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Just got 23&me results in; can anyone deconstruct contradictions

Discussion in 'Genetic Testing and SNPs' started by overtrain, Aug 6, 2013.

  1. overtrain

    overtrain Medical Mafia needs to die via this virus.

    Hello! So here are some 23&me results just in. I see some contradictions, so I don’t know how to deconstruct the data. If any of you have any input, that would be so swell. THANK YOU (I feel a bit less CFSy on 2 days of a lot of methylfolate, charcoal, & extra b12!)

    Mutations detected: C282Y, H63D
    rs1799945 H63D C to G CG
    i3002468 S65C A to T AA

    I think that means high levels of homocysteine. “According to Dr. Ben Lynch, impaired function of the enzyme can cause or contribute to conditions such as… Chronic Fatigue Syndrome…” (‘ya think?)

    Hemochromatosis? Iron overload, though rare, or “mild” if have these 2 mutations together, I guess. Well, something is clearly not “mild” in my CFS.

    Other results:

    * SNP: rs1801133 (A or G)
    * Anon's Genotype: AA
    * Gene: MTHFR
    * Chromosome: 1
    * SNP: rs1801131 (G or T)
    * Anon's Genotype: TT
    * Gene: MTHFR
    * Chromosome: 1

    You have 0 homozygous (+/+) mutations and 5 heterozygous (+/-) mutations.
    Here are your heterozygous mutations as indicated in your SNP gene table above (not including MTHFR):

    * VDR Bsm
    * VDR Taq
    * MTRR A66G
    * CBS C699T
    * CBS A360A

    “CBS defects are actually upregulations. This means the enzyme works too fast. In these patients, it's common to see low levels of cystathionine and homocysteine since there is a rapid conversion to taurine.”

    HUH? Aren’t I supposed to already have too high homocysteine? So do these two factors then cancel each other out, so it means my homo. Is fine?

    “This leads to high levels of taurine and ammonia. If taurine climbs one may need to address ammonia. Yucca Root and Charcoal/Magnesium flushes can help address high ammonia levels. High doses of L-Ornithine may be effective as well according to medical studies.

    The CBS mutation not only leads to excess taurine, but can also lead to excess sulfur groups. There are many things one may need to avoid with a CBS upregulation. Some of the items include garlic, broccoli, eggs, onions, legumes, meat, Epsom salt baths, alpha lipoic acid, glutathione, chelating agents such as DMPS, NAC, Milk Thistle, various other supplements, and much more.”

    (No beans? Like that's going to happen. I'm a vegetarian.)

    COMT V158M rs4680 GG -/-
    (I think means increased dopamine, not a bad thing, right?)
    COMT H62H rs4633 CC -/-
    COMT P199P rs769224 GG -/-
    GSTP1 I105V rs1695 AG +/-
    GSTP1 A114V rs1138272 CT +/-
    GSTT1 Absent* (23 doesn’t test for this)

    “Methyl B12 is usually much easier to tolerate for those that are COMT (-/-). Patients with MTR/MTRR may also benefit from the combination of GABA and L-Theanine. L-Theanine is a methyl donor. They may also benefit from taurine, Pycnogenol® pine bark extract, and grape seed extract.”

    HUH? Am I not too high in taurine already? >>face palm

    “With COMT V158M + and a VDR Taq + status, the body may have further trouble tolerating methyl donors.”

    Another contradiction… aren’t I supposed to tolerate methyl group best?

    Methylation Analysis Results

    Gene & Variation rsID Alleles Result
    COMT V158M rs4680 GG -/-
    COMT H62H rs4633 CC -/-
    COMT P199P rs769224 GG -/-
    VDR Bsm rs1544410 CT +/-
    VDR Taq rs731236 AG +/-
    MAO A R297R rs6323 GG -/-
    ACAT1-02 rs3741049 GG -/-
    MTHFR C677T rs1801133 AA +/+
    MTHFR 03 P39P rs2066470 GG -/-
    MTHFR A1298C rs1801131 TT -/-
    MTR A2756G rs1805087 AA -/-
    MTRR A66G rs1801394 AG +/-
    MTRR H595Y rs10380 CC -/-
    MTRR K350A rs162036 AA -/-
    MTRR R415T rs2287780 CC -/-
    MTRR A664A rs1802059 GG -/-
    BHMT-02 rs567754 CC -/-
    BHMT-04 rs617219 AA -/-
    BHMT-08 rs651852 CC -/-
    AHCY-01 rs819147 TT -/-
    AHCY-02 rs819134 AA -/-
    AHCY-19 rs819171 TT -/-
    CBS C699T rs234706 AG +/-
    CBS A360A rs1801181 AG +/-
    CBS N212N rs2298758 GG -/-
    SHMT1 C1420T rs1979277 GG -/-

