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rs numbers of variants

PostPosted: Wed Dec 03, 2014 3:19 am
by StevetT
I've recently had my DNA analysed by 23andme.com and have downloaded the raw data which provide the two character values of rs numbers in my DNA.

The documents regarding the genetic variants related to TMAU which I have found online do not refer to rs numbers. Can you please point me to an online resource where the relevant variants are identified using rs numbers?

Re: rs numbers of variants

PostPosted: Sun Dec 07, 2014 1:04 pm
by StevetT
I've found the answer to my question (thanks to a link in annie's post "This research" in the "Read it here" forum which I followed down): http://databases.lovd.nl/shared/variants/FMO3

I've also learned that the 23andme results do not contain relevant SNPs for TMAU as their test is of a custom set of SNPs (not whole genome sequencing).

Re: rs numbers of variants

PostPosted: Sun Dec 07, 2014 7:03 pm
by PoetFire
Hi. Dr Dolphin can correct any mistakes I make if he wishes.

I did the 23andme test too and has to 'translate' them too. As you say they only test a few 'codons', about 20 in all (out of 532), although most of them are known common 'variants' (such as 158, 308 etc). The coding part of FMO3 DNA makes a 532 amino acid sequence. But you can also have DNA faults in the non-coding part (introns) and the promoter region etc which can affect function apparently, so even the full sequence FMO3 coding sequence test can still leave you not knowing if you have a fault I guess (in other parts, not the coding region).

The table you linked to I think is kept by Prof Elizabeth Shephard. I think I got the codons from the Pumbed site.

I have more to write about this which I will write later

Re: rs numbers of variants

PostPosted: Wed Dec 10, 2014 1:58 am
by StevetT
Thanks, PoetFire for the info. Could you also please post the URL for the "Pumbed" database which you mentioned?

Re: rs numbers of variants

PostPosted: Sun Dec 14, 2014 2:21 pm
by PoetFire
Hi Steve.

I don't recall how I found the RS numbers now

This is the page where I got a lkot of info on the sequence though :
http://www.ncbi.nlm.nih.gov/CCDS/CcdsBr ... A=CCDS1292

Re: rs numbers of variants

PostPosted: Thu Mar 26, 2015 10:18 pm
by FADworker
Hi

Sorry I'm late to the game here - have had other things to think about lately such as finding a new job. rs prefixes refer to any SNP - single nucleiotide polymorphisms - many of which will be functionally (with respect to the final TMA oxidase activtiy of the encoded FMO3 enzyme) silent. Sequence changes in the FMO3 gene that actually affect the function of the final FMO3 protein may not be included as they are relatively rare. You are really interested in rare sequence changes that affect the function of the FMO3 protein either by inactivating the enzyme altogether with respect to TMA oxidation, such as the relatively common proline to leucine change at amino acid position 153, or result in a partial reduction of activity.

Happy to try and answer any specific queries with respect to mutational effects.