Casp7 rs10553596 explains 44 non AD?

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J11
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Casp7 rs10553596 explains 44 non AD?

Postby J11 » Mon Jul 04, 2016 5:43 pm

The minor allele of rs10553596 appears to have Large importance for epsilon 44s, though not for 34s.
pan-caspase inhibitors might help those 44s without the right genotype.

Interestingly the frequency of the protective allele is much higher in African populations.

http://www.ncbi.nlm.nih.gov/pubmed/2735 ... t=Abstract
Last edited by J11 on Tue Jul 05, 2016 9:50 am, edited 2 times in total.

J11
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Re: Casp7 rs10553596 explains 44 non AD?

Postby J11 » Mon Jul 04, 2016 7:53 pm

Just wanted everyone to know that this one could be a real nail bitter.

I checked with The Broad. No proxies.
http://www.broadinstitute.org/mpg/snap/ldsearch.php

Checked the Exome file, not there.
Checked 23andme not on v3, though snpedia is reporting that it is on 23andme somewhere.

{Note: It seems that it is probably not on 23andme. Snpedia provided a link to 23andme: I thought
that this meant that the SNP would be on one of the gene chips, though this does not appear to be necessarily true.
Snpedia usually shows which specific gene chip a SNP is on. There are no 23andme gene chips showing that have this
SNP.}

Even checked the imputation file. Not there! Very unusual.
This is a fairly common SNP MAF=.29.
Not sure why it is so elusive.

I am sure a fair number on this thread who are 44 would be very interested in this genotype.
might have to go full genome to find out.
Last edited by J11 on Tue Jul 05, 2016 9:53 am, edited 1 time in total.

J11
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Re: Casp7 rs10553596 explains 44 non AD?

Postby J11 » Mon Jul 04, 2016 8:16 pm

Just double checked the exome file.
rs10553596 was not mentioned in the VCF file.

rs10553596 is right in the middle of exon 1 in the CASP7 gene.
When I looked at the pile-up, this SNP was pretty much right in the centre.
Appears almost certain that our loved one is wild type for this variant.

Matisse
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Re: Casp7 rs10553596 explains 44 non AD?

Postby Matisse » Tue Jul 05, 2016 12:30 am

It's not on the V4 chip either. I checked.

J11
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Re: Casp7 rs10553596 explains 44 non AD?

Postby J11 » Tue Jul 05, 2016 11:02 am

I continue to be quite surprised every time a new report emerges with large protective effects.
How is it that a common variant with such large benefits has not been found before?

It is now understood that there are likely no common variants left that have increase AD by a large amount.
What seems strange to me is why these common variants with large protective effects would not have been
found simply by thinking of the common SNP as producing a large increase in risk. Wouldn't risk and protection
be linked in this way in the large GWAS?

I'll be interested to see how many 44s on the forum might now consider doing an exome scan to find out their rs10553596 status.


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