Ataxia Syndrome With Hearing Loss and Nephronophthisis Associated With a Novel Homozygous Variant in XPNPEP3

A 53-year-old man from the Norrbotnian region in Sweden with a history of chronic kidney disease and gout presented with action and postural tremor, involuntary jerks, gait difficulties, falls, dysarthria, and loss of sensation in his feet. Onset was insidious and occurred during his late teens; this disorder was progressive and motivated the use of a walker a few months before his last visit. He was diagnosed with bilateral sensorineural hearing loss and stuttering speech at age 4 years; he reached his developmental milestones as expected and attended a regular school but had trouble acquiring motor skills (e.g., ride a bicycle and doing winter sports). His mother and deceased father have ancestry in the Finnish side of the Tornio valley, and none of them suffered from neurologic disease (Pedigree shown in eFigure 1, links.lww.com/NXG/A631). At age 23 years, the patient was evaluated for mitochondrial disease; however, a muscle biopsy and analyses of respiratory chain complexes were interpreted as normal then. EMG demonstrated mild myopathic abnormalities. Protein electrophoresis, cytology analysis, lactate, and protein levels in the CSF were normal. EEG demonstrated bilateral synchronous slow wave activity. Targeted analysis of common disease-causing variants in mitochondrial DNA (mtDNA) did not detect m.3243A>G, m.8344A>G, or m.8993T>G/C. Examination at age 53 years demonstrated predominant axial ataxia, dysmetria, dysarthria, postural and action tremor, slow vertical saccades, and ptosis were also found (Video 1 and eFigure 2, links.lww.com/NXG/A632). Examination with scale and rating of ataxia (SARA) yielded 17 points. In addition, the Romberg test was abnormal, pinprick sensation was reduced in both feet, and vibratory sensation was absent in the left lateral malleolus. During the examination, intermittent dystonic postures (feet and neck) and myoclonic jerks were also found. Muscle tonus was normal, but strength was reduced in both hands and legs (eAppendix 1, links.lww.com/NXG/A630), reflexes were symmetrical, and plantar response was flexion. Treatment with clonazepam reduced his myoclonic jerks. Neurography demonstrated a moderate axonal sensorimotor neuropathy and increased thresholds for temperature. Brain MRI demonstrated severe and progressive cerebellar atrophy and global cortical atrophy grade 1–2 more pronounced in the frontoparietal lobes (Figure 1, A and B). Extended laboratory work-up for ataxias, including for neurometabolic disorders, did not provide any diagnostic clues other than mild CK and neurofilament elevation in plasma. A recent echocardiography ruled out cardiomyopathy.

A psychometric evaluation demonstrated mild impairments, the patient obtained 76–90 index points on the working memory part (12th percentile) and 74–88 points on the perceptual function part (9th percentile) of WAIS-IV. The patient demonstrated perseveration, reduced concentration capacity and slower processing speed. Chronic kidney failure was diagnosed at age of 23 years. A kidney biopsy displayed features interpreted as glomerulonephritis (eAppendix 1, links.lww.com/NXG/A630). Estimated glomerular filtration rate was 40 mL/min/1.73 m² at age 23 years and slowly declined to 17 mL/min/1.73 m² at his latest visit and urea was 35.6 mmol/L (normal value: 3.5–8.2 mmol/L) (Table 1). Alport's disease was considered at this point, but no variants in COL4A5 were identified. A re-evaluation of earlier kidney biopsy was pursued based on the genetic findings. Indeed, the biopsy demonstrated abnormalities compatible with nephronophthisis. Looming dialysis has raised kidney transplantation into consideration.

WGS of DNA derived from blood detected a novel homozygous nonsense variant, c.766C>T, (p.Gln256*), in exon 4 of XPNPEP3 (NM_022098.4). His mother is heterozygous carrier of the variant. No DNA from the father was available for analysis. The variant is rare with a frequency of 24/251140 alleles in the general population and no homozygous individuals have been found, according to GnomAD (v2.1.1). The analysis detected also the heterozygous variant c.1997C>T, (p.Ala666Val), in PUM1 (NM_001020658.2) inherited from the healthy mother, which was interpreted as a variant of uncertain significance (eAppendix 1, links.lww.com/NXG/A630). WGS of DNA extracted from muscle did not detect any pathogenic variants in mtDNA.

A skin biopsy and a second muscle biopsy were obtained at age 53 years. COX negative fibers and a few ragged red fibers (RRF) were found under light microscopy, whereas electron microscopy demonstrated paracrystalline “parking lot” inclusions and rounded electron dense structures within the mitochondria as well as abnormal cristae (Figure 2, A–D). In mitochondria isolated from muscle, ATP production using the complex IV dependent substrate combination TMPD+Ascorbate was reduced (eFigure 3A, links.lww.com/NXG/A633). Also, activity for the respiratory chain complex IV (CIV) was decreased (eFigure 3B). Respiratory chain enzymes in mitochondria isolated from fibroblasts showed decreased activity for CIV and an activity in the lower normal range for complex I (CI) (eFigure 3C). Coenzyme Q10 in the muscle specimen was 1.43 ng/unit CS (Normal value >1.18), treatment with coenzyme Q10 was started despite the normal value. Western blot analysis confirmed loss of XPNPEP3 protein in both cultured fibroblasts and muscle tissue from the patient (eFigure 4, A and B, links.lww.com/NXG/A634). In healthy controls, protein expression was much lower in skeletal muscle compared to cultured fibroblasts. This finding is somewhat in line with previous work. We applied the same antibody for XPNPEP3 reported in the Human Protein Atlas (Tissue expression of XPNPEP3 - Staining in skeletal muscle - The Human Protein Atlas, proteinatlas.org/). In this atlas no expression of XPNPEP3 is found; however, we found a low degree of expression in skeletal muscle (eFigure 4B).