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Can someone help me with SNPs too?

Discussion in 'Genetic Testing and SNPs' started by wordweaver27, Sep 11, 2013.

  1. wordweaver27

    wordweaver27

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    Hello everyone,

    I'm de-lurking finally. I've got my 23andme results and with all of this brain fog cannot wrap my head around everything. I appreciate any assistance you may be able to give me in helping me figure this out before I begin communicating with my doc about it. Here goes:

    Detox (I'm only including Homozygous because Hetero are way too many to list)
    PON1 Q192R rs622 ++ CC

    IgE
    C3 rs366510 ++ GG
    FCER1A/OR10J2P rs2494262 ++ AA

    Methylation
    Homozygous
    AGT M235R/C4072T rs699 ++ GG
    CBS A360A rs1801181 ++ AA
    FUT2 rs492602 ++ GG
    FUT2 rs601338 ++ AA (yup, I'm immune to the Norovirus.)
    FUT2 rs602662 ++ AA
    GAD1 rs769407 ++ CC
    GAD1 rs3791851 ++ CC
    GAD1 rs3791878 ++ TT
    GAD1 rs701492 ++ TT
    GAD1 rs769395 ++ GG
    MTHFD1 C105T rs6362 ++ CC
    MTHFR 03 P39P ++ AA
    MTHFR A1298C ++ GG
    MTHFR A1572G ++GG
    MTHFR 6 more unnamed variants ++
    MTHFS rs6495446 ++ CC
    PEMT rs4244593 ++TT
    TCN2 C766G rs1801198 ++ GG

    Heterozygous
    BHMT - all those listed on MTHFRSupport report
    COMT rs6269 +-
    COMT H62H rs 4633 +-
    COMT V158M rs4680 +-
    DAO rs2070586 +-
    DAO rs2111902 +-
    DHFR
    GAMT rs55776826
    GIF (TCN3) +-
    MAO A R297R +-
    MTHFD1 G1958A +-
    MTHFD1L rs11754661 +-
    MTHFD1L rs6922269 +- (anyone notice this rs# is a palindrome?)
    MTHFR G1793A (R594Q) +-
    MTR A2756G +-
    MTRR A66G +-
    MTRR H595Y +-
    MTRR K350A +-
    MTRR rs10520873
    MTRR rs9332
    NOS2 - two of these are hetero on MTHFRSupport report
    NOS3 - two of these are hetero
    PEMT rs7946 +-
    SMHT2 rs34095989 +-
    SCL19A1 - both hetero
    VDR Bsm +-
    VDR Taq +- (I looked this one up in my raw data)


    Mitochondrial Function & Sulfonotransferase
    There are a handful of Homozygous and heterozygous mutations which I can post if you think they are relevant but my eyes are starting to cross just now.

    Besides the usual suspects, the ones that pop out at me to investigate further are PON1, PEMT, TCN2 and GIF(TCN3). What do you think?
    Thank you! :)
     
  2. Crux

    Crux Senior Member

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    Hi wordweaver;

    You've got a long list of snps, and I would tip over trying to figure all of them. ( still trying to understand mine:confused:)

    The TCN2 is a big one. Transcobalamin 2 is involved with B12 transport.
    GIF is involved with intrinsic factor, a B12 binding protein. GIF snps are associated with Pernicious Anemia.
    http://ghr.nlm.nih.gov/gene/GIF

    I've read conflicting info about FUT2. ( B12)

    GAD1 is involved with forming enzymes for synthesis of GABA.

    DAO is for histamine metabolism. ( B6, vitamin C, copper)

    You're probably familiar with the MTHFR, MTR, and MTRR.

    This is all I can do for now, but it would be good to have doc check B12, folate, homocysteine, mma.
    Possibly check for intrinsic factor antibodies, and parietal cell antibodies.
     
  3. roxie60

    roxie60 Senior Member

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    How do we know your homozygs are the bad (risk) ones? Just having a ++ doesnt always mean you interpret it bad or good, I think you need to know the risk alelle. I could be wrong, JMO.

