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The highly polymorphic DRD4 gene has a number of frequent functional variants in the populations [ 88].
Using this technology as a screening tool reveals tens to hundreds of genes harboring frequent functional variants affecting RNA expression in the human brain.
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The most frequent scenario, however, is that functional variants are mildly deleterious and, since purifying selection tends to avoid their fixation, the ratio of functional to neutral divergence between species is smaller than the analogous ratio for polymorphism.
In the discussion we provide our thoughts and literature analysis on why these genes have been reported as disease-associated despite being among the frequent genes to harbor rare functional variants.
One challenge in applying association methodology is to identify functional variants without analysing every polymorphism in a genomic region, which may be as frequent as 1/1000 base pairs in regions of the genome.
We identified 28 novel variants including potential functional variants in the intron region and one rare missense variant (R150S).
Heron, S. E. et al. Extended spectrum of idiopathic generalized epilepsies associated with CACNA1H functional variants.
Sontheimer, E.J. & Steitz, J.A. Three novel functional variants of human U5 small nuclear RNA.
Interference between the effects of multiple functional variants at a locus can even completely hide the nature of true causal variants for a non-trivial fraction of analyses60.
We did include the DAT1 VNTR35 because there are fewer functional variants and the major functional distinction is between the 9 and 10 base pair repeat.
Variants designated as non-functional in Findlay and colleagues' analysis generally corresponded with those annotated as deleterious in the database, and, reassuringly, nearly all functional variants corresponded with those annotated as benign.
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