In a screen of the MYO1A gene in 230 Italian patients with sensorineural hearing loss who were negative for mutations in GJB2. This variant was found in a 5-year-old male patient with mild hearing loss, and was not found in 200 population matched control chromosomes (we assume this represents 100 control individuals). The authors note this position is not evolutionarily conserved and state that follow-up observations will be needed to determine whether the variant is pathogenic. Counting carriers this is case+: 1, case-: 229, control+: 0, control-: 100.
Notably, this paper is investigating the new hypothesis that variants in this gene may cause hearing loss. The authors list 8 total variants impacting protein structure found in a screen of 230 unrelated patients (one nonsense, one in-frame trinucleotide insertion, and 6 missense) and state that these variants were not seen in 200 control chromosomes (which we treat as 100 control individuals). Notably, they do not mention how many other variants impacting protein structure (nonsynonymous substitutions, etc) were found in the controls (this would be the appropriate test). Even if there were none, these numbers for gene data taken as a whole (case+: 8, case-:222, control+: 0, control-:100) do not appear to be significant: two-tailed Fisher’s exact test gives a p-value = 0.112. Another of the 8 variants reported by these authors (S797F) has been observed in a healthy PGP participant with no hearing loss.