1. Guest, the 'News in Brief' for the week beginning 21st September 2020 is here.
    Dismiss Notice
  2. Welcome! To read the Core Purpose and Values of our forum, click here.
    Dismiss Notice

ABCC6 and pathogenic SNPs

Discussion in 'General ME/CFS News' started by mariovitali, Mar 22, 2020.

Tags:
  1. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362
    Dear All,


    I am preparing an email to a number of researchers for the gene called ABCC6. Looking for further information regarding its function, one can find that it is a gene responsible for Pseudoxanthoma Elasticum (PXE) but the techniques i use suggest otherwise, meaning it should be further investigated.

    Interestingly, a website discussing about PXE shows the following information in its FAQ :


    PXE snapshot.png


    Please report on any of the SNPs shown below, despite the mention that an epidemiological study has been made between 1997 and 2001.


    Here is the list of the SNPs. :

    https://www.ncbi.nlm.nih.gov/snp/?term=rs2238472
    Pathogenic

    rs59513011 - Risk T
    rs2606921 - Risk A
    rs55778939 : Risk T
    (New addition) rs58668703 - Risk T
    (New addition) rs41278172 - Risk A
    Likely benign :

    rs72657698 : Risk C



    Thank you for your help.
     
    Last edited: Mar 23, 2020
    ukxmrv, merylg, ScottTriGuy and 3 others like this.
  2. Kitty

    Kitty Senior Member (Voting Rights)

    Messages:
    1,035
    Likes Received:
    7,661
    I only have one showing up on this gene, rs58668703, which is assessed as rare, clinically significant, and pathogenic. However, PXE is a recessive disease and my type's heterozygous, so whilst I might be a carrier, I don't have symptoms.
     
    ScottTriGuy and mariovitali like this.
  3. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362
    For the record :


    Here are the results from 5 out 7 patients for whom i have full gemome data


    rs2238472 : p1,p2,p3
    rs59513011 : p1
    rs2606921 : p1
    rs72657698 : p3,p4,p5
    rs55778939 : p4
     
    merylg, ScottTriGuy and Kitty like this.
  4. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362
    Thank you so much for this. Pathogenic + rare. I added it to the original post

    As disucssed in my initial post, this gene may be much more important than what it seems.
     
    merylg, ScottTriGuy and Kitty like this.
  5. ScottTriGuy

    ScottTriGuy Senior Member (Voting Rights)

    Messages:
    654
    Likes Received:
    5,849
    Location:
    Toronto
    I didn't find any of the 6 you listed.
     
    Kitty, merylg and mariovitali like this.
  6. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362

    Did you look for this information at full genome data (e.g DanteLabs) or you looked it up on 23andme data?
     
    Last edited: Mar 22, 2020
    Kitty and ScottTriGuy like this.
  7. ScottTriGuy

    ScottTriGuy Senior Member (Voting Rights)

    Messages:
    654
    Likes Received:
    5,849
    Location:
    Toronto
    On my 23andme / Genetic Genie.
     
    Kitty and mariovitali like this.
  8. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

    Messages:
    807
    Likes Received:
    5,418
    Some info from NIH site about this gene.
    https://ghr.nlm.nih.gov/gene/ABCC6#
     
    Kitty and mariovitali like this.
  9. wigglethemouse

    wigglethemouse Senior Member (Voting Rights)

    Messages:
    807
    Likes Received:
    5,418
    Please, please, please check OpenSNP and dBSNP for allele and genotype frequency. Cross reference with kaviar frequency and CADD score. Provide links to ClinVar. rs2238472 for example has an allele frequency of 25% (dnSNP) and a genotype frequency of 46%=CT+TT (OpenSNP). This is in line with the 3 out of 7 that you quote in your small sample.

    If you do not get your facts and analysis 200% validated researchers may tune out your future emails and ignore you.
     
    Kitty and mariovitali like this.
  10. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362
    Right, the likely benign one. Thank you @wigglethemouse i will remove it.
     
    wigglethemouse and Kitty like this.
  11. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362
    @wigglethemouse

    I forgot to write that a prominent ME researcher has previously identified ABCC6 SNPs to ME patients.
     
  12. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362

    It's possible that these SNPs are not analysed from 23andme. Perhaps someone can confirm.
     
    ScottTriGuy and Kitty like this.
  13. Kitty

    Kitty Senior Member (Voting Rights)

    Messages:
    1,035
    Likes Received:
    7,661
    None of these (including the newly-added one that came from my WGS) appear in my 23andMe data from 2017.

    ETA: the 'likely benign' rs72657698 does appear, but in my case is not genotyped.
     
  14. Ravn

    Ravn Senior Member (Voting Rights)

    Messages:
    1,106
    Likes Received:
    9,240
    I don't have the snps on your list (Dante) but I do have some others on the ABCC6 gene.
    Have attached screenshot of list, in case it's of any use (note that 1 snp is listed twice, once as pathogenic, once as benign :confused:).

    snps ABCC6.JPG
     
    mariovitali likes this.
  15. mariovitali

    mariovitali Senior Member (Voting Rights)

    Messages:
    425
    Likes Received:
    2,362
    rs41278172 is actually pathogenic according to the DBSNP and should be added to the list on the first post.

    Thank you!
     
    ukxmrv and Ravn like this.

Share This Page