FMO1

flavin containing dimethylaniline monoxygenase 1, the group of Flavin containing monooxygenases

Basic information

Region (hg38): 1:171248470-171285978

Links

ENSG00000010932 ∙ NCBI:2326 ∙ OMIM:136130 ∙ HGNC:3769 ∙ Uniprot:Q01740 ∙ 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 FMO1 gene.

• Inborn genetic diseases (23 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FMO1 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				1		1
missense			23	2	2	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	23	3	3

Variants in FMO1

This is a list of pathogenic ClinVar variants found in the FMO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-171258092-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-171258098-G-A		not specified	Uncertain significance (Apr 25, 2023)
1-171258106-A-G		not specified	Uncertain significance (Jun 22, 2023)
1-171258154-G-A		not specified	Uncertain significance (May 23, 2023)
1-171258209-G-C		not specified	Uncertain significance (Mar 24, 2023)
1-171267550-T-C		not specified	Uncertain significance (May 31, 2023)
1-171267555-G-A		not specified	Uncertain significance (Mar 16, 2022)
1-171267570-C-A		not specified	Uncertain significance (Apr 07, 2022)
1-171267618-T-C		not specified	Uncertain significance (Jun 22, 2023)
1-171275402-G-T		not specified	Uncertain significance (Jul 09, 2021)
1-171275479-A-G		not specified	Uncertain significance (Dec 02, 2022)
1-171278719-T-C			Benign (Jun 29, 2018)
1-171278738-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-171278760-T-A		not specified	Uncertain significance (Dec 28, 2022)
1-171278764-C-T		not specified	Uncertain significance (Feb 13, 2024)
1-171278765-G-A		not specified	Uncertain significance (Feb 09, 2022)
1-171280818-G-A			Likely benign (Aug 01, 2022)
1-171280832-T-C		not specified	Uncertain significance (Jun 26, 2023)
1-171280846-C-A		not specified	Uncertain significance (Dec 16, 2023)
1-171280910-T-C			Likely benign (Apr 24, 2018)
1-171280937-T-C		not specified	Uncertain significance (Jan 10, 2023)
1-171282129-T-C			Benign (Jun 29, 2018)
1-171282208-A-G		not specified	Uncertain significance (Jan 03, 2022)
1-171282228-C-T			Likely benign (May 24, 2018)
1-171282268-A-G			Benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FMO1	protein_coding	protein_coding	ENST00000354841	8	37480

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.12e-11	0.474	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	235	285	0.825	0.0000139	3500
Missense in Polyphen		78	104.59	0.74575		1271
Synonymous	-0.748	113	103	1.09	0.00000515	1025
Loss of Function	1.20	19	25.5	0.745	0.00000158	276

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000314	0.000314
Ashkenazi Jewish	0.00	0.00
East Asian	0.000825	0.000816
Finnish	0.00	0.00
European (Non-Finnish)	0.000274	0.000273
Middle Eastern	0.000825	0.000816
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This protein is involved in the oxidative metabolism of a variety of xenobiotics such as drugs and pesticides. Form I catalyzes the N-oxygenation of secondary and tertiary amines.
• Pathway: Drug metabolism - cytochrome P450 - Homo sapiens (human);Busulfan Pathway, Pharmacodynamics;Tamoxifen Pathway, Pharmacokinetics;Tamoxifen Action Pathway;Tamoxifen Metabolism Pathway;Catalytic cycle of mammalian Flavin-containing MonoOxygenases (FMOs);Tamoxifen metabolism;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;FMO oxidises nucleophiles;Biological oxidations;Metabolism;Selenoamino acid metabolism;nicotine degradation IV (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.688
• rvis_EVS: 1.09
• rvis_percentile_EVS: 91.85

Haploinsufficiency Scores

• pHI: 0.501
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Fmo1

Gene ontology

• Biological process: organic acid metabolic process;xenobiotic metabolic process;response to osmotic stress;toxin metabolic process;drug metabolic process;response to lipopolysaccharide;NADPH oxidation
• Cellular component: endoplasmic reticulum lumen;endoplasmic reticulum membrane;integral component of membrane;organelle membrane
• Molecular function: monooxygenase activity;N,N-dimethylaniline monooxygenase activity;protein binding;flavin adenine dinucleotide binding;NADP binding