Whole Genome Sequencing Identifies a 78 kb Insertion from Chromosome 8 as the Cause of Charcot-Marie-Tooth Neuropathy CMTX3

Abstract

With the advent of whole exome sequencing, cases where no pathogenic coding mutations can be found are increasingly being observed in many diseases. In two large, distantly-related families that mapped to the Charcot-Marie-Tooth neuropathy CMTX3 locus at chromosome Xq26.3-q27.3, all coding mutations were excluded. Using whole genome sequencing we found a large DNA interchromosomal insertion within the CMTX3 locus. The 78 kb insertion originates from chromosome 8q24.3, segregates fully with the disease in the two families, and is absent from the general population as well as 627 neurologically normal chromosomes from in-house controls. Large insertions into chromosome Xq27.1 are known to cause a range of diseases and this is the first neuropathy phenotype caused by an interchromosomal insertion at this locus. The CMTX3 insertion represents an understudied pathogenic structural variation mechanism for inherited peripheral neuropathies. Our finding highlights the importance of considering all structural variation types when studying unsolved inherited peripheral neuropathy cases with no pathogenic coding mutations.

Structural variations causing inherited peripheral neuropathies: A paradigm for understanding genomic organization, chromatin interactions, and gene dysregulation

“…Our laboratory has recently identified two novel SVs as the underlying genetic causes of an X‐linked form of CMT (CMTX3, OMIM:%302802) (Brewer et al., ); and an autosomal dominant form of distal HMN (DHMN1, OMIM:%182960) (Drew et al., ). Linkage analyses in large families mapped the respective disease loci to chromosome Xq26.3‐q27.3 for CMTX3 (Huttner, Kennerson, Reddel, Radovanovic, & Nicholson, ) and chromosome 7q34‐q36.2 for DHMN1 (Gopinath, Blair, Kennerson, Jennifer, & Nicholson, ).…”

“…The 78 kb CMTX3 duplication of chromosome 8q24.3 contains a partial transcript (exons 1–7) of the ARHGAP39 (OMIM:*615880) gene which is encoded on the negative strand. The duplicated chromosome 8q24.3 sequence is inserted into an intergenic region of chromosome Xq27.1 with LOC389895 and SOX3 (OMIM:*313430) being the nearest flanking genes (Brewer et al., ) (Figure ). The 1.35 Mb DHMN1 SV duplication of chromosome 7q36.3 involves five protein‐coding genes ( LOC389602 , RNF32 (OMIM:*610241), LMBR (OMIM:*605522), NOM1 (OMIM:*611269), MNX1 (OMIM:*142994)), a partial transcript of the UBE3C (OMIM:*614454) gene (exons 1–9), three long noncoding RNAs (lncRNA; LOC285889 , LINC01006 , MNX1 ‐ AS1) and several putative enhancers and promoters.…”

“…For both CMTX3 and DHMN1, trisomy of any gene transcripts (whole or partial) within the inserted DNA may result in gene dosage effects and produce neuropathy. For CMTX3, differential expression of ARHGAP39 in lymphoblasts using qPCR was not observed between patients and controls suggesting that trisomy of the partial transcript was not likely to be the mechanism underlying CMTX3 pathology (Brewer et al., ). When testing genes for DHMN1, the expression of the partial transcript UBE3C was higher in patients when compared to controls which may suggest a gene dosage mechanism for DHMN1 (unpublished data).…”

“…A simple SV event may be part of a more complex rearrangement involving 2 or more types of SV. Such examples include translocation insertions (Antonarakis, Kazazian, & Tuddenham, 1995;Brewer et al, 2016), translocation deletions (Barber, Ford, Harris, Harrison, & Moorman, 2004), and inversion duplications (Kostiner, Nguyen, Cox, & Cotter, 2002). The scale and complexity of SV can therefore cause major re-organization of the regulatory landscape of genomic loci.…”

“…In these cases where exome sequencing has failed to identify mutations in specific genes, it is likely a proportion of the neuropathy cases may be due to noncoding DNA or structural variation (SV) mutations. We have recently identified novel SV mutations causing two forms of IPN – X‐Linked Charcot‐Marie‐Tooth neuropathy (CMTX3) (Brewer et al., ) and distal hereditary motor neuropathy (DHMN1) (Drew, Cutrupi, Brewer, Nicholson, & Kennerson, ). Our findings have added to the spectrum of mutations causing IPN and highlight the importance of interrogating the noncoding genome for SV mutations for IPN families that have been excluded for genome wide protein coding mutations.…”