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"no call" for all GSTT1 genes. What does this mean?

Discussion in 'Genetic Testing and SNPs' started by kday, Feb 15, 2013.

  1. kday

    kday Senior Member

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    This is weird. Why would this happen? It kinda freaked me out a bit.

    [​IMG]

    [​IMG]
  2. kday

    kday Senior Member

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    Ok, do I not have the gene? It says enzyme activity is absent in 20% of caucasians. Does this mean I wouldn't have any SNPs. Do I have a gene deletion? I'll be the first to say that I don't really understand this.

    Does anybody else get "no call" for all GSTT1 SNPs?

  3. Helen

    Helen Senior Member

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    Sweden
    GSTM1 deletion and/or GSTP1 polymorphisms seem to be more common among ME/CFS people according to Genovations (DetoxiGenomic) gene tests that I have received from people. Maybe it is the same with the GSTT1 . It would not surprise me.

    Are the GSTM1 and GSTP1 genes also analysed in the test from 23andme
    ?
  4. kday

    kday Senior Member

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    Yes, however, all of the SNPs are there for all 40 of GSTM1 and GSTP1 SNPs. 23andMe does not report my GSTT1 as a deletion (they say they don't regularly keep track of deletions), but instead says "no call" for all SNPs. However, I think it's logical that it is probably a deletion. But I sent in a support ticket asking them if it could be.
  5. Helen

    Helen Senior Member

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    Hi Kday,
    Did you get any reply from 23andme?
  6. frenchmoxie

    frenchmoxie

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    Yes, I've been waiting to see if 23andme got back with you on this issue. I didn't get a no-call for this, but just a straight up deletion I think.
  7. Sea

    Sea Senior Member

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    NSW Australia
    I have a "no call" for 12 out of the 14 snps tested for GSTT1. I've just assumed it's a deletion since it's not uncommon for there to be significant deletions in this gene.
  8. Mogwai

    Mogwai

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    Auckland, NZ
    Same here:

    GSTT1 - Absent*

    *It is likely that you are missing this gene and have a deletion. However, since this type of testing isn't technically designed to detect deletions, it isn't with 100% certainty.
    Valentijn likes this.
  9. Critterina

    Critterina Senior Member

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    Arizona, USA
    Me, too. I have rs11550605 TT and rs11550605 is AA. The rest are no call. Sea, Are these the same ones you have?
    In areas where I have an insertion or deletion, I get an I or D in my report, instead of A,C,G, or T.
  10. Sea

    Sea Senior Member

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    Yes, I have the same two snps - assuming you mean 11550605 TT and 11550606 AA. According to SNPedia these are both the ancestral allele, but according to the human gene compendium the 11550606 AA is the variant and is a missense mutation. I don't know which one is more reliable.
    http://www.genecards.org/cgi-bin/carddisp.pl?gene=GSTT1&snp=133#snp

    I got my 23andme results in March this year. How long have you had your results? They may have changed the way they report. I remember reading somewhere on their site that they would go back to no call results and update them as they got new information.

    I have some II and DD elsewhere in my report
    Critterina likes this.
  11. Critterina

    Critterina Senior Member

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    Arizona, USA
    I got my results late July (~26th). I just poked into 'browse' to respond to this post, though, so my no-calls were from their website the day I made the post.
    Sea likes this.
  12. aquariusgirl

    aquariusgirl Senior Member

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    no call here too, except for the 11550606 AA. Rich would be all over this...god bless him...
  13. Valentijn

    Valentijn Activity Level: 3

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    23andMe gives a lot of no calls on GSTT1 because they don't actually test most of the SNPs they have listed on it. If any results are present on the gene, then you have it. If literally all of them are missing, then you don't have it.
  14. Jackie M

    Jackie M

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    Illinois USA
    I got tested in July 2014 with the V4 chip. I have no call on all except 3 of the SNPs 23andMe shows for GSTT1.

    rs1130990: CC (less common than G but not rare)
    rs11550605: GT (occurs <.05%)
    rs2266636: CT (appears to occur < 1% looking at openSNP, but didn't come up in rare allele program, unsure)

    Here is a resource I hadn't seen before: Wolfram
    Last edited: Aug 14, 2014
  15. Valentijn

    Valentijn Activity Level: 3

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    If you have any SNPs on GSTT1, then you have the gene.

    23andMe lists a lot of SNPs on that gene, but usually just tests a few for most customers, hence they show a lot of no call results.

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