News & Views on Systemic Body Odor and Halitosis such as trimethylaminuria TMAU. If you have fecal odors or bowel odors it may be metabolic/systemic

14 January 2018

the 'big 3' FMO3 variants : a cheap way to test

There are 3 common variants for FMO3, that perhaps most 'FMO3 smell people' carry. The easiest and cheapest way to find out is to do the 23andme.com test, or an ancestry test that lets you download the raw data.

FMO3 is a 532 amino acid sequence, and 23andme only test about 50 of the 532, but it does test the 3 main variants at codons 158, 257, 308.
It would be interesting to see if most of carry 2 or more of these.

Estimates of carriers of the 3 main variants :
E158K : 40% people ?
E308G : 20% ?
V257M : 10% ?

DIY STUDY
We should be aiming to flood PUBMED with papers about TMAU, SysBO/Hali etc.
PUBMED is where researchers look to see whats going on.

But for now, as beggars, we can try a DIY STUDY.

Question 
Do you carry E158K, V257M and/or E308G ?

Feel free to put your result in the COMMENT SECTION.
Anon if you want ?
e.g.
E158K : AG
V257M : AA
E308G : AG

HOW CAN I TEST FOR THIS ?
A cheap and easy way to test for the 3 most common FMO3 variants is :

1. Find and buy an ancestry test that lets you download the RAW DATA ...
or buy 23andme.com test.

2. Look for these 3 variants :


rs2266782
variant known as E158K
normal : GG
variant : A

rs1736557
variant known as V257M
normal : GG
variant : A

rs2266780
variant known as E308G
normal : AA
variant : G


FMO3 PROTEIN is a 532 amino acid sequence, but there are 3 most common variants. E158K V257M E308G . Many people carry these faults (Whites carry maximum for the 3 : 45%, 25% 10% ...  estimate from memory). No-one is bothered much to find out if they are 'pathogenic' or not, but it would be interesting to see if those who identify with metabolic malodor tend to carry them in a mix.

My own current view :
I suspect most cases of 'metabolic/systemic body odor' are due to weakness in the FMO3 enzyme, but there may be other enzyme disorders too.

COMMENT SECTION
Feel free to put your result in the comment section. Anon if you want.


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8 comments:

sysbodyodor said...

I have
E158K (carry)
E308G (carry)

Anonymous said...

Hello, I have been participating in a study based in Germany from the same persons that run the bodyodorresearch.blogspot.com website. Thought I'd update you with some interesting information. Im not sure the exact method but the exome data was run through some sort of supercomputer analysis type program and they were able to scan my fmo3 Gene in it's entirety and found that there is no mutation. This is weird because when I eat eat fish I start to smell like it. There was another suspected Gene that they scanned (carns1) based on certain elevated aminos and that showed no mutation either, but that could be due to a not so good scan of that particular enzyme which they are now testing to see if that's the case.

sysbodyodor said...

Hi. I know if that study and support what they are doing.
I guess there could be a few reasons for your result :
1. You may not be TMAU1 but TMAU2.
2. It might be something else.

The ones I want to point out :
3. It seems people can have faults in the 'intron' part of the gene, mostly thought as 'junk part', or the promoter region etc, which can cause TMAU1. This wouldn't show up in the coding sequence.
4. Most 'faults' for FMO3 are probably currently not known what effect they have, and so wouldn't be listed 'pathogenic' in a list. So an app may check your code and not have a fault as being pathogenic.
5. Maybe you could try putting your code through an app such as promethease (not used it), or post it here or even send it to me if its just the FMO3 gene (i.e. I dont want your full exome, genome etc).
It would depend how they chart it but I might be able to read.
nucleotides are like AAA.
amino level are like AA.
AGTC etc

3 nucleotides = an amino acid.

sysbodyodor said...

Thanks for the data.
I don't think I will suggest promethease again.
Don't like their 'storefront' presentation of disorders etc.

I looked around for FMO3.
It seems they list 17 rs things.

It looks like you carry E158K same as me.
But maybe 40% whites carry it, so it alone doesn't seem to cause smells.
The FMO3 data is basic and I would need to look around to try and make sense. But that's the only one I could see in this time.
I'm guessing the rest are 'normal'.

With SNP VARIANTS, it can be one or other. Theres a major and a minor option. Often its unknown what effect either will be (it seems).
I think often our group carry combos, with E158K being the anchor. Especially with E308G.

I will look around a bit more but expect the other 16 to be the 'major' (normal ?, or 'wild type' as they call it).

CYP enzymes are related to FMO3 and carry out the same type of job (broad spectrum oxidizers). Most peoples CYPs vary, so can't tell if that is significant. I talk of FMO3 a lot but CYPs are also on my mind (still have a bias for fmo3).

I wonder if biotinidase (sp?) might have any effect, probably not.

sysbodyodor said...

just noticed you carry 257 too
V257M : AG

An issue with the sites is that they won't flag things as 'suspicious' in their headline details.
Mainly cos no-one is interested in many genes so no-one knows the effect of variants.

so (far) you are :
E158K : AG (normal : GG)
V257M : AG (normal : AA)

My current (10% confidence)) guess is these 2 together may be a factor in your smell problem but may not.
Not seen anything about this combo I can recall.

Most of us I think are a combo of very mild TMAU1 and TMAU2 as a syndrome.

Anonymous said...

Thing is that FMO3 wouldn't be able to explain phenylalanine & fecal type odors really. if you look at the map of metabolic body odors on the bodyodorresearch blog CARNS1 hits them all perfectly. Do you think whole genome testing give me a for sure answer? Also, I have taken an organic acids test which is where the researcher got the idea for CARNS1 from. I've attached it if you want to take a look at it.

sysbodyodor said...

I noticed your biotin was low. I was too. Theres enzymes that deal with biotin. I was ok. Your dna data showed up biotinadase but I cant recall why. maybe worth looking at.

Im a fan of genova in spirit but not a great fan of their tests. Somehow they miss the point imho. i have used them too. THey are part of the 'functional medicine' movement. For smells I think we would be looking at metabolites far from the mainstream.

sysbodyodor said...

FMO3 oxidizes 1000s of sulfides/amines of a particular shape. I doubt most with TMAU1 smell of TMA. probably sulfides more. also i think gut flora generate a lot of our biotin (not proven).

At this stage we can all speculate what the causes are, cos nobody knows. bit like a religious convention to discuss which religion is right.

so no-ones right/wrong atm imho.
depends where everyone wants to focus.

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Update Aug 17 :
Genos is back with it's EXOME test
link

Note :
Exome/Genome testing may be better option than single gene testing.

See this post : link

Note : Genos Exome Testing.

Exome testing is almost the same price now as single gene testing. Also Genos is consumer friendly, which standard DNA labs are not.

So the blog offer to test solely for FMO3 is almost obsolete, and so no longer offered.


Does Genos fully sequence FMO3 gene ?

At the moment it is not clear, but hoped this will become clear over the next few months

Note : possible 'wild west' way of testing FMO3
Use an ancestry dna site and rummage through the raw data

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