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Glycogen Storage Disease SNPs

Discussion in 'Genetic Testing and SNPs' started by Valentijn, Jan 13, 2014.

  1. Valentijn

    Valentijn Activity Level: 3

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    @Radio asked me about how these are looking for us, so here's the 23andMe results for 12 ME/CFS patients and 12 controls.

    A purple box means that the genotype is usually prevalent in less than 1% of the population, red = 1 - 2.5%, orange = 2.5 - 5%, and yellow = 5 - 10%. SNPs with no variation for patients and controls are not shown, nor SNPs with no uncommon genotypes, nor duplicate SNPs which are always identical to other SNPs which are shown.

    SLC2A.gif

    PHK-PFK.gif

    glycogen_misc.gif

    Totals are weighted based on rare genotypes are: purple = x10, red = x5, orange = x2, and yellow = x1. Totals are shown for patients and controls as a group, as well as the ratio for the patient group compared to the control group. Thus a ratio greater than 1 indicates more rare genotypes for the patients, and a ratio of less than 1 indicates more rare genotypes for controls.

    Overall there is not a big difference, with a weighted total of 297 for patients and 242 for controls, resulting in a ratio of 1.2. Some exceptions are the SLC2A genes, with a ratio of 1.4, mostly due to increased rare genotypes for patients in SLC2A9 (1.7) , SLC2A11 (2.2), and SLC2A12 (2.0). SLC2A9 was especially interesting, since there was a lot of research into those SNPs regarding uric acid levels (high in gout and metabolic syndromes, low in MS or due to mineral deficiencies). A lot of us have alleles associated with lower-than-normal levels of uric acid, some as a missense mutation.

    GYS2 also had quite a few more rare allele for patients, with a ratio of 3.2 This includes a heterozygous pathogenic missense known to cause hypoglycemia and ketonuria when compound heterozygous.

    The SNPs which have research available regarding their impact are bolded, underlined, and italicized. The description and links to that research are at:
    G6PC2 rs560887 TT = lower glucose
    GYS2 i5002300 (rs121918424) G = pathogenic missense mutation, http://omim.org/entry/138571#0006
    SLC2A9 rs16890979 T = lower uric acid : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2779583/
    SLC2A9 rs734553 G = lower uric acid : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683940/
    SLC2A9 rs737267 T = lower uric acid : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2657564/
    SLC2A9 rs12498742 G = lower uric acid : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683940/
    SLC2A9 rs7442295 GG = lower uric acid : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253977/
    PFKP rs6602024 AA = 1.81+ BMI : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1934391/ , AG = higher BMI : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2795983/
     
    merylg, Radio and Waverunner like this.

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