Novel mutation in AP1S1 causing MEDNIK and lack of improvement of hepatopathy with zinc chelation.
Bryce P. Comstock1, Natalie S. Hauser2, Christine Reyes1, Carlos R. Ferreira1,3
1 Division of Genetics & Metabolism, Children’s National Medical Center, Washington, DC 20010, USA
2 Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia 22042, USA
3 Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
MEDNIK is characterized by Mental retardation, Enterophothy, Deafness, Neuropathy, Icthyosis, and Keratoderma. MEDNIK was first reported in 2005 in 4 affected individuals from an isolated area in Southern Quebec settled by French settlers in the 17th century. MEDNIK is an autosomal recessive disorder caused by recessive mutations in the AP1S1 gene, which encodes a small subunit of the adaptor protein 1 complex. This complex is involved in protein trafficking by clathrin-coated vesicles between the Golgi apparatus and plasma membrane. While the precise pathogenesis of MEDNIK is unknown, copper metabolism is severerly impacted, likely due to abnormal intracellular trafficking of copper transporters such as ATP7A and ATP7B. Thus, patients with MEDNIK present a combination of copper deprivation in certain tissues–as seen in Menkes disease–and copper accumulation in other tissues such as the liver–as seen in Wilson disease. There can also be mistrafficking of other transporters, such ABCD1, leading to mild elevation of very long chain fatty acids.
Our patient presented initially with enteropathy leading to dependence on total parenteral nutrition, sensorineural hearing loss detected through newborn hearing screen, and liver disease. His AST ranged from 57 to 355 IU/L, ALT from 81 to 663 IU/L, alkaline phosphatase from 675 to 1,584 U/L, total bilirubin from 1.3 to 2.9 mg/dL, and conjugated bilirubin from 1.0 to 2.3 mg/dL. Serum copper and ceruloplasmin were normal; urine copper, however, was markedly increased at 209 mcg/L/24 hours (reference: 2-30). Very low chain fatty acid analysis revealed a C22:0 level of 81.2 umol/L (ref: 28-93.5), C24:0 of 70.5 umol/L (ref: 24.3-77.8) and C26:0 of 0.73 umol/L (ref: 0.17-0.73).
A liver biopsy was performed at 4 months of age and revealed bridging fibrosis primarily, but with one nodule with disrupted architecture and no central vein, raising suspicion for early cirrhosis. There was chronic inflammation within the triads, mostly lymphocytes with rare eosinophils and histiocytes. The hepatocytes showed abundant cholestasis, with cholangiolar plugging. There was feathery degeneration of hepatocytes, with rare multinucleated cells and nucleoli. No copper was seen with special stains. Liver copper was measured by Dynamic Reaction Cell-Inductively Coupled Plasma-Mass Spectrometry (DRC-ICP-MS) and the concentration was found to be normal at 13 mcg/g dry weight (reference: 10-35).
Whole exome sequencing performed on the patient revealed a homozygous canonical splice site mutation in AP1S1 (NM_001283.3:c.291+2T>A). This variant is novel, but is well conserved, has a CADD Phred-scaled score of 25.4, is rare in the general population (allele frequency of 2/163,022 in gnomAD), and more importantly it explains the patient's clinical presentation. Based on the current ACMG standards and guidelines for the interpretation of variants, this was interpreted as pathogenic: PVS1 (canonical splice site) + PM2 (extremely low frequency) + PP3 (computational evidence supports deleterious effect).
Given prior reports of improvement of cholestasis with zinc chelation, we attempted this strategy. However, when copper levels were lowered belowe the reference range, the patient developed metaphyseal fractures and cytopenias. Chelation was thus restricted in order to keep copper levels around the lower limit of normal. Despite chelation, there was no decrease in ALT, AST, or alkaline phosphatase, but bilirubin levels normalized. Over time, he was noted to have developmental delay and icthyosis.
In conclusion, we report a new case of MEDNIK associated with a novel mutation. The liver involvement is likely not solely caused by copper accumulation, as our patient had normal liver copper concentrations, and copper chelation resulted in no improvement in liver function.