ClinVar Genomic variation as it relates to human health
NM_001002294.3(FMO3):c.458C>T (p.Pro153Leu)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Pathogenic(5); Uncertain significance(1)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001002294.3(FMO3):c.458C>T (p.Pro153Leu)
Variation ID: 16308 Accession: VCV000016308.14
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 1q24.3 1: 171107811 (GRCh38) [ NCBI UCSC ] 1: 171076952 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Oct 8, 2024 Dec 8, 2023 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_001002294.3:c.458C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001002294.1:p.Pro153Leu missense NM_001319173.2:c.398C>T NP_001306102.1:p.Pro133Leu missense NM_001319174.2:c.269C>T NP_001306103.1:p.Pro90Leu missense NM_006894.6:c.458C>T NP_008825.4:p.Pro153Leu missense NC_000001.11:g.171107811C>T NC_000001.10:g.171076952C>T NG_012690.1:g.21935C>T P31513:p.Pro153Leu - Protein change
- P153L, P90L, P133L
- Other names
- -
- Canonical SPDI
- NC_000001.11:171107810:C:T
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
Exome Aggregation Consortium (ExAC) 0.00099
The Genome Aggregation Database (gnomAD), exomes 0.00102
The Genome Aggregation Database (gnomAD) 0.00149
Trans-Omics for Precision Medicine (TOPMed) 0.00168
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
FMO3 | - | - |
GRCh38 GRCh37 |
178 | 265 | |
LOC126805916 | - | - | - | GRCh38 | - | 70 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
|
Dec 8, 2023 | RCV000017701.40 | |
Conflicting interpretations of pathogenicity (3) |
criteria provided, conflicting classifications
|
Jan 20, 2023 | RCV002223760.5 | |
FMO3-related disorder
|
Pathogenic (1) |
no assertion criteria provided
|
Jul 12, 2024 | RCV004755741.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Uncertain significance
(Jun 08, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV003251245.1
First in ClinVar: Feb 07, 2023 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 153 of the FMO3 protein (p.Pro153Leu). … (more)
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 153 of the FMO3 protein (p.Pro153Leu). This variant is present in population databases (rs72549326, gnomAD 0.2%). This missense change has been observed in individual(s) with trimethylaminuria (PMID: 8401051, 9398858, 11191884, 12893987, 16601883, 17224546, 21422137, 31240165). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 16308). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Experimental studies have shown that this missense change affects FMO3 function (PMID: 9282831, 9398858, 9536088, 17531949). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
|
|
Pathogenic
(Sep 06, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Trimethylaminuria
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV000351243.3
First in ClinVar: Dec 06, 2016 Last updated: May 24, 2019 |
Comment:
The FMO3 c.458C>T (p.Pro153Leu) missense variant is reported widely reported in the literature and is noted to be one of the most common variants in … (more)
The FMO3 c.458C>T (p.Pro153Leu) missense variant is reported widely reported in the literature and is noted to be one of the most common variants in the FMO3 gene associated with disease (Philips et al. 2015). Across a selection of the available literature, the p.Pro153Leu variant was identified in a total of 14 individuals with trimethylaminuria, including eight homozygotes and six compound heterozygotes. Four unaffected family members were identified as heterozygotes for the p.Pro153Leu variant (Dolphin et al. 1997; Treacy et al. 1998; Dolphin et al. 2000; Chalmers et al. 2006). The variant was found in one of 108 control chromosomes, and is reported at a frequency of 0.00337 in the European American population of the Exome Sequencing Project. Functional analysis by several groups demonstrated that the p.Pro153Leu variant abolishes the catalytic activity of FMO3 (Dolphin et al. 1997; Cashman et al. 1997; Treacy et al. 1998). Based on the collective evidence, the p.Pro153Leu variant is classified as pathogenic for trimethylaminuria. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. (less)
|
|
Pathogenic
(Mar 17, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Not provided
Affected status: yes
Allele origin:
germline
|
AiLife Diagnostics, AiLife Diagnostics
Accession: SCV002502436.1
First in ClinVar: Apr 23, 2022 Last updated: Apr 23, 2022 |
Number of individuals with the variant: 1
Secondary finding: no
|
|
Pathogenic
(Feb 02, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Trimethylaminuria
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV000893233.2
First in ClinVar: Mar 31, 2019 Last updated: Dec 31, 2022 |
|
|
Pathogenic
(Jan 20, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Not provided
Affected status: unknown
Allele origin:
germline
|
Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV004226538.1
First in ClinVar: Jan 06, 2024 Last updated: Jan 06, 2024 |
Comment:
PP3, PP4, PM3, PS3, PS4_moderate
Number of individuals with the variant: 1
|
|
Pathogenic
(Dec 08, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Trimethylaminuria
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004242010.1
First in ClinVar: Feb 04, 2024 Last updated: Feb 04, 2024 |
Comment:
Variant summary: FMO3 c.458C>T (p.Pro153Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging … (more)
