Interesting CBS Variations

[Valentijn]

Edit edit: reread a thrid time and conculde GG should mean higher homocystiene. I have 'GG' but my homocystiene when tested has been on the low end of range. So still confused. Something else must be mucking up the works, now concerned if get everything working that might end up with high homocystiene. Catch 22. Is my conclussion about GG and higher homocystiene correct?

That's right, C699T GG is the version which has a risk of higher homocysteine.

But there are three different ways in which homocysteine is disposed of: via CBS, via BHMT, and via MTR/MTRR. So even if your CBS is a little slow, the others (which are the more useful ones as well) might be functioning well enough to handle any excesses.

As far as getting things "working" and ending up with high homocysteine, it depends on what you're trying to do. If you want to slow down CBS, etc, then higher homocysteine might result.

 

[roxie60]

Interesting, I have the GG variant yet low homocystiene which is a good thing. I am just wondering since I do not know what is keeping the homocystiene low as I work on improving methylation cycle if that would then cause a new problem, mainly homocystiene rising? Catch 22.

 

[Valentijn]

Interesting, I have the GG variant yet low homocystiene which is a good thing. I am just wondering since I do not know what is keeping the homocystiene low as I work on improving methylation cycle if that would then cause a new problem, mainly homocystiene rising? Catch 22.

Good methylation should result in "normal" (low) levels of homocysteine. But slowing down CBS further probably wouldn't be helpful for methylation.

 

[Bluebell]

Roxie60, I am not a medical person, but I cannot see how improving your methylation cycle and getting everything flowing well would cause you to have poorer health (such as a worse homocysteine level).

Just like the VDR situation, I would say this isn't a big thing to worry about.

 

[Bluebell]

Indeed, there are some that are worse than MTHFR C677T. MTHFR W339G (rs267606886) CC reduces gene functioning to 21% of normal, and MTHFR N324S (rs267606887) CC reduces gene functioning to 36% of normal. There's also another MTHFR SNP which takes it down to 10%, but isn't part of the 23andMe results. When C677T is added to the mix, functionality of those reduces by half again. So W339G is then down to about 10%, and N324S to 18%.

V, those rs numbers are not in my 23andme data. They look a little longer than normal - do they really have 9 digits?

None of my MTHFR SNP rs numbers start with 2676, nor end with 887 or 886.

 

[Valentijn]

V, those rs numbers are not in my 23andme data. They look a little longer than normal - do they really have 9 digits?

Ah, those have "i" numbers. i5003529 and i5003530 respectively.

 

[Bluebell]

Ah, those have "i" numbers. i5003529 and i5003530 respectively.

Thanks for checking. I'm AA and TT respectively, so neither is the risky one.

 

[SuckSmoothie]

Sorry to pull a necromancer here but is p5p useful for CBS upregulations or downregulations? I've tested my urine sulfate and whenever it's above 1600 I react badly to p5p, but whenever it's lower p5p is a godsend on my cognition.

I have +/- for C699T and C19150T, -/- for A360A and +/+ for A13637G

 

[john6]

Sorry to pull a necromancer here but is p5p useful for CBS upregulations or downregulations? I've tested my urine sulfate and whenever it's above 1600 I react badly to p5p, but whenever it's lower p5p is a godsend on my cognition.

I have +/- for C699T and C19150T, -/- for A360A and +/+ for A13637G

There aren't any CBS upregulations, but P-5-P can be helpful to get CBS working to lower homocysteine. CBS function is best viewed in light of the whole methylation cycle.

 

[sleepingbeautycan]

How do I find the i5003529 in 23andme? I tried entering it into both fields and nada. Then I looked on the MTHFR gene and it has i5003527, i5003530 and i5003528. And where is the government website that allows the translation of the i numbers to the rs numbers. I think I have version4 from 23andme and some of the tests stopped being tested.

Thanks so much, your knowledge is amazing.

 

[Valentijn]

How do I find the i5003529 in 23andme? I tried entering it into both fields and nada.

It isn't tested on the V4 chip.

And where is the government website that allows the translation of the i numbers to the rs numbers.

"i" numbers are 23andMe's private ID system for SNPs. If you ask them, they'll say they just use it for testing SNPs which don't have an rs ID yet. But they're lying - they usually will also use i numbers to make it harder to find your results on known pathogenic mutations.

There's no website for converting them that I'm aware of. The government certainly would not be interested in doing so But if you look up an adjacent SNP on dbSNP and do the math (accounting for 23andMe using version 37 build and the default view in dbSNP using version 38 to determine position on the chromosome), you might be able to find it on the map view.

 

[sleepingbeautycan]

"i" numbers are 23andMe's private ID system for SNPs. If you ask them, they'll say they just use it for testing SNPs which don't have an rs ID yet. But they're lying - they usually will also use i numbers to make it harder to find your results on known pathogenic mutations.

There's no website for converting them that I'm aware of. The government certainly would not be interested in doing so But if you look up an adjacent SNP on dbSNP and do the math (accounting for 23andMe using version 37 build and the default view in dbSNP using version 38 to determine position on the chromosome), you might be able to find it on the map view.

Oh darn! I thought someone had mentioned a government site and reading lots of small numbers. I really have no idea what I'm talking about.

So the map view is ordered by location, and if I find the allele before or the allele after and there is a i number in the corresponding spot, then that is our winner??? We should add this information to snpedia (or some other site) for everyone else to use.

 

[Valentijn]

So the map view is ordered by location, and if I find the allele before or the allele after and there is a i number in the corresponding spot, then that is our winner???

Unfortunately it's usually not that easy, since 23andMe doesn't test every allele. Typically they'll be hundreds or thousands of positions apart.

 

[Sea]

@sleepingbeautycan go to Variation Viewer
http://www.ncbi.nlm.nih.gov/variation/view/
Click the "read our overview" link and you can learn how to navigate the site. You'll find the rs numbers for some of the i numbers by searching using the chromosome location (which is in the column beside the i numbers in 23andme)
Under "pick assembly" make sure you choose: GRCh37.p13: Annotation Release 105

 

[sleepingbeautycan]

Thank you @Sea and @Valentijn I was able to look up an i number using variation viewer!!