Mutational analysis of the three putative genes in stuttering
A total of 64 unrelated probands with non-syndromic persistent stuttering (sex ratio - 12:1; 59:5; mean age at onset of 5.13 years) were screened for the recurrence of mutations in the three stuttering implicated genes. Sixty seven percent (43/64) of them had family history. More than 50% of PWS were found to be severe; 53.1% severe (34/64), 28.1% moderate (18/64) and 18.8% mild (12/64).
Mutation screening of the twelve specific exons previously reported (figure 1), identified a total of 12 variants that includes five nonsynonymous missense variants, five synonymous and two non coding variants (tables 1 and 2; figures A1-A3). The distribution of these 12 variants among the 64 probands are shown in figure 2a. Variants observed in NAGPA (n=6) were higher than that of GNPTAB(n=2) and GNPTG (n=4) (figure 2b).
Only three unrelated probands (STU 29, STU 63 and STU 34), harbored heterozygous likely pathogenic missense variants (c.3598G>A in GNPTAB , c.802A>C in GNPTG and c.131G>C in NAGPA respectively) with an overall frequency of 4.7% (3/64*100) and an allele frequency of 2.3% (3/128 * 100). None of the three showed more than one pathogenic allele but there was co-occurrence of synonymous and non-coding variants (table 3).
The two missense variants (c.139C>T & c.1394 C>T) in NAGPA, had low conservation scores and were found in high frequency in the ExAC database supporting their benign nature. Hence, segregation analysis and genotype-phenotype correlations were analyzed only for the three likely pathogenic variants (figure 3-5). Only two variants (c.3598G>A and c.802A>C) co-segregated (table 4) with the affected status, reducing the likely pathogenic allele frequency to 1.6% (2/128 *100).