The 12th Invest in ME Conference, Part 1
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Snps on the OTC gene Rs4621959 Rs5963418 Rs5963419

Discussion in 'Genetic Testing and SNPs' started by sleepingbeautycan, May 9, 2016.

  1. sleepingbeautycan

    sleepingbeautycan

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    I've been fascinated by the CBS effect on ammonia debate and in my research it occurred to me that maybe there is a small defect on a urea cycle gene that works with the CBS gene causing problems. My hypothesis is that there is a slow down in the urea cycle converting ammonia to urine and that coupled with CBS increasing the amount of ammonia. Does this make sense, even if you disagree with Yasko?

    So I went through every 23andme OTC gene on SNPedia and came up with homozygous ancestral every time. I think that this makes sense because it seems like a person with a snp in a heavily researched urea cycle location would probably not make it to adulthood. So then I looked for heterozygous alleles especially in locations that had not been researched at all.

    So, for me I came up with three:
    Rs4621959 Wild:A 30% MAF (very common with no studies)
    Rs5963418 Wild:A 4% MAF (relatively rare with no studies)
    Rs5963419 Wild:T 36% MAF (increasingly common)

    So I am wondering if anyone else has either of these heterozygous alleles? Do you think you have a problem with ammonia? Did you feel anxious when you went on MeFolate or MeB12?

    They may have absolutely no effect on anything. It is just something that I am really interested in and wondering if anyone has any info.
     
  2. ahmo

    ahmo Senior Member

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    I have all 3. And I have ammonia issues. I had transient anxiety sometimes when I increased folate. It was more like euphoria, as Fred described it. But could include breathlessness.

    Rs4621959: GG
    Rs5963418: GG
    Rs5963419: CT
     
  3. Oci

    Oci Senior Member

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    I have the same as Ahmo. I don't know what "wild" means or "ancestral". I don't think I have ammonia issues.
     
  4. sleepingbeautycan

    sleepingbeautycan

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    Sorry, I used those terms because some of the others on here are careful on their terminology. What I mean by the wild type is *usually* the one that is the problem. Ancestral type is the one that most people have and is *usually* the safer one. So if you have the same as Ahmo, you have:

    Rs4621959: GG
    Rs5963418: GG
    Rs5963419: CT

    The wild type in Rs4621959 is an A, and since neither of you have that genetic letter you don't have that genetic mistake. The wild type for Rs5963418 is also A and again since you have GG you don't have that problem either.

    For Rs5963419, T is the wild type. And you have that as a genetic change from normal. Thank you @ahmo and @Oci for responding.

    As well if you are interested the MAF percentage is the number of times that wild type shows up in 100 chances. So 36% means that 36/100 letters will be the wild type. So it is fairly common.
     
  5. sleepingbeautycan

    sleepingbeautycan

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    It is good that it doesn't seem to be stopping you from taking your Mefolate!! Thanks for taking time to respond.
     
  6. Oci

    Oci Senior Member

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    Now I am very confused! According to snpedia https://www.snpedia.com/index.php/Glossary

    Wild-type: For a given SNP, allele, genotype or gene, the form that was either first discovered or is the most common is considered the reference against which all other forms are compared. This reference form is called the wild-type form.
     
  7. alicec

    alicec Senior Member

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    Australia
    Wildtype and ancestral are the same thing, the original allele in a population. A changed allele is a variant. It can't be assumed that this is "risk", it may or may not be, it may be beneficial.
     
    Valentijn likes this.
  8. sleepingbeautycan

    sleepingbeautycan

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    You are right!! I am learning more every day. I am sorry to confuse you, but welcome to the club (we like to refer to ourselves as the chronically confused chromosome club -- membership is free)

    Yes, that is true but isn't it true that if the variant has any clinical effect it is negative? There are some that are protective but not many. And a lot are beneficial in some circumstances and negative in others.

    Thank you so much for correcting me.
     

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