1. DISEASE CHARACTERISTICS
1.1 Name of the disease (synonyms)
Trimethylaminuria (fish-odour syndrome, fish malodour syndrome, stale fish syndrome).
1.2 OMIM# of the disease
602079.
1.3 Name of the analysed genes or DNA/chromosome segments
FMO3.
1.4 OMIM# of the gene(s)
136132.
1.5 Mutational spectrum
More than 30 mutations have been reported to cause trimethylaminuria. Most are missense mutations, but nonsense mutations, small (1 or 2 bp) deletions and one large (12.2 kb) deletion, have been reported. The most common mutations identified to date are p.Pro153Leu1 and p.Glu305X.2 In one case, the haplotype in which a mutation occurs is important: p.Val187Ala has no effect on FMO3 activity, but when it occurs in cis with the common polymorphism p.Glu158Lys it severely affects enzyme activity.3 A human FMO3 database has been established,4 and causative mutations identified to date have been reported.5, 6 In addition to rare causative mutations, 15 non-synonymous single-nucleotide polymorphic (SNP) variants of FMO3 have been identified.7 Of these, only one, p.Asn61Lys, which occurs at low frequency, results in a severe reduction of enzyme activity.8 However, some polymorphic variants (eg, p.Glu158Lys and p.Glu308Gly) when present in cis can cause a moderate decrease in enzyme activity.7, 9 When present in the homozygous state, they may cause mild or transient trimethylaminuria, particularly in infants and young children,10, 11 who have low expression of FMO3.12 Two FMO3 haplotypes that contain promoter-region SNPs have been reported to severely reduce expression in vitro.13 Although the impact of these haplotypes in vivo has not been validated, it is possible that they contribute to the disorder in the absence of coding-region mutations.
1.6 Analytical methods
The most common method is amplification of the eight coding exons by PCR with exon-specific primers, followed by DNA sequencing of the amplicons. Large deletions are rare, being identified in only one individual,14 and can be identified by multiplex ligation-dependent probe amplification.
1.7 Analytical validation
Both the strands of DNA should be sequenced. Identified variants should be compared with databases and the literature to establish whether they correspond to known causative mutations. If a novel mutation is found, it is important to establish that it abolishes or substantially reduces the ability of FMO3 to catalyze the N-oxygenation of trimethylamine (TMA), as assessed by assay of heterologously expressed mutant protein.1, 15, 16 If an individual is heterozygous for two different causative mutations, analysis of the parents’ DNA will establish whether the mutations are in trans. If an individual is homozygous or compound heterozygous17 for loss-of-function mutations of FMO3, diagnosis is confirmed.
1.8 Estimated frequency of the disease in Germany (incidence at birth (‘birth prevalence’) or population prevalence)
For severe, inherited trimethylaminuria, the incidence of heterozygous carriers in the white British population is 0.5–1.0%.18 The frequency of the severe type of the disorder in this population could thus be as high as 1 in 40 000. The true prevalence of the disorder is unknown; however, of patients referred to a malodour clinic in Philadelphia, 35% had trimethylaminuria.19
1.9 If applicable, prevalence in the ethnic group of investigated person
The incidence of heterozygous carriers is higher in other ethnic groups studied: 1.7% in Jordanian, 3.8% in Ecuadorian and 11.0% in New Guinean populations,20 suggesting the frequency of the disorder may be as high as 1 in 3000 and 1 in 400 in the latter two groups, respectively.
1.10 Diagnostic setting
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Comment: Trimethylaminuria usually presents with a body odour resembling that of rotten or decaying fish, the result of excess excretion of TMA in the breath, sweat, urine and reproductive fluids.21, 22, 23, 24 Individuals complaining of or exhibiting a fishy odour should be tested for urinary excretion of TMA, ideally on two separate occasions. Genetic testing should be offered to individuals who, under normal dietary conditions, excrete more than 10% of total TMA as the free amine. Molecular diagnosis can identify affected individuals and heterozygous carriers. It can also distinguish primary genetic trimethylaminuria (including severe presentations, caused by loss-of-function mutations in FMO3, and milder presentations, commonly resulting from compound heterozygosity for milder missense mutations and polymorphisms that affect FMO3 activity) from other, less common forms of trimethylaminuria such as
-
1)
An intermittent form, associated with menstruation,25, 26 probably related to decreased expression of FMO3 in response to steroid hormones. The effect is more pronounced in women homozygous for combinations of polymorphisms that affect FMO3 activity.26
-
2)
A rare transient childhood presentation, as a consequence of immature FMO3 expression, which is switched on after birth and increases with age;12 young children who are heterozygous for a loss-of-function mutation or have certain combinations of polymorphisms of FMO3 may exhibit mild symptoms of the disorder, which disappear with age.10, 11, 27
-
3)
Unusually, as a consequence of viral hepatitis, liver disease, or major transient overload of dietary precursors of TMA with the coexistence of function-altering polymorphisms of FMO3. Prenatal diagnosis is possible if the disease-causing mutations in the family have been identified.