    For example on TCN2 I am GG (homozyg) but it is the risk alelle 'G' that tells me this could be a problem for me. So are you GG on TCN2, I cant tell by just a ++ and I think if you want fed back from others your alelles need to be included.
     
  4. caledonia

    caledonia

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    Check the link to the MTHFRsupport radio show on the SNPs (below in my signature).
     
  5. Crux

    Crux Senior Member

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    Hi roxie60;

    TCN2,GG, surely can cause big problems with getting B12 into the cells, brain, spine, etc.
    I noticed that some of the symptoms you've been having still may be that of B12 deficiency. ( fatigue of course, tinnitus, pain, even hyperpigmentation -- there is hyperpigmentation in B12 deficiency too.)

    I'm just hetero TCN2,(CG), but I need at least 15mg daily subs. to keep from, well, dying.

    I do hope you're getting enough.:)
     
  6. roxie60

    roxie60 Senior Member

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    thx Crux, I understand homozyg GG TCN2 is something I need to manage best as possible, thx for input. But I was mostly using as example for Op that people would need more info, specificaly the alelles associatedc with her homozyg genes. If she is CC then it is not an issue for her. Your response solidified my point, once you knew I was GG you knew based on your research tha could be a problem for me.

    You also just reminded me I had not taken my MB12 5000 mcg yet today ;)
     
  7. roxie60

    roxie60 Senior Member

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    Sadly I have given up hope of ever getting rid of this tinnitus....:cry: I would like to see a healthy person with absolutely no issues just take on this one symptom, 24x7 tinnitus and come back a year later and see how well they have faired.
     
  8. Crux

    Crux Senior Member

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    It's true that the not knowing of risk alleles can be confusing. Some of the analysis reports don't include risk alleles.
    I've noticed that there are discrepancies in which are risk and not. It gets even more confusing when I read some articles that don't jibe with others.

    Genetics analysis is inexact, researchers are estimating tendencies. We're looking for clues, patterns.

    Tinnitus is miserable.:ill: Luckily, mine stopped, but my husband still has it. ( He takes 5mg daily mb12.) He has familial hearing loss. We keep trying to make it stop, but I don't know what else to try. ( There was zinc, CoQ10, Ginkgo, etc.)
     
    roxie60 likes this.
  9. roxie60

    roxie60 Senior Member

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    I'm trying / have tried bioflavanoids (which once I read the label most was in stuff already taking so to me just another marketing spiel), CoQ10, B's (lots of em), multivit w/ zinc, white noise, fan, phone sleep apps like Lightning Bug). Sadly only way I can go to sleep is tv on which is not usually a good option for many reasons but it is all that has worked. Drs put me down for doing it, that watching tv not a good method, I tell them I'm not watching it, I put the same DVDs in and play them over and over, I'm not watching but once again they just dont listen - I found something that helps me get to sleep with tinnitus and they want to tell me I'm wrong. Tell ya waht medicos you find a 100% resolution for tinnitus and I'll turn the tv off.

    I feel for you husband and I'm glad yours stopped (becareful what meds you take cause mine use to stop when stopped certain meds but the last time I stopped what I was using when it started again appears to have done permanent damage). It is so annoying but really only understood by those that suffer with or have had it.
     
    Crux likes this.
  10. wordweaver27

    wordweaver27

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    Yes, I'm GG for TCN2. I edited my OP to add the Homozygous alleles. I forgot to mention originally that my information was based off of the MTHFRSupport report so all of my ++ that I listed are the risk alleles (nice reds that pop right off the page).

    Thank you for looking :)
     
    roxie60 likes this.
  11. wordweaver27

    wordweaver27

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    Yes, the TCN2 and GIF are popping out at me and may be a major key to the puzzle that I have become. And yes, there are a lot of them.

    Regarding MTR/MTRR, I still don't really get how that works, especially with MTHFR. I obviously need more B12. The question is, what kind?

    What's really interesting is that a lot of my heterozygous snps and quite a few of my homozygous are related to neural tube defects, cleft lip/palate and congenital heart disease. My second child had multiple congenital anomalies including cleft lip/palate and a heart defect, as well as a few others. Very intriguing and Makes me question having a third.
     
