The allelic spectrum of Charcot-Marie-Tooth disease in over 17,000 individuals with neuropathy

Abstract

We report the frequency, positive rate, and type of mutations in 14 genes (PMP22, GJB1, MPZ, MFN2, SH3TC2, GDAP1, NEFL, LITAF, GARS, HSPB1, FIG4, EGR2, PRX, and RAB7A) associated with Charcot-Marie-Tooth disease (CMT) in a cohort of 17,880 individuals referred to a commercial genetic testing laboratory. Deidentified results from sequencing assays and multiplex ligation-dependent probe amplification (MLPA) were analyzed including 100,102 Sanger sequencing, 2338 next-generation sequencing (NGS), and 21,990 MLPA assays. Genetic abnormalities were identified in 18.5% (n = 3312) of all individuals. Testing by Sanger and MLPA (n = 3216) showed that duplications (dup) (56.7%) or deletions (del) (21.9%) in the PMP22 gene accounted for the majority of positive findings followed by mutations in the GJB1 (6.7%), MPZ (5.3%), and MFN2 (4.3%) genes. GJB1 del and mutations in the remaining genes explained 5.3% of the abnormalities. Pathogenic mutations were distributed as follows: missense (70.6%), nonsense (14.3%), frameshift (8.7%), splicing (3.3%), in-frame deletions/insertions (1.8%), initiator methionine mutations (0.8%), and nonstop changes (0.5%). Mutation frequencies, positive rates, and the types of mutations were similar between tests performed by either Sanger (n = 17,377) or NGS (n = 503). Among patients with a positive genetic finding in a CMT-related gene, 94.9% were positive in one of four genes (PMP22, GJB1, MPZ, or MFN2).

Keywords: Charcot–Marie–Tooth disease; genetic testing; high-throughput nucleotide sequencing; molecular epidemiology; peripheral neuropathy.

Figure 1

The mutation frequency of Charcot–Marie–Tooth disease genes in a large cohort (n = 17,377) analyzed at a commercial laboratory. The pie chart shows the percentage of positive results attributed to each gene by color out of the total number of genetically positive patients (n = 3216) as determined by Sanger sequencing and MLPA. Mutations in four genes (PMP22 dup/del, GJB1, MPZ, and MFN2) accounted for 94.9% of the genetically positive patients in our cohort. PMP22 duplications (dup) accounted 56.7% of positive patients, PMP22 deletions (del) 21.9%, GJB1 6.7%, MPZ 5.3%, MFN2 4.3%, PMP22 0.9%, SH3TC2 0.8%, GDAP1 0.7%, NEFL 0.7%, LITAF 0.5%, GARS 0.4%, HSPB1 0.3%, GJB1 del 0.3%, FIG4 0.3%, EGR2 0.1%, RAB7A 0.1%, and PRX 0.03%.

Figure 2

The distribution of pathogenic sequencing mutation types in Charcot–Marie–Tooth disease. The pie chart shows the percentage of mutation types by color out of the total number of genetically positive patients (n = 3216) as determined by Sanger sequencing and MLPA. Missense mutations accounted for the majority (70.6%) of pathogenic sequencing variants identified in this cohort, followed by nonsense 14.3%, frameshift 8.7%, and splice site 3.3% mutations. Other mutation types accounted for the remaining 3.1% of pathogenic mutations.

Figure 3

The distribution of pathogenic sequencing mutation types per Charcot–Marie–Tooth disease gene. The bar graph shows the distribution of mutation types by color for each CMT gene. Missense mutations accounted for a majority of pathogenic variants identified in most genes. Pathogenic mutations identified in the SH3TC2 and PRX genes were mostly nonsense mutations.