A Second Case With the V374A KCND3 Pathogenic Variant in an Italian Patient With Early-Onset Spinocerebellar Ataxia.

Background and
Objectives: To date, approximately 20 heterozygous mainly loss-of-function variants in KCND3 have been associated with spinocerebellar ataxia (SCA) type 19 and 22, a clinically heterogeneous group of neurodegenerative disorders. We aimed at reporting the second patients with the V374A KCND3 mutation from an independent family, confirming its pathogenic role.
Methods: We describe the clinical history of a patient with SCA and conducted genetic investigations including mitochondrial DNA analysis and exome sequencing.
Results: This male patient was reported to have unstable gait with tremors at the lower limbs and dysarthric speech since childhood. A neurologic examination also showed dysarthria, nystagmus, action tremor, dysmetria, and weak deep tendon reflexes. He had marked cerebellar atrophy at brain MRI, more evident at vermis. Molecular analysis, including exome sequencing and an in silico panel analysis of genes associated with SCA, revealed the c.1121T>C [p.V374A] mutation in KCND3. Discussion: This report consolidates the pathogenicity of the V374A KCND3 mutation and suggests that the ataxic paroxysmal exacerbations are not a key phenotypic feature of this mutation.

KCND3 gene encodes the voltage-dependent potassium channel Kv4.3, an alpha subunit of the Shal family of A-type K+ channels, essential in membrane repolarization in excitable cells. Heterozygous loss-of-function mutations in KCND3 have been associated with spinocerebellar ataxia type 19 and 22 (SCA19/22), a clinically heterogeneous group of neurodegenerative disorders characterized by variable degrees of cerebellar ataxia, parkinsonism, cognitive dysfunction, epilepsy, and extrapyramidal signs (MIM#607346).[1-3] Recently, it has been reported a case with paroxysmal ataxia exacerbations carrying the heterozygous pathogenic variant V374A in the KCND3 gene.[4] In this study, we present a second case carrying the same pathogenic variant, confirming this genotype-phenotype association.

Case Report

This male patient, now aged 50 years, with a negative family history, had unstable gait with tremors at the lower limbs and dysarthric speech since childhood. Our first evaluation was at age 40 years. A neurologic examination showed dysarthria, nystagmus in all directions of gaze, action tremor, dysmetria, weak deep tendon reflexes, truncal ataxia, ataxic gait, and instability in upright position with a positive Romberg sign. He also had bilateral pes cavus. He had marked cerebellar atrophy at brain MRI, more evident at vermis