    Gene & Variation rsID Alleles Result
    CYP1A1*2C A4889G rs1048943 TT -/-
    CYP1A1 m3 T3205C rs4986883 TT -/-
    CYP1A1 C2453A rs1799814 GG -/-
    CYP1A2 164A>C rs762551 CC +/+
    CYP1B1 L432V rs1056836 CG +/-
    CYP1B1 N453S rs1800440 TT -/-
    CYP1B1 R48G rs10012 CG +/-
    CYP2A6*2 1799T>A rs1801272 AA -/-
    CYP2A6*20 rs28399444 II -/-
    CYP2C9*2 C430T rs1799853 CT +/-
    CYP2C9*3 A1075C rs1057910 AA -/-
    CYP2C19*17 rs12248560 CC -/-
    CYP2D6 S486T rs1135840 CG +/-
    CYP2D6 100C>T rs1065852 GG -/-
    CYP2D6 2850C>T rs16947 AG +/-
    CYP2E1*1B 9896C>G rs2070676 CC -/-
    CYP2E1*1B 10023G>A rs55897648 GG -/-
    CYP2E1*4 4768G>A rs6413419 GG -/-
    CYP3A4*1B rs2740574 TT -/-
    CYP3A4*2 S222P rs55785340 AA -/-
    CYP3A4*3 M445T rs4986910 AA -/-
    CYP3A4*16 T185S rs12721627 GG -/-
    GSTP1 I105V rs1695 AG +/-
    GSTP1 A114V rs1138272 CT +/-
    SOD2 A16V rs4880 AG +/-
    NAT1 R187Q rs4986782 GG -/-
    NAT1 R64W rs1805158 CC -/-
    NAT2 I114T rs1801280 CT +/-
    NAT2 R197Q rs1799930 AG +/-
    NAT2 G286E rs1799931 GG -/-
    NAT2 R64Q rs1801279 GG -/-
    NAT2 K268R rs1208 AG +/-

    Also also said I have Alpha-1 Antitrypsin Deficiency.

    Lastly, for fun, my supposed increased risk of these:

    Compared to Average
    Venous Thromboembolism
    Established Research: Multiple studies with 750+ participants
    35.4% 9.7% 3.63x
    Woo hoo! (I have Factor V Leiden blood disorder so no surprise there)

    Atrial Fibrillation
    Established Research: Multiple studies with 750+ participants
    20.5% 15.9% 1.29x


    Rheumatoid Arthritis
    Established Research: Multiple studies with 750+ participants
    8.6% 4.2% 2.03x


    Parkinson's Disease
    Established Research: Multiple studies with 750+ participants
    2.0% 1.6% 1.26x

    Much appreciation if anyone responds. :lol:
  2. Valentijn

    Valentijn Activity Level: 3

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    I've deleted the -/- results and crossed out the ones with no research showing that there's any risk factors associated.

    VDR might indicate that you're a little slow in forming dopamine, hence you might have an excess of the methyl groups which help form dopamine.

    MTHFR C677T is a pretty major problem with creating methylfolate. When homozygous it's functioning at about 30% of normal. You might want to check the list at http://forums.phoenixrising.me/index.php?threads/interesting-mthfr-variations.24543/ to see if you have any other MTHFR risk factors, since C677T has a habit of making those even worse.

    MTRR indicates you might need some B12. Due to your vegetarian lifestyle, you should probably be supplementing B12 anyhow. And because of the potential trouble with methyl groups, hydroxoB12 might be the safest version, but based on the data here there's no reason to think that methylB12 will cause major problems (though watch out for potassium issues with methylB12).

    I read CBS C699T backwards compared to Yasko and genetic genie, so I see the hetero version as causing a bit of a downregulation compared to the faster (better) version. B6 can help if there's a problem there.

    SUMMARY:
    B12 is probably a very good idea, and supplementing methylfolate may be essential. You might want to consider getting levels of those tested regularly, due to your diet and genetic predispositions. B6 may also help.

    If you want to take methylB12 instead of hydroxoB12, then supplementing vitamin D might also help, to speed up your methyl use in forming dopamine. But that might affect your neurotransmitter levels, so watch out for any side effects.
    overtrain likes this.
  3. taniaaust1

    taniaaust1 Senior Member

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    If Im reading that correctly, you have two copies of C667T MTHFR C667T .. its extremely important that that gets the right treatment, treating that could really improve things for you.

