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Lactase Persistence Variants

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  • Lactase Persistence Variants

    You may already be aware of this, but if you all are interested in checking your Family Finder and other autosomal DNA raw data for the lactase persistence variants, I am posting a table of the two most common LP variants among Europeans and the descendants of Europeans. Here's how you do that: Download your Family Finder raw data. Open the file using 7-Zip or WinZip or some similar program. Hold down the ctrl key in the lower left corner of your keyboard and type the letter f. A Find box will open up in the upper right of your screen. Type the rs (RefSNP) number of the LP variant you're checking on in the box and click the down arrow. That variant will be highlighted. Check to see if you have at least one copy of the risk allele. If you do, you are a carrier of that variant. You might have two copies of the variant. That's what I have for both. You can also check your AncestryDNA and 23andMe raw data for the variants. The table below shows the two most common LP variants.

    If you have 23andMe test results, checking for LP variants is really easy. Just go to your 23andMe homepage. Click on the down arrow next to your name in the upper right and then on Browse Raw Data. Type the rs (RefSNP) number in the search box and then type the enter key. Again, if you have at least one risk allele, you're a carrier of that LP variant.

    Lactase persistence is the ability to continue producing the enzyme lactase after childhood. Lactase enables one to digest the milk sugar lactose. Lactase persistence is the opposite of lactose intolerance. Sometimes one can be a carrier of an LP variant and still be lactose intolerant due to allergies or other causes, but most of the time LP variants impart the ability to continue consuming milk and other dairy products beyond childhood without difficulty.

    The NCBI web site here mentions C as a risk allele for rs4988235 in addition to A, but I've never heard of that. As far as I know, the risk allele is A, but I thought I would mention it.

    European Lactase Persistence Variants Table.jpg

  • #2
    There are some interesting lactase persistence frequency maps at the site at the link below:

    Interactive Lactase Persistence Maps


    • #3
      Just curious: Did anyone here check his or her LP variants after reading the first post above? How'd that go?


      • #4
        I downloaded the paper from your link in your May 21 post, in order to enlarge the maps. The additional SNPs for lactase persistence in that study were, as labeled in the legend of figure 4:
        -14990 T>G ss820486563
        -13907 C>G rs41525747
        -13495 C>T rs4954490
        -13915 T>G rs41380347
        -13910 C>T rs4988235
        -14010 G>C rs145946881

        The two SNPs of the above list that are associated with Europe on the Fig. 4 map are in bold; one (rs4988235) is shown in the two Stevo listed, the other (rs4954490) in bold is not in his list. In addition to the two SNPs that Stevo listed, I also checked for rs4954490, but it didn't show up in any 23andMe v. 3, Ancestry (for me only, in 2017) or FTDNA results from kits processed in 2013-2014.

        Results from my kits and other kits that I manage (all of European ancestry):

        Person and at which company they tested SNP SNP
        rs4988235 rs182549
        23andMe v. 3 chip:
        KATM AA TT
        Father AG CT
        Family Finder (whatever chip used in 2013-2014):
        My maternal Uncle AG not found
        My maternal Aunt AG TC
        Father's sister (my paternal aunt) AA TT
        Paternal 1st cousin of father & aunt AA TT

        I do ingest dairy products regularly, and only have digestive problems when the fat content is high. I don't recall my father or his sister having issues with lactase intolerance. Their paternal first cousin has all Irish ancestry. My paternal side has Irish, German, and Swiss ancestry.

        My mother never did DNA testing, but we can see that I must have received my second A and T from her. Two of her then-still-living siblings have tested at FTDNA, though: her brother and one of her sisters. My maternal side is of Greek and Maltese ancestry.


        • #5
          I’ll have to check my parents’ Family Finder raw data again to find out whether they were homozygous or heterozygous, but obviously they were carriers of both the variants I listed in the post that started this thread, or I wouldn’t be homozygous for both of them like I am.

          I only listed the two most common European variants, although, as KATM pointed out, there are other LP variants.
          Last edited by Stevo; 3 October 2022, 10:29 AM.