  12. roxie60

    roxie60 Senior Member

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    radio show link ???? Is Sterling doing a radio show?
     
  13. roxie60

    roxie60 Senior Member

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    (anyone notice this rs# is a palindrome?) - I had not until I saw your note - probably cause look at so many Rs#'s dont look for patterns.
     
  14. roxie60

    roxie60 Senior Member

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    double whammy on A1298C. and also TCN2 - You probably know - check your B12.

    Here is what I found on TCN2


    Transcobalamin II Function: Primary vitamin B12-binding and transport protein. Delivers cobalamin to cells; This gene encodes a member of the vitamin B12-binding protein family. This family of proteins, alternatively referred to as R binders, is expressed in various tissues and secretions. This plasma protein binds cobalamin and mediates the transport of cobalamin into cells. ; Homozyg TCN2 deficiency?; Effect of TCN2 766C>G on B12 cellular availability in renal disease; Increased TCN2 levels - related issues lower B12 levels, increased RA activity, renal activity; Possible risks with SNPs in methionine synthase ; http://www.wikigenes.org/e/gene/e/6948.html ; http://ghr.nlm.nih.gov/gene/TCN2 ; http://www.genecards.org/cgi-bin/carddisp.pl?gene=TCN2
     
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  15. roxie60

    roxie60 Senior Member

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    What I found for C3 (I am also GG and have asthma and allergies although asthma has improved later in life)


    Associated w/ asthma and common allergens; Age Related Macular Degeneration

    Here is another related C3 gene - http://www.snpedia.com/index.php/Rs2230199
     
  16. roxie60

    roxie60 Senior Member

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    Is it true that CC on a plus strand would be the same as GG on the minus strand?

    EG : rs2230201 G is risk alelle. I am CC on the plus strand and in SNPedia is shows GG as the risk alelle (minus strand).

    GG - >1.4x risk of lupus

    Wish I had $5 each time a Dr asked me if I had Lupus just looking at my face (there must b something about lupus and how ones face looks). Of course my blood test came back a year ago negative for lupus. Many years ago it came back Lupus suspect but not high enough titer...

    UPDATE: well now I'm not sure of the above, just found a SNP (rs2241394) that says GG on the minus but I'm GG on the plus strand per 23and Me. :mad::confused: just when I think I get it :confused:
     
  17. Sea

    Sea Senior Member

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    Yes
    So in this instance you have the risk allele
    Same principle applies. So for this one you you would be CC on the minus strand and not have the risk allele.

    It's easiest to get confused when the two allele choices are the ones that complement each other
     
    roxie60 likes this.
  18. Crux

    Crux Senior Member

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    Hi wordweaver;
    Sorry that your child has health conditions. It would be a good idea to have them checked too.
    NTDs are associated with MTHFR mutations, but B12 is also very important.

    Caledonia has provided a great many references in her signature that describe the importance of treating these snps. Thanks caledonia!

    Regarding the type of B12 and folate needed... It's difficult to say, when one is heterozygous for COMT. ( There are other snps that may indicate whether someone is sensitive to methyl groups. ) Caledonia and Valentijn are the experts here.

    I would definitely avoid folic acid, found in supplements, enriched and fortified foods. Folic acid is more bioavailable, but more difficult to convert and utilize. (It can become neurotoxic.)

    Methylcobalamin is easier to find, and less expensive. For some people, it is too stimulating, so they prefer Hydroxocobalamin.

    With MTHFR A1298C ++, methylfolate is usually recommended because it is much more difficult to convert folates to the active forms, with this snp.
     
  19. frenchmoxie

    frenchmoxie

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    I'm also homozygous for TCN2, but past testing has revealed normal levels of MMA.
     
  20. Crux

    Crux Senior Member

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    Yes, A couple of people that posted here also had normal, (low?), MMA.
    There still isn't a 'gold standard' test yet.

    In the case of MMA, here's an article by Kara Fitzgerald ND, who believes that the normal range for MMA is incorrect. ( similar to serum B12 range)

    This means alot of people are being missed.

    http://www.metametrixinstitute.org/...hrinking-Brain-A-Story-of-B12-Deficiency.aspx
     

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