    Take care... my first specialist who I went to to get that treated didnt use the right forms of supplements/vitamins for it and hence it wasnt helped, I see another specialist for it now and are now on better forms of things for it and they certainly do help. Dr. Ben Lynch has a lot of good info out on treating this polymorphism.
    overtrain likes this.
  4. Bluebell

    Bluebell Senior Member

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    V, would they need to be taken together (the D and the methylB12) to work best for speeding up the methyl use in forming dopamine, or would taking them an hour or two apart be okay and have the same result?

    (That is a general question I have -- do any pairs or groups of methylation supplements need to be taken at the very same time in order to be processed by the body in the way that we intend them to be? And/or, are there some that should be taken quite separately in order to be processed in the way we wish them to be? I'm not asking you that huge question here -- but if you have any information on it, and wish to answer, feel free!)
  5. Bluebell

    Bluebell Senior Member

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    Hi Overtrain,

    I am interested to learn how you are using charcoal (how much, when), and what benefits you are noticing from it.

    As Taniaaust1 wrote, the homozygous MTHFR C677T is a biggie, and Dr. Benjamin Lynch has a website pretty much devoted to it: mthfr.net.

    He's done a video about it that you might want to watch, on his site seekinghealth.com (it's also on youtube - same video).

    Those links and more are provided in my big list of methylation links - hyperlink is below my signature line -->
    overtrain likes this.
  6. Valentijn

    Valentijn Activity Level: 3

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    No idea :p
  7. overtrain

    overtrain Medical Mafia needs to die via this virus.

    THANK YOU, everyone, for the responses! I really appreciate your time & energy. It looks like I've been taking wrong things like NAC, which only backfired the last year.... & the wrong folate, the wrong b12.... the list goes on. Gluthione. I thought M.E./CFS was a methylation issue in part.... so I was trying to improve my methylation by putting cart before horse. It's funny, because I said, way back when I still WENT to doctors, that I felt "something is missing" in my body. Yeah, you know the drill.... hello, psych eval?

    Fascinates me we know this stuff & mainstream med mafia doesn't. Isn't it common sense that a blood # for, say, b12, doesn't reflect HOW the body utilizes it, same as the TSH #?

    However, I'm still in the dark about the contradictions between results. I guess it's one of those try & see what helps as time goes on.

    If anyone- I can search for this- but if you have the stats on how many of us on this site or who have ME/CFS in general populations around the globe have 677 gene mutation, that might be enlightening. Studies must have been done..... or.... not..... :rolleyes:
  8. overtrain

    overtrain Medical Mafia needs to die via this virus.

    Bluebell,
    Good grief, this is great, thank you so much.

    Activated Charcoal: Last summer I accidently swallowed a small rock thinking it was a vitamin... which got me thinking about poison control in general... (I knew burned toast is good for a stomach ache.) Saw it on sale 4 bucks at drugstore. Left it unopened but eventually read somewhere it was good for digestion in general or something, so started taking 1 a day (sensitive body, to see what happ), then read it's good for ph balance... then after MTHFR read it's good for that. Now with bad tooth read today it can be used in gauze...

    I have Nature's Way 560mg, of which I'm taking 6 a day. (Either before or after meals.) My stomach feels less upset & digestion easier in general. Also feel a bit less constipated. There's prob. purer forms or fresher charcoal, or cheaper. Hasn't been a major difference like night & day, just an ease in the body. At some point I'll stop & see what happens. ;)
  9. overtrain

    overtrain Medical Mafia needs to die via this virus.

    Thank you.... until rdg your post I didn't understand the double-positive thing, though it should have clicked, what with those two plus signs.... I'm so glad the correct supps helped you.... that gives me hope. I need to now try the right b12, etc. Good luck!
  10. overtrain

    overtrain Medical Mafia needs to die via this virus.

    Valentijn likes this.
  11. Bluebell

    Bluebell Senior Member

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    Overtrain, make sure to indicate whom you are addressing your posts to! It's not entirely clear in your post that I quoted here whose post you were responding to.

    You can either just write their name in your response (like you did with Valentijn, just above), or hit "reply" to their post which will quote it in your response, or you can do the "at" symbol and then their user name, like this: overtrain.
  12. Bluebell

    Bluebell Senior Member

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    Hi Overtrain, glad you liked it.

    (I think you were referring to my big list of methylation links, or maybe the Lynch site and video.)

    IMPORTANT: You need to stop taking the charcoal in this way!!!

    Charcoal should be taken at least 3 hours before and after you ingest any food or any supplements --- and preferably 4 hours away from any food or supplements. If it's taken any closer than 3 hours, in your digestive system it will bind up the nutrients that are in your food and supplements and will usher them out of your body partly UNABSORBED.

