gain1.0000
1:171199467:GCTGA:Gdonor_gain1.0000
1:171199468:C:Gdonor_gain1.0000
1:171204046:GCCT:Gdonor_gain1.0000
1:171204065:G:GGdonor_gain1.0000
1:171207786:GACCT:Gdonor_gain1.0000
1:171207791:G:GGdonor_gain1.0000
1:171185360:G:GGdonor_gain0.9900
1:171185844:AA:Adonor_gain0.9900

AlphaMissense

3547 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:171196765:C:GC146W0.990
1:171185834:T:AW41R0.989
1:171185834:T:CW41R0.989
1:171193394:A:CK64N0.985
1:171193394:A:TK64N0.985
1:171193389:A:CS63R0.983
1:171193391:C:AS63R0.983
1:171193391:C:GS63R0.983
1:171196700:T:AW125R0.979
1:171196700:T:CW125R0.979
1:171199378:A:CS173R0.979
1:171199380:C:AS173R0.979
1:171199380:C:GS173R0.979
1:171193410:A:CS70R0.977
1:171193412:T:AS70R0.977
1:171193412:T:GS70R0.977
1:171185836:G:CW41C0.975
1:171185836:G:TW41C0.975
1:171196755:T:AV143D0.975
1:171196763:T:CC146R0.974
1:171193393:A:TK64I0.972
1:171185803:C:GC30W0.971
1:171193443:T:CF81L0.971
1:171193445:C:AF81L0.971
1:171193445:C:GF81L0.971
1:171196764:G:AC146Y0.970
1:171203874:A:CS213R0.970
1:171203876:C:AS213R0.970
1:171203876:C:GS213R0.970
1:171185730:C:AA6D0.969

dbSNP variants (sampled 300 via entrez): RS1000197051 (1:171201443 CCTT>C), RS1000255077 (1:171211147 A>C), RS1000297217 (1:171201778 A>C), RS1000497999 (1:171192532 C>A,T), RS1000614168 (1:171192747 C>T), RS1000669906 (1:171205942 G>T), RS1000680585 (1:171210286 G>A), RS1000860168 (1:171213174 A>G), RS1000865408 (1:171187122 A>C,G), RS1000942844 (1:171205345 G>C), RS1001214700 (1:171209363 T>C), RS1001268975 (1:171210363 T>G), RS1001294108 (1:171184582 C>A,T), RS1001500898 (1:171212803 A>G), RS1001582474 (1:171209025 G>A)

Disease associations

OMIM: gene MIM:603955 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3542432 (PROTEIN FAMILY)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases expression3
Resveratrolaffects cotreatment, decreases expression2
Air Pollutantsdecreases expression, increases abundance2
Nickeldecreases expression2
Tobacco Smoke Pollutionaffects expression, decreases expression2
fluxapyroxaddecreases expression1
2-phenylphenoldecreases expression1
testosterone enanthateaffects expression1
lasiocarpinedecreases expression1
chlortolurondecreases expression1
sodium arsenatedecreases expression, increases abundance1
benzydamine N-oxideincreases chemical synthesis, increases oxidation1
azoxystrobindecreases expression1
CGP 52608affects binding, increases reaction1
cyproconazoledecreases expression1
Docetaxelaffects response to substance1
Arsenicincreases abundance, decreases expression1
Benzo(a)pyreneincreases methylation1
Benzydamineincreases oxidation, increases chemical synthesis1
Calcitrioldecreases expression1
Copperaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Ethionamideincreases oxidation1
Ethylenethioureaincreases oxidation, decreases oxidation1
Methimazoledecreases oxidation, increases oxidation1
Plant Extractsaffects cotreatment, decreases expression1
Propranololincreases oxidation1
Silicon Dioxidedecreases expression1
Smokeincreases abundance, decreases expression1
Tetrachlorodibenzodioxindecreases expression1

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)

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

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