2. TEST CHARACTERISTICS
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2.1 Analytical sensitivity (proportion of positive tests if the genotype is present)
Insufficient data to comment.
2.2 Analytical specificity (proportion of negative tests if the genotype is not present)
Insufficient data to comment.
2.3 Clinical sensitivity (proportion of positive tests if the disease is present)
The clinical sensitivity can be dependent on variable factors such as age or family history. In such cases a general statement should be given, even if a quantification can only be made case by case.
Unknown. However, molecular genetic tests should distinguish between mutations that abolish or severely affect FMO3 activity and, thus, cause severe primary trimethylaminuria, from those that have a relatively moderate effect, resulting in mild or transient forms of the disorder. But acquired and secondary forms of trimethylaminuria, which are not caused by mutations, would not give a positive genetic test.
2.4 Clinical specificity (proportion of negative tests if the disease is not present)
The clinical specificity can be dependent on variable factors such as age or family history. In such cases a general statement should be given, even if a quantification can only be made case by case.
Only individuals who have tested positive for trimethylaminuria by urinary analysis, or their relatives, will be genetically tested.
2.5 Positive clinical predictive value (life-time risk to develop the disease if the test is positive)
Unknown. Only those with a biochemical diagnosis of trimethylaminuria are tested.
2.6 Negative clinical predictive value (probability not to develop the disease if the test is negative)
Assume an increased risk based on family history for a non-affected person. Allelic and locus heterogeneity may need to be considered.
Index case in that family had been tested:
Close to 100%, if known causative mutations have been identified in the index patient.
Index case in that family had not been tested:
Unknown. Only patients that present with symptoms are analysed.
3. CLINICAL UTILITY
3.1 (Differential) diagnosis: The tested person is clinically affected
(To be answered if in 1.10 ‘A’ was marked)
3.1.1 Can a diagnosis be made other than through a genetic test?
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3.1.2 Describe the burden of alternative diagnostic methods to the patient
Very low. However, one individual developed an adverse reaction, with fever and vomiting, after a choline challenge.33
3.1.3 How is the cost effectiveness of alternative diagnostic methods to be judged?
The initial diagnosis of trimethylaminuria is usually biochemical. Genetic testing will help to confirm the diagnosis, distinguish the various genetic and non-genetic forms of the disorder and identify asymptomatic heterozygous carriers.
3.1.4 Will disease management be influenced by the result of a genetic test?
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3.2 Predictive setting: The tested person is clinically unaffected but carries an increased risk based on family history
(To be answered if in 1.10 ‘B’ was marked)
3.2.1 Will the result of a genetic test influence lifestyle and prevention?
If the test result is positive (please describe):
Not applicable.
If the test result is negative (please describe):
Not applicable.
3.2.2 Which options in view of lifestyle and prevention does a person at-risk have if no genetic test has been done (please describe)?
Not applicable.
3.3 Genetic risk assessment in family members of a diseased person
(To be answered if in 1.10 ‘C’ was marked)
3.3.1 Does the result of a genetic test resolve the genetic situation in that family?
A genetic test should distinguish primary inherited and secondary forms trimethylaminuria, mild and severe forms of the inherited disorder, and identify heterozygous carriers.
3.3.2 Can a genetic test in the index patient save genetic or other tests in family members?
The parents and offspring of an individual affected by primary inherited trimethylaminuria will be obligate heterozygotes. Sibs of an affected individual would have to be genetically tested to establish whether they were affected, unaffected or a heterozygous carrier.
3.3.3 Does a positive genetic test result in the index patient enable a predictive test in a family member?
Not applicable.
3.4 Prenatal diagnosis
(To be answered if in 1.10 ‘D’ was marked)
3.4.1 Does a positive genetic test result in the index patient enable a prenatal diagnostic?
Yes, but it is not indicated.
4. IF APPLICABLE, FURTHER CONSEQUENCES OF TESTING
Please assume that the result of a genetic test has no immediate medical consequences. Is there any evidence that a genetic test is nevertheless useful for the patient or his/her relatives? (Please describe)
Affected individuals and their families benefit from counselling. Realization that the problem is the result of a recognized medical condition may help.
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Acknowledgements
This work was supported by the CIBERER, EuroGentest2 (Unit 2: ‘Genetic testing as part of health care’), a Coordination Action under FP7 (Grant Agreement Number 261469) and the European Society of Human Genetics.
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Shephard, E., Treacy, E. & Phillips, I. Clinical utility gene card for: Trimethylaminuria. Eur J Hum Genet 20, 4–5 (2012). https://doi.org/10.1038/ejhg.2011.214
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DOI: https://doi.org/10.1038/ejhg.2011.214