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Assume that a read aligns to multiple pseudogenomes that straddle an informative variant caused by a SNP.
A variant caused by a G-to-A transition at codon 158 of the COMT gene, results in a valine-to-methionine substitution [ 32].
It is a rare complication of HIV, and while the symptoms can be self-limited, a rapidly progressive variant caused by cytomegalovirus infection of peripheral nerves has been described in the setting of advanced immunosuppression.
Otherwise, G6PD Mahidol is a common deficient variant caused by a (163 glycine-serine mutation that occurs in about 163 glycine-serine in populations across Southeast Asia [ 7, 8].
Epidemiologically, there are two main variants of AD, a rare familial early-onset variant, caused by mutations in amyloid precursor protein (APP), presenilin 1 (PSEN1) or presenilin 2 (PSEN2), and a sporadic late-onset variant, representing 95% of cases and for which only one gene, APOE, has been clearly associated as a risk factor (Querfurth et al., 2010).
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Mannstadt M, Magen D, Segawa H, Stanley T, Sharma A, Sasaki S, Bergwitz C, Mounien L, Boepple P, Thorens B, Zelikovic I, Jüppner H. Fanconi-Bickel syndrome and autosomal recessive proximal tubulopathy with hypercalciuria (ARPTH) are allelic variants caused by GLUT2 mutations.
In our approach, we used a two-part, complementary method to identify variants caused by MMC treatment in C. elegans.
In addition, these methods cannot follow the exponential increase in the number of newly discovered protein sequences or their variants, caused by improved sequencing technologies.
Using a file of amino-acid variants caused by the SNPs, one can identify which of the SNPs leads to a predicted change in protein structure.
This was recently shown for other dominantly inherited Charcot Marie Tooth variants caused by mutations in TRPV4 and GDAP1 (Zimon et al., 2010, 2011).
The most frequent opa alleles, wild-type opa31 and opa32, also have the most derived variants caused by single synonymous substitutions at the nucleotide sequence level.
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