    This timing should be on the label. Indeed, this IS on the label, because I have the same charcoal supplement that you do. You need to follow instructions, young man! :nerd:
    :)

    -----
    From what I've read - though I have only seen a few mentions about it, and I don't have a good feeling for it yet -- people who use charcoal as part of a Yasko-influenced methylation protocol seem to take it one day a week at the most and they take it right before bed, as far from anything else as possible, with a glass of water and sometimes a capsule of magnesium (the magnesium is there to stimulate the bowels, because in some people charcoal can slow down the bowels).
    overtrain and Valentijn like this.
  13. caledonia

    caledonia

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    overtrain Yep, the charcoal will clog you up good if you keep taking it on a daily basis - don't ask me how I know this - lol.

    I'll try and get back later with a more extensive analysis. In the meantime, check out all the links in my signature.
  14. kday

    kday Senior Member

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    overtrain - I wanted to add this about GSTT1... 23andMe isn't designed to detect deletions but based on the fact that that you show no call for all the GSTT1 SNPs, you probably have a deletion. I emailed 23andMe and they explained other factors (such as a difficult to genotype region of DNA). However, from what I can see, the no call rate for these SNPs is about 23% when I examined data from openSNP, so I feel pretty confident these are all deletions. The higher than 15% could reflect the type of population that uses OpenSNP.

    However, there are some people that have all GSTT1 missing except 3 if I remember right. I don't know what to make of this, so I don't count it as a deletion as of now.

    While a GSTT1 deletion is common, I think it is significant if you have acquired environment illness (e.g. xenobiotics). Would be more significant if I could tell if one has a GSTT1 and GSTM1 deletion, but unfortunately, it doesn't look like 23andMe's chip sequences GSTM1 null alleles correctly.

    However, defects of MTHFR, MTRR, GSTT1, GSTP1, CYP1a2 is a great setup for environmental toxicity, so you just might be at the right place. ;)

    Given that you are ill and there may be environmental factors (such as xenobiotics) at play, I think you may notice a lot of detox from a methylation protocol and increasing your glutathione. Assuming you don't have problems with protein sulfur you can also boost glutathione with things like Whey Protein, S-Acetyl Glutathione. Immunocal or ImmunoPro Rx are effective whey proteins. Most other whey proteins just simply don't work, so just don't pick up any from the store. NAC helps some and is shown to boost glutathione in studies, but I am not a huge fan of it and some people here warn against it. Liposomal glutathione and IV glutathione might help if you never tried it before (but IV is very high cost per dose).
    Valentijn likes this.
  15. caledonia

    caledonia

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    The apparent contradictions in homocysteine are due to a concept called gene expression. For example, if CBS is expressed it will run faster. If it's not expressed, it won't. There are various test methods to determine if CBS is expressed. You can also go by symptoms. If you're getting stress/anxiety reaction from even tiny amounts of methyl donors, then CBS is expressed and you'll need to treat that first. Otherwise you're going to have trouble completing a methylation program.

    So your homocysteine may or may not be fine depending on gene expression. This is why functional testing in addition to SNP testing is also a good idea.
  16. overtrain

    overtrain Medical Mafia needs to die via this virus.

    Caledonia, Hi... I'm a little late to the party here- I often miss notifications. Thank you for the charcoal info. This is what brainfog has done to my two Masters degrees in the English language.... dosing? rdg bottle instruction? Oh my. However, one thing I know is I'm not young, nor male... ;)

    Thank you for the other info. re CBS. I need to research this & post back. At first the methyl 12 & folic made me feel better but I'm crashing now. Things like SAM.e kill me, & I am right now moving slowly out of a mold/roach/bedbug infested place where I noticed my symptoms got much worse. Was also working at respiratory care unit when became ill, as well as a second job cleaning w heavy industrial cleaners that made me feel nuked when I used them.

    Sulphur I read I have to avoid.
  17. Bluebell

    Bluebell Senior Member

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    Sorry that I thought you were a young man -- I think I read it in someone's description of themselves here -- it was probably another member whose thread I had replied to just before or after I posted on your thread.

    But you mixed me up with Caledonia, so maybe we are even. :D

    I hope you were able to get out of the unhealthy living situation and stop working with industrial cleaners! No wonder your health is a little affected!

    With all that, and working two jobs, plus the willy-nilly use of charcoal's negating ALL your nutrition, you must have a mighty strong constitution, actually!
  18. overtrain

    overtrain Medical Mafia needs to die via this virus.


    Does charcoal do away with it all? Or just within a hour of taking it? No matter, as I stopped altogether. The charcoal. But yes, I do have a strong constitution, thanks, & I moved from a mold/roach infested apt. to a safe, clean, amazing place with a jacuzzi 1 mo. ago! And now even laun soap is hypoallergenic. And I don't work. At all. Ever.

    I hope your healing is going well. :)

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