Late-onset epi-cblC methylmalonic aciduria with tissue-variable MMACHC promoter methylation due to a stop retained PRDX1 variant.

Mutations in the MMACHC gene lead to autosomal recessive combined methylmalonic aciduria and homocystinuria (cblC type). Additionally, specific mutations in the downstream, inversely oriented PRDX1 gene that result in aberrant PRDX1 transcripts overlapping the MMACHC promoter lead to its methylation and consequent downregulation of expression. This type is called epi-cblC and can be due to bi-allelic PRDX1 mutations causing MMACHC epimutation, or it can be digenic with heterozygous PRDX1 and MMACHC pathogenic variants located in trans. We identified a patient with an unusually late-onset epi-cblC type due to the compound heterozygous recurrent pathogenic MMACHC:c.271dup, p.(Arg91Lysfs*14) variant and a novel PRDX1:c.599G > A, p.(Ter200=) variant. We found that the PRDX1 stop retained variant caused activation of a cryptic acceptor splice site and production of an aberrant transcript overlapping the MMACHC promoter. We confirmed hemimethylation of the MMACHC promoter in the blood of the patient and her daughter, also a carrier of the PRDX1 stop retained variant. Interestingly, the methylation level was much lower in the patient's fibroblasts. In line with these methylation data, expression of the MMACHC gene was attenuated in blood, while it was preserved in the fibroblasts of the proband. The difference in methylation could be explained by a lower proportion of aberrant PRDX1 transcripts detected in fibroblasts compared to blood. In conclusion, we describe a rare example of a stop retained variant causing aberrant splicing with a tissue-dependent level of expression. These differentially expressed splicing changes presumably lead to varying degrees of MMACHC promoter methylation and gene expression observed in blood and fibroblasts. We suggest that preserved MMACHC expression from one allele in a subset of tissues could explain the unusual late onset and milder form of the disease in the epi-cblC type patient.