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SNPs for Nitric Oxide Synthase (NOS3) - alternative(s) to Yasko's marker

Discussion in 'Genetic Testing and SNPs' started by nandixon, Sep 21, 2012.

  1. nandixon

    nandixon Senior Member

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    23andMe doesn't provide the SNP marker for dysfunction in the endothelial nitric oxide synthase (NOS3) enzyme that Yasko uses, i.e., D298E (rs1799983). They do however give data for some 30+ other SNPs, including rs2070744. (https://www.23andme.com/you/explorer/gene/?gene_name=nos3) This SNP, while not a proxy/substitute for Yasko's, appears to be functionally as important, and might suggest the need for ammonia support/neutralization where the risk allele is present. A number of other SNPs reported by 23andMe may be significant as well.

    So other people can check their results, here are the SNPs currently found on SNPedia for NOS3 (http://www.snpedia.com/index.php/NOS3) with my personal results and the "normal" (common) alleles in parentheses. Where I'm homozygous for the risk allele (+/+) I've also made some notations and given the percentage frequency of occurrence in the general population using the data from openSNP. I think I double-checked all my homozygous results against the actual research articles that SNPedia cited, so hopefully this is pretty accurate.

    I had delayed looking into my NOS3 results because when I first checked them, all 30+ were showing as homozygous and so I figured I was fairly safe. That was not a good assumption:

    rs11771433 No Data
    rs1799983 No Data (Yasko marker D298E)
    rs1800779 +/+ GG (AA) (associated w/ hypoxic-ischemic encephalopathy; 17% frequency)
    rs180783 +/+ AA (TT) (proxy for rs4496877 - see below; 17% frequency)
    rs2070744 T(-786)C +/+ CC (TT) (major issues w/ ammonia detoxification if similar to D298E => take yucca with meals and activated charcoal at bedtime; significantly lower promoter of endothelial NOS => reduced nitric oxide production; increased risk of rheumatoid arthritis, bladder cancer, progression of prostate cancer; 13% frequency)
    rs3918188 -/- CC (CC)
    rs3918226 -/- CC (CC)
    rs3918227 -/- CC (CC)
    rs4496877 +/+ AA (GG) (significantly increased nephropathy risk in type-1 diabetes; 13% frequency)
    rs743507 +/+ CC (TT) (significant association w/ diabetic nephropathy; 7% frequency)
    rs7830 -/- GG (TT)
     
  2. merylg

    merylg Senior Member

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    Sydney, NSW, Australia
    [​IMG] NOS3 150689397 rs1800783 A or T AT
    [​IMG] NOS3 150689943 rs1800779 A or G AG
    [​IMG] NOS3 150689970 rs2243311 C or T CC
    [​IMG] NOS3 150690079 rs2070744 C or T CT
    [​IMG] NOS3 150690176 rs3918226 C or T CC
    [​IMG] NOS3 150695726 rs1549758 C or T CC
    [​IMG] NOS3 150699877 rs2853792 A or G AA
    [​IMG] NOS3 150700946 rs3918227 A or C CC
    [​IMG] NOS3 150702219 rs3918184 C or T CC
    [​IMG] NOS3 150702331 rs3918185 A or G GG
    [​IMG] NOS3 150702432 rs3918186 A or T AT
    [​IMG] NOS3 150702591 rs3918187 A or G AA
    [​IMG] NOS3 150702781 rs3918188 A or C CC
    [​IMG] NOS3 150703041 rs2566511 C or T no call
    [​IMG] NOS3 150703130 rs3918229 C or T CC
    [​IMG] NOS3 150703242 rs2853795 A or G AG
     
  3. merylg

    merylg Senior Member

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    Sydney, NSW, Australia
    [​IMG] NOS3 150703414 rs2566513 G or T TT
    [​IMG] NOS3 150703915 rs2853796 G or T GT
    [​IMG] NOS3 150704843 rs891511 A or G AA
    [​IMG] NOS3 150705413 rs3918230 C or G GG
    [​IMG] NOS3 150705842 rs3918196 A or G GG
    [​IMG] NOS3 150706383 rs753482 A or C AA
    [​IMG] NOS3 150706640 rs3918232 A or G GG
    [​IMG] NOS3 150706915 rs743506 A or G AA
    [​IMG] NOS3 150707117 rs3730009 C or T TT
    [​IMG] NOS3 150707344 rs3918201 G or T GG
    [​IMG] NOS3 150707488 rs743507 C or T TT
    [​IMG] NOS3 150707943 rs867225 A or G GG
    [​IMG] NOS3 150708089 rs891512 A or G GG
    [​IMG] NOS3 150708302 rs1808593 G or T TT
    [​IMG] NOS3 150708923 rs3918235 A or G GG
    [​IMG] NOS3 150709291 rs3918236 A or G GG
    [​IMG] NOS3, ATG9B 150709571 rs7830 G or T TT
    [​IMG] NOS3, ATG9B 150709904 rs3918208 C or T TT
    [​IMG] NOS3, ATG9B 150710907 rs3918211 C or T TT
    [​IMG] intergenic 150680506 rs4496877 G or T GT
     
