Novel homozygous mutations in Pakistani families with Charcot-Marie-Tooth disease

Abstract

Background: Charcot-Marie-Tooth disease (CMT) is a group of genetically and clinically heterogeneous peripheral nervous system disorders. Few studies have identified genetic causes of CMT in the Pakistani patients.

Methods: This study was performed to identify pathogenic mutations in five consanguineous Pakistani CMT families negative for PMP22 duplication. Genomic screening was performed by application of whole exome sequencing.

Results: We identified five pathogenic or likely pathogenic homozygous mutations in four genes: c.2599C > T (p.Gln867*) and c.3650G > A (p.Gly1217Asp) in SH3TC2, c.19C > T (p.Arg7*) in HK1, c.247delG (p.Gly83Alafs*44) in REEP1, and c.334G > A (p.Val112Met) in MFN2. These mutations have not been reported in CMT patients. Mutations in SH3TC2, HK1, REEP1, and MFN2 have been reported to be associated with CMT4C, CMT4G, dHMN5B (DSMA5B), and CMT2A, respectively. The genotype-phenotype correlations were confirmed in all the examined families. We also confirmed that both alleles from the homozygous variants originated from a single ancestor using homozygosity mapping.

Conclusions: This study found five novel mutations as the underlying causes of CMT. Pathogenic mutations in SH3TC2, HK1, and REEP1 have been reported rarely in other populations, suggesting ethnic-specific distribution. This study would be useful for the exact molecular diagnosis and treatment of CMT in Pakistani patients.

Keywords: Charcot–Marie–Tooth disease (CMT); Consanguinity; Homozygosity; Pakistan; Whole exome sequencing.

Fig. 1

Five Pakistani consanguineous pedigrees with autosomal recessive CMT. Genotypes of pathogenic or likely pathogenic mutations are indicated at the bottom of all the examined family members. Black and white symbols represent affected and unaffected individuals, respectively. The affected individuals subjected to whole exome sequencing are indicated by an asterisk (□: male, and ○: female). a PaC2 family with c.2599C > T (p.Gln867*) in SH3TC2, b PaC3 family with c.3650G > A (p.Gly1217Asp) mutation in SH3TC2, c PaC4 family with c.19C > T (p.Arg7*) mutation in HK1, d PaC6 family with c.247delG (p.Gly83Alafs*44) mutation in REEP1, and e PaC14 family with c.334G > A (p.Val112Met) mutation in MFN2

Fig. 2

Identification of novel homozygous variants thought to be the underlying causes of CMT. a Sequencing chromatograms of c.2599C > T and c.3650G > A in SH3TC2, c.19C > T in HK1, c.247delG in REEP1, and c.334G > A in MFN2. b Conservation of two missense mutation sites. The amino acids at the mutation sites are highly conserved among vertebrate species. c Domain structure and location of the mutations of SH3TC2, and MFN2. The p.Gly1217Asp in SH3TC2, and the p.Val112Met in MFN2 are located in the tetratricopeptide repeats (TPR) and GTPase domains, respectively

Fig. 3

Homozygosity mapping of the chromosomal regions around the pathogenic mutations for the affected individuals from the consanguineous Pakistani CMT families. Genes and SNP numbers located at the ends of the homozygous blocks (HBs) and their approximate chromosomal positions (indicating by Mbp) are shown at the top and bottom of the maps, respectively. a 16 Mbp HB from FGF1 to THG1L in the PaC2 family with SH3TC2 mutation. b 12 Mbp HB from PKD2L2 to SLC6A7 in the PaC3 family with SH3TC2 mutation. c 38 Mbp HB from PPYR1 to NRG3 in the PaC4 family with HK1 mutation. d 53 Mbp HB from CTNNA2 to MZT2A in the PaC6 family with REEP1 mutation. e 14 Mbp HB from NADK to CLCNKB in the PaC14 family with MFN2 mutation