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All 33 variants were missense variants and affected 173 alleles.
In the discovery cohort (n=186), a total of 206 different sequence alterations were recorded in the exons and intron exon boundaries of USH2A; 88 variants were missense, coding insertions/deletions or splice site changes.
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Only a small portion of these variants is missense.
Similarly, since many mitochondrial variants are missense variants, evidence criteria for truncating variants will likely not be helpful.
Of the identified variants, 6 were missense, 1 was an in-frame deletion, and 5 were LoF variants (see Additional file 1: Table S2).
Seven of the variants identified were missense changes, six in CTNNA3 and one in LRRTM3.
Of these 15 common variants, seven were missense changes and eight synonymous changes, and only one, rs1801516 (encoding an Asp1853Gln change), had a MAF greater than 5%.
Of the twenty-three likely benign variants five were intronic, 13 were synonymous and 5 were missense variants.
Of them, six were missense variants and two were frameshift-causing variants (Table 1).
Eight of the changes were missense variants, six were silent changes, and twenty of the variants took place in introns, 5'UTR, or 3'UTR regions.
In this study, the term "functional variants" refers to variants that are missense, nonsense or fall within a splice site window (see below for specifics).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com