FMO2

flavin containing dimethylaniline monoxygenase 2, the group of Flavin containing monooxygenases

Basic information

Region (hg38): 1:171185248-171212686

Links

ENSG00000094963 ∙ NCBI:2327 ∙ OMIM:603955 ∙ HGNC:3770 ∙ Uniprot:Q99518 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FMO2 gene.

• Inborn genetic diseases (15 variants)
• not provided (8 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMO2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			15	3		18
nonsense					1	1
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	15	5	3

Variants in FMO2

This is a list of pathogenic ClinVar variants found in the FMO2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-171185770-G-T		not specified	Uncertain significance (Jan 08, 2024)
1-171193337-G-A			Likely benign (Aug 01, 2022)
1-171193344-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-171196663-TG-T		not specified	Benign (Mar 28, 2016)
1-171196723-C-T			Likely benign (Jan 26, 2018)
1-171196724-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-171196728-A-T		not specified	Uncertain significance (Dec 02, 2021)
1-171199358-T-C			Likely benign (Apr 06, 2018)
1-171199382-G-A			Likely benign (Jan 24, 2018)
1-171199432-G-A		not specified	Uncertain significance (Oct 27, 2022)
1-171203866-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-171203956-G-A		not specified	Uncertain significance (May 17, 2023)
1-171203961-A-G		not specified	Uncertain significance (May 05, 2023)
1-171203974-T-C		not specified	Uncertain significance (Dec 20, 2023)
1-171205299-T-A		not specified	Uncertain significance (Nov 18, 2022)
1-171205323-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-171205361-A-G		not specified	Uncertain significance (Jan 24, 2024)
1-171205418-G-A		not specified	Uncertain significance (Nov 06, 2023)
1-171205432-T-G		not specified	Uncertain significance (Feb 27, 2024)
1-171205463-C-T		not specified	Uncertain significance (Jan 23, 2023)
1-171205496-A-G		not specified	Uncertain significance (Dec 17, 2023)
1-171205550-G-A		not specified	Uncertain significance (Oct 03, 2022)
1-171205551-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-171205578-G-A		not specified	Uncertain significance (Jan 18, 2022)
1-171205599-A-G		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FMO2	protein_coding	protein_coding	ENST00000441535	8	27476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.14e-7	0.783	111898	842	13007	125747	0.0567

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0993	256	261	0.983	0.0000136	3111
Missense in Polyphen		86	98.658	0.8717		1233
Synonymous	0.567	85	91.9	0.925	0.00000486	876
Loss of Function	1.36	13	19.5	0.667	9.05e-7	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.323	0.324
Ashkenazi Jewish	0.0896	0.0901
East Asian	0.000872	0.000870
Finnish	0.0240	0.0237
European (Non-Finnish)	0.0481	0.0478
Middle Eastern	0.000872	0.000870
South Asian	0.0533	0.0528
Other	0.0530	0.0525

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the N-oxidation of certain primary alkylamines to their oximes via an N-hydroxylamine intermediate. Inactive toward certain tertiary amines, such as imipramine or chloropromazine. Can catalyze the S-oxidation of methimazole. The truncated form is catalytically inactive. {ECO:0000269|PubMed:9804831}.
• Pathway: Drug metabolism - cytochrome P450 - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;Catalytic cycle of mammalian Flavin-containing MonoOxygenases (FMOs);Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;FMO oxidises nucleophiles;Biological oxidations;Metabolism;Selenoamino acid metabolism;nicotine degradation IV (Consensus)

Intolerance Scores

• loftool: 0.941
• rvis_EVS: 2.47
• rvis_percentile_EVS: 98.61

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.285
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.229

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Fmo2

Gene ontology

• Biological process: organic acid metabolic process;NADP metabolic process;xenobiotic metabolic process;toxin metabolic process;drug metabolic process;NADPH oxidation;oxygen metabolic process
• Cellular component: endoplasmic reticulum membrane;membrane;organelle membrane
• Molecular function: monooxygenase activity;N,N-dimethylaniline monooxygenase activity;flavin adenine dinucleotide binding;NADP binding