Contiguous 1.4Mb 17p12 Deletion Associated with Axonal Neuropathy
Analysis of patient 1 CNVs identified a known pathogenic contiguous 1.4Mb 17p12 deletion associated with hereditary neuropathy and liability to pressure palsy (HNPP) (Li, 2012; van Paassen et al., 2014). This deletion includes all coding exons of PMP22 encoding peripheral myelin protein 22, which is essential for nerve myelination and cell proliferation (Adlkofer et
al., 1995). On the other hand, duplication of the same 1.4Mb 17p12 region including PMP22
is associated with CMT type 1A (CMT1A). However, patient 1 did not manifest the HNPP phenotype and instead had an axonal neuropathy reminiscent of CMT1A. Although
uncommon, patients harbouring the PMP22 deletion presenting severe axonal neuropathy instead of HNPP have been reported (Chance et al., 1993; Bergamin et al., 2014). CMT disease due to PMP22 deletion or duplication is one of the most common neurological disorders in North East England with an estimated minimum prevalence of 11.8 per 100,000 (Foley et al., 2012). Given that neuropathy is a common feature of adult-onset Mendelian mtDNA maintenance disorders (Chapter 3), digenic disorders of mitochondrial PEO and CMT could be under recognised in this cohort of patients. However, this requires the further genetic studies of patients with PEO and neuropathy to ascertain any prevalence.
Isolated Cystinuria Type A Due to Recessive SLC3A1 Mutations
The presence of cystinuria together with PEO and multiple mtDNA deletions in patient 19 was an unusual finding that suggested the presence of a second Mendelian disorder. Since patient 19 had received penicillamine to treat the cystinuria, it was presumed that PEO and fatigue was penicillamine-induced myasthenia gravis (Drosos et al., 1993). However, this was not the case following withdrawal of penicillamine, leading to the diagnosis of mitochondrial myopathy. WES of analysis SLC3A1 and SLC7A9 identified the two most common
pathogenic SLC3A1 variants associated with isolated cystinuria. As of August 2016, over 150 different SLC3A1 variants have been associated with isolated cystinuria type A (SLC3A1, 2016). To date, the p.Met467Thr missense change and exon 5-9 duplication are the most common pathogenic SLC3A1 variants associated with isolated cystinuria type A in the United Kingdom and other Western European countries (Rhodes et al., 2015; Wong et al., 2015), but are not as common in South East Europe (Popovska-Jankovic et al., 2013).
MYH14 p.Gly384Cys Variant is Not Associated with Non-Syndromic Hearing Loss
In the patient 6, a heterozygous p.Gly384Cys MYH14 missense change previously reported as pathogenic, causing autosomal dominant non-syndromic hearing loss (DFNA4, OMIM #600652). The variant had been reported as pathogenic, occurring de novo in a 9 year old Italian girl and was annotated as pathogenic due to the evolutionary conservation of the Gly384 residue, absence from tested controls and since the girl was the only affected family member (Donaudy et al., 2004). This variant could serve to explain the history of hearing loss affecting the family of patient 6. However, thanks to NGS and the sharing of variant
frequency data over the past decade it has been revealed that a number of annotated ‘rare’ and ‘pathogenic’ variants associated with various Mendelian disorders actually occur at MAFs that suggest that these are not rare within the general population. A significant re-assessment of previously reported pathogenic variants can be attributed to the ExAC database (Lek et al., 2016). Re-assessment of ‘pathogenic’ HCM variants in 7,855 cases found that some variants were occurring at MAFs too common to cause penetrative Mendelian disease (Walsh et al., 2016). Assessing the MYH14 p.Gly384Cys missense change, it also occurs more frequently than would be expected for a disease-causing mutation. In ExAC, it occurs in 343/119994 heterozygous alleles (MAF=0.002858, 0.028%) and when further sub-categorised by ethnicity, the variant occurs in 275/66322 non-Finnish European alleles (MAF=0.004146, 0.041%). Similarly, the variant was identified in 36/12712 alleles (MAF=0.0023832, 0.024%) from NHLBI ESP and in 12/4996 alleles (MAF=0.002, 0.02%) in the 1000 Genomes Project databases. Hence, it the opinion of this study that the MYH14 p.Gly384Cys mutation is not associated with hearing loss. Thus, this serves to highlight the importance of variant classification and the need to functionally validate candidate variants.
Although excluded from WES analysis for adult-onset PEO with multiple mtDNA deletions, a second heterozygous MYH14 missense change (p.Arg1729Trp) was also identified in patient 13 through analysis of known autosomal dominant and recessive hearing loss genes.
Therefore it was concluded that the MYH14 change identified in patient 13 was the most likely aetiology for his SNHL since it occurred at a low MAF and affected a conserved residue.
4.5.6 Concluding Remarks
the expected predominance of autosomal dominant mutations (Chapter 3), almost all proposed likely causative and VUS were heterozygous. Nonetheless, it is important to acknowledge that segregation and further functional studies are necessary to validate the pathogenicity of identified variants. The identification of a heterozygous somatic mosaic
TWNK missense change is also suggestive of an under recognised phenomenon of mosaicism
in autosomal dominant Mendelian mitochondrial disease, that is detectable by WES even at low mutational levels. Owing to this, careful curation and annotation of electropherograms generated from diagnostic targeted gene sequencing will be needed. This study has also identified the only known patient harbouring a dominant RRM1 mutation to date, with further contributions to this emerging story anticipated. Irrespective of the custom filtering strategy that has been devised and employed, the interactome of mitochondrial function and mtDNA maintenance is not yet complete as highlighted by the identification of a novel SEPT2 mutation. Secondary, actionable mutations causing other Mendelian disorders are also not prioritised by the filtering strategy devised here and are instead dependent upon thorough clinical phenotyping that can direct this additional variant prioritisation. Segregation studies will also greatly improve confidence in likely causative variants and VUS identified, although it is accepted that this is difficult when studying a late-onset disorder.