Variant summary: FMO3 c.458C>T (p.Pro153Leu) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.001 in 251080 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in FMO3 causing Trimethylaminuria (0.001 vs 0.0056), allowing no conclusion about variant significance. c.458C>T has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Trimethylaminuria (e.g., Dolphin_1997, Treacy_1998), and the variant has been shown to segregate with disease in related individuals (e.g., Dolphin_1997). These data indicate that the variant is very likely to be associated with disease. Several publications report experimental evidence evaluating an impact on protein function, finding that the variant results in undetectable or severely reduced (<10%) enzymatic activity relative to the wild type (e.g., Dolphin_1997, Treacy_1998, Yeung_2007). The following publications have been ascertained in the context of this evaluation (PMID: 9398858, 9536088, 17531949). Four submitters have reported clinical-significance assessments for this variant to ClinVar after 2014 with conflicting interpretations (pathogenic, n = 3; VUS, n = 1). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
|
|
Pathogenic
(Dec 01, 1997)
|
no assertion criteria provided
Method: literature only
|
TRIMETHYLAMINURIA
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000037978.3
First in ClinVar: Apr 04, 2013 Last updated: Apr 21, 2017 |
Comment on evidence:
In a brother and sister with trimethylaminuria (TMAU; 602079), Dolphin et al. (1997) identified a homozygous 551C-T transition in the FMO3 gene, changing a CCC … (more)
In a brother and sister with trimethylaminuria (TMAU; 602079), Dolphin et al. (1997) identified a homozygous 551C-T transition in the FMO3 gene, changing a CCC proline triplet at codon 153 to a CTC leucine triplet (P153L). Their unaffected parents and a third sib were heterozygous for the mutation. The authors found the same mutation in 2 other trimethylaminuria kindreds, in which it also cosegregated with the disorder. In the first kindred studied, the leu153 allele was found to carry a polymorphism at codon 158, namely glu158. Among 30 unrelated, non-trimethylaminuric individuals, pro153 was found in all, whereas glu158 and lys158 occurred in frequencies of approximately 50% each. (less)
|
|
Pathogenic
(Jul 12, 2024)
|
no assertion criteria provided
Method: clinical testing
|
FMO3-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV005366501.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The FMO3 c.458C>T variant is predicted to result in the amino acid substitution p.Pro153Leu. This variant is recognized as one of the most common pathogenic … (more)
The FMO3 c.458C>T variant is predicted to result in the amino acid substitution p.Pro153Leu. This variant is recognized as one of the most common pathogenic variants associated with trimethylaminuria (Dolphin et al. 1997. PubMed ID: 9398858; Chalmers et al. 2006. PubMed ID: 16601883; Doyle. 2019. PubMed ID: 31240165). We interpret this variant as pathogenic. (less)
|
|
not provided
(-)
|
no classification provided
Method: literature only
|
Trimethylaminuria
Affected status: not provided
Allele origin:
unknown
|
GeneReviews
Accession: SCV000041186.2
First in ClinVar: Apr 04, 2013 Last updated: Oct 01, 2022 |
|
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
Impact of trimethylaminuria on daily psychosocial functioning. | Roddy D | JIMD reports | 2020 | PMID: 33473342 |
Precision medicine integrating whole-genome sequencing, comprehensive metabolomics, and advanced imaging. | Hou YC | Proceedings of the National Academy of Sciences of the United States of America | 2020 | PMID: 31980526 |
Primary Trimethylaminuria. | Adam MP | - | 2020 | PMID: 20301282 |
Optimizing clinical exome design and parallel gene-testing for recessive genetic conditions in preconception carrier screening: Translational research genomic data from 14,125 exomes. | Capalbo A | PLoS genetics | 2019 | PMID: 31589614 |
The genetic and biochemical basis of trimethylaminuria in an Irish cohort. | Doyle S | JIMD reports | 2019 | PMID: 31240165 |
Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults. | Perkins BA | Proceedings of the National Academy of Sciences of the United States of America | 2018 | PMID: 29555771 |
Fish Malodour syndrome in a child. | Oliveira A | BMJ case reports | 2015 | PMID: 25870212 |
Fish odour syndrome. | Li M | CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne | 2011 | PMID: 21422137 |
Functional characterization of genetic variants of human FMO3 associated with trimethylaminuria. | Yeung CK | Archives of biochemistry and biophysics | 2007 | PMID: 17531949 |
Trimethylaminuria (fish-odor syndrome): a case report. | Arseculeratne G | Archives of dermatology | 2007 | PMID: 17224546 |
Diagnosis and management of trimethylaminuria (FMO3 deficiency) in children. | Chalmers RA | Journal of inherited metabolic disease | 2006 | PMID: 16601883 |
Deleterious mutations in the flavin-containing monooxygenase 3 (FMO3) gene causing trimethylaminuria. | Zhang J | Pharmacogenetics | 2003 | PMID: 12893987 |
Compound heterozygosity for missense mutations in the flavin-containing monooxygenase 3 (FM03) gene in patients with fish-odour syndrome. | Dolphin CT | Pharmacogenetics | 2000 | PMID: 11191884 |
Mutations of the flavin-containing monooxygenase gene (FMO3) cause trimethylaminuria, a defect in detoxication. | Treacy EP | Human molecular genetics | 1998 | PMID: 9536088 |
Missense mutation in flavin-containing mono-oxygenase 3 gene, FMO3, underlies fish-odour syndrome. | Dolphin CT | Nature genetics | 1997 | PMID: 9398858 |
Human flavin-containing monooxygenase form 3: cDNA expression of the enzymes containing amino acid substitutions observed in individuals with trimethylaminuria. | Cashman JR | Chemical research in toxicology | 1997 | PMID: 9282831 |
The fish odour syndrome: biochemical, familial, and clinical aspects. | Ayesh R | BMJ (Clinical research ed.) | 1993 | PMID: 8401051 |
click to load more click to collapse |
Text-mined citations for rs72549326 ...
HelpRecord last updated Oct 13, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.