  4. nandixon

    nandixon Senior Member

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    Thanks Meryl! I've combined our total 23andMe results together below (mine first, your's second in each line) and corrected two transcription errors made in my original post above. [Where I typed "rs4496877 +/+ AA (GG)," the "AA" should have been TT. And where I typed "rs7830 -/- GG (TT)," the "TT" should have been GG.]

    NOS3:
    rs1800783 T>A AA (++), AT (+-) fn1
    rs1800779 A>G GG (++), AG (-+) fn2
    rs2243311 C>T CC (--), CC (--)
    rs2070744 T>C CC (++), CT (+-) fn3
    rs3918226 C>T CC (--), CC (--)
    rs1549758 C>T TT (++), CC (--) fn4
    rs2853792 A>G GG (++), AA (--) fn5
    rs3918227 C>A CC (--), CC (--)
    rs3918184 C>T CC (--), CC (--)
    rs3918185 G>A GG (--), GG (--)
    rs3918186 A>T AA (--), AT (-+)
    rs3918187 A>G AA (--), AA (--)
    rs3918188 C>A CC (--), CC (--)
    rs2566511 C>T CC (--), no call
    rs3918229 C>T CC (--), CC (--)
    rs2853795 A>G AA (--), AG (-+)
    rs2566513 T>G TT (--), TT (--)
    rs2853796 G>T GG (--), GT (-+)
    rs891511 G>A GG (--), AA (++) fn6
    rs3918230 G>C GG (--), GG (--)
    rs3918196 G>A GG (--), GG (--)
    rs753482 A>C CC (++), AA (--) fn7
    rs3918232 G>A GG (--), GG (--)
    rs743506 A>G GG (++), AA (--) fn8
    rs3730009 T>C TT (--), TT (--)
    rs3918201 G>T GG (--), GG (--)
    rs743507 T>C CC (++), TT (--) fn9
    rs867225 G>A GG (--), GG (--)
    rs891512 G>A AA (++), GG (--) fn10
    rs1808593 T>G GG (++), TT (--) fn11
    rs3918235 G>A GG (--), GG (--)
    rs3918236 G>A GG (--), GG (--)
    rs7830 G>T GG (--), TT (++) fn12
    rs3918208 T>C TT (--), TT (--)
    rs3918211 T>C TT (--), TT (--)
    rs4496877 G>T TT (++), GT (-+) fn13

    Footnotes (fn):
    1 Proxy for rs4496877 (see fn13); 17% frequency
    2 Associated w/ hypoxic-ischemic encephalopathy; 17% freq
    3 Major issues w/ ammonia detoxification if similar to Yasko's D298E (rs1799983) => might take yucca with meals and activated charcoal at bedtime; significantly lower promoter of endothelial NOS => reduced nitric oxide production; increased risk of rheumatoid arthritis, bladder cancer, progression of prostate cancer; 13% freq
    4 Possible association w/ Parkinson's Disease; increased susceptibility to steroid-induced osteonecrosis of femoral head (ONFH); may be linked with Yasko's marker; 8% freq
    5 Significance?; 19% freq
    6 Significance?; 13% freq
    7 High risk of restenosis and cardiovascular events in type-2 diabetes; 4% freq
    8 Relation in migraine; 9% freq
    9 Significant association w/ diabetic nephropathy; 7% frequency
    10 Associated w/ hypertension in type-2 diabetes; 4% freq
    11 Associated w/ hypoxicischemic encephalopathy and acute mountain sickness; 7% freq
    12 Significant association w/ "ABI" marker for peripheral arterial disease; 11% freq
    13 Significantly increased nephropathy risk in type-1 diabetes; 13% freq
     
    roxie60 likes this.
  5. roxie60

    roxie60 Senior Member

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    is 'no call' when they dont give you letters for the SNP just -- ?
     
  6. roxie60

    roxie60 Senior Member

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    Hi nan, I was wondering are the footnotes in relation to the 'common' SNP or the 'uncommon' SNPs?

    e.g. 13Significantly increased nephropathy risk in type-1 diabetes; 13% freq - this applies to the 'uncommon variety which would be TT, am I reading/interpreting this correctly?

    what is the source for your footnotes?
     
  7. roxie60

    roxie60 Senior Member

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    Note as of 1/9/2013 there are 35 NOS3 SNPs from 23andMe (incase this changes overtime as we have seen with other SNPs).
     
  8. roxie60

    roxie60 Senior Member

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    I have added mine to the list. Also added the tracking convention used in other threads I think is helpful. I have copied a dup of the list cause my OCD is kicking in and I like to see things line up as best possible. Use which ever one you want to add new data. I wonder if we should put 'common' = 1 with orientation in parentheses? Just an organization suggestion, did not change what you started nan, just addded mine and the tracking row. My values are in red.

    1=nandixon, 2=merylg, 3=roxie60

    NOS3:
    rs1800783 T>A... AA (++), AT (+-) , TT(--)fn1
    rs1800779 A>G... GG (++), AG (-+), AA(--) fn2
    rs2243311 C>T.... CC (--), CC (--), CC(--)
    rs2070744 T>C.... CC (++), CT (+-), (--, no call?) fn3
    rs3918226 C>T.... CC (--), CC (--), CC (--)
    rs1549758 C>T.... TT (++), CC (--), CC (--) fn4
    rs2853792 A>G... GG (++), AA (--), AA (--), fn5
    rs3918227 C>A... CC (--), CC (--), CC (--),
    rs3918184 C>T.... CC (--), CC (--), CT (-+),
    rs3918185 G>A... GG (--), GG (--), GG(--)
    rs3918186 A>T.... AA (--), AT (-+), AA(--)
    rs3918187 A>G... AA (--), AA (--), AA(--)
    rs3918188 C>A... CC (--), CC (--), AC(+-)
    rs2566511 C>T.... CC (--), no call, CT(-+)
    rs3918229 C>T.... CC (--), CC (--), CC(--)
    rs2853795 A>G... AA (--), AG (-+), AG(-+)
    rs2566513 T>G.... TT (--), TT (--), TT(--)
    rs2853796 G>T.... GG (--), GT (-+), TT(--)
    rs891511 G>A..... GG (--), AA (++), AG(+-) fn6
    rs3918230 G>C... GG (--), GG (--), GG (--)
    rs3918196 G>A... GG (--), GG (--), GG (--)
    rs753482 A>C..... CC (++), AA (--), AA(--) fn7
    rs3918232 G>A... GG (--), GG (--), GG(--)
    rs743506 A>G..... GG (++),AA (--), AA(--) fn8
    rs3730009 T>C.... TT (--), TT (--), TT(--)
    rs3918201 G>T.... GG (--), GG (--), GG(--)
    rs743507 T>C...... CC (++),TT (--), TT(--) fn9
    rs867225 G>A..... GG (--), GG (--), GG(--)
    rs891512 G>A..... AA (++),GG (--), GG(--) fn10
    rs1808593 T>G.... GG (++),TT (--), TT(--) fn11
    rs3918235 G>A.... GG (--), GG (--), GG(--)
    rs3918236 G>A.... GG (--), GG (--), GG(--)
    rs7830 G>T.......... GG (--), TT (++), GT(-+) fn12
    rs3918208 T>C.... TT (--), TT (--), TT(--)
    rs3918211 T>C.... TT (--), TT (--), TT(--)
    rs4496877 G>T.... TT (++),GT (-+), GG(--) fn13

    Footnotes (fn):
    1 Proxy for rs4496877 (see fn13); 17% frequency
    2 Associated w/ hypoxic-ischemic encephalopathy; 17% freq
    3 Major issues w/ ammonia detoxification if similar to Yasko's D298E (rs1799983) => might take yucca with meals and activated charcoal at bedtime; significantly lower promoter of endothelial NOS => reduced nitric oxide production; increased risk of rheumatoid arthritis, bladder cancer, progression of prostate cancer; 13% freq
    4 Possible association w/ Parkinson's Disease; increased susceptibility to steroid-induced osteonecrosis of femoral head (ONFH); may be linked with Yasko's marker; 8% freq
    5 Significance?; 19% freq
    6 Significance?; 13% freq
    7 High risk of restenosis and cardiovascular events in type-2 diabetes; 4% freq
    8 Relation in migraine; 9% freq
    9 Significant association w/ diabetic nephropathy; 7% frequency
    10 Associated w/ hypertension in type-2 diabetes; 4% freq
    11 Associated w/ hypoxicischemic encephalopathy and acute mountain sickness; 7% freq
    12 Significant association w/ "ABI" marker for peripheral arterial disease; 11% freq
    13 Significantly increased nephropathy risk in type-1 diabetes; 13% freq
     
  9. roxie60

    roxie60 Senior Member

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    not sure what happened to formatting, maybe I hit a limit. Will try and edit post to fix formatting where last few SNPs ended up in one line
     
  10. roxie60

    roxie60 Senior Member

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    Here is the list without orientation (although I think that is important to understand and make observations) to make room for other members data, if you want or continue to use format with orientation.

    1=nandixon, 2=merylg, 3=roxie60

    NOS3:
    rs1800783 T>A... AA, AT, TT, fn1
    rs1800779 A>G... GG, AG, AA, fn2
    rs2243311 C>T.... CC, CC, CC,
    rs2070744 T>C.... CC, CT, (--, no call?) fn3
    rs3918226 C>T.... CC, CC, CC,
    rs1549758 C>T.... TT, CC, CC, fn4
    rs2853792 A>G... GG, AA, AA, fn5
    rs3918227 C>A... CC, CC, CC,
    rs3918184 C>T.... CC, CC, CT,
    rs3918185 G>A... GG, GG, GG,
    rs3918186 A>T.... AA, AT, AA,
    rs3918187 A>G... AA, AA, AA,
    rs3918188 C>A... CC, CC, AC,
    rs2566511 C>T.... CC, no call, CT,
    rs3918229 C>T.... CC, CC, CC,
    rs2853795 A>G... AA, AG, AG,
    rs2566513 T>G.... TT, TT, TT,
    rs2853796 G>T.... GG, GT, TT,
    rs891511 G>A..... GG, AA, AG, fn6
    rs3918230 G>C... GG, GG, GG,
    rs3918196 G>A... GG, GG, GG,
    rs753482 A>C..... CC, AA, AA, fn7
    rs3918232 G>A... GG, GG, GG,
    rs743506 A>G..... GG, AA, AA, fn8
    rs3730009 T>C.... TT, TT, TT,
    rs3918201 G>T.... GG, GG, GG
    rs743507 T>C...... CC,TT, TT, fn9
    rs867225 G>A..... GG, GG, GG,
    rs891512 G>A..... AA,GG, GG, fn10
    rs1808593 T>G.... GG,TT, TT, fn11
    rs3918235 G>A.... GG, GG, GG,
    rs3918236 G>A.... GG, GG, GG,
    rs7830 G>T.......... GG, TT, GT, fn12
    rs3918208 T>C.... TT, TT, TT,
    rs3918211 T>C.... TT, TT, TT,
    rs4496877 G>T.... TT,GT, GG, fn13

    Footnotes (fn):
    1 Proxy for rs4496877 (see fn13); 17% frequency
    2 Associated w/ hypoxic-ischemic encephalopathy; 17% freq
    3 Major issues w/ ammonia detoxification if similar to Yasko's D298E (rs1799983) => might take yucca with meals and activated charcoal at bedtime; significantly lower promoter of endothelial NOS => reduced nitric oxide production; increased risk of rheumatoid arthritis, bladder cancer, progression of prostate cancer; 13% freq
    4 Possible association w/ Parkinson's Disease; increased susceptibility to steroid-induced osteonecrosis of femoral head (ONFH); may be linked with Yasko's marker; 8% freq
    5 Significance?; 19% freq
    6 Significance?; 13% freq
    7 High risk of restenosis and cardiovascular events in type-2 diabetes; 4% freq
    8 Relation in migraine; 9% freq
    9 Significant association w/ diabetic nephropathy; 7% frequency
    10 Associated w/ hypertension in type-2 diabetes; 4% freq
    11 Associated w/ hypoxicischemic encephalopathy and acute mountain sickness; 7% freq
    12 Significant association w/ "ABI" marker for peripheral arterial disease; 11% freq
    13 Significantly increased nephropathy risk in type-1 diabetes; 13% freq
     
  11. roxie60

    roxie60 Senior Member

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    I think it is important that we add 'common and orientation as the first entry in all the SNPs data we are trying to capture so people at a glance can see where they stand, what do you think?
     
  12. roxie60

    roxie60 Senior Member

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    Dont know if this effort will amount to much. It seems we should only record data from 23andMe since there is a risk other data is using info from different location of the gene. Feels like a rabbit hole or back hole. I know we want answers but wondering if we are the ones that will figure it all out...hum
     
  13. Leon

    Leon

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    Thank you for posting this nandixon - I'm homozygous for the C allele.

    I can find reference to rheumatoid arthritus (which is very interesting, given my maternal grandmother was housebound from a young age due to this) and cardiovascular risk; but I can't find any reference to ammonia issues. I'm certain I have ammonia issues (e.g. I can't currently eat animal/fish protein or ingest glutamine). Have you had any more thoughts about whether this is a useful marker for the rs1799983 SNP?
     
  14. roxie60

    roxie60 Senior Member

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    Does '--' on that SNP mean I dont have it or they couldnt figure it out?
     
  15. Valentijn

    Valentijn Activity Level: 3

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    Yes :p

    It can mean either of those. Or that the chip they used to process your sample doesn't test for that SNP.
     

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