Email from FMO3 DNA tester : About those with primary TMAU in urine but normal in DNA test

As time goes by and awareness of test results amongst the community surfaces, it has become clear there is a pattern in the UK of a few testers getting a result that implies 'primary TMAU' in their phenotype (urine) test, but when they do the DNA test for confirmation, no suspect FMO3 copies are found. A geneticist with expertise in FMO3 DNA clinical testing, Richard Kirk, MSc FRCPath Lead Clinical Scientist, was asked about this, and this was his response to this anomaly :

Q : I understand your lab does the FMO3 DNA test. I was wondering if the test also looks for only mutants and not polymorphisms/variants/wild-type ? We seem to have a few people who would seem primary TMAU cases in the urine test, but the DNA test says they are normal.

I also had in mind this 2007 paper about FMO3 function and menstruation
http://www.biomedcentral.com/1471-2350/8/2

A :Thank you for your email.
Our FMO3 DNA test is done by sequencing all the parts of the FMO3 gene that code for the FMO3 protein/enzyme ('exons' in genetics terms). This means that we do pick up neutral polymorphisms and variants, as well as pathogenic mutations. In particular, we can and do detect the p.[Glu138Lys;Glu308Gly] variant haplotype that is mentioned in the 2007 paper, and others. If we find this variant haplotype on one or both copies of the gene, we include it in our reports.
There are certainly individuals that appear to have primary TMAU on the urine test, but nothing on our DNA test.
Although our test will pick up all the mutations that have been described in this gene, we cannot exclude rare mutation mechanisms such as mutations deep within introns (the non-coding DNA between the exons) or mutations affecting the controlling mechanisms for the gene. There is also a theoretical possibility that other related proteins/enzymes could be affected. Unfortunately, investigating these possibilities would be research, and beyond the current scope of a diagnostic service like ours.
I hope this information is of help.

...The one addition I would make is that we also cannot exclude a non-genetic cause for a 'primary' result on the urine test. Further biochemical and microbiological follow-up can sometimes help to give a full picture. Unfortunately in some of these cases our current laboratory testing cannot come up with a final answer.

Richard Kirk MSc FRCPath
Lead Clinical Scientist - Inborn Errors of Metabolism Section

Sheffield Diagnostic Genetics Service

Sheffield Children's NHS Foundation Trust
Western Bank

SHEFFIELD S10 2TH
UK

This pattern seemd to be also demonstrated in a dissertation paper in the USA, where 12 people known to have been diagnosed as primary TMAU in the urine test were then DNA tested, and 8 found to not have the textbook genetic model of the disorder, namely 2 mutant FMO3 copies.
http://digitalcommons.library.tmc.edu/dissertations/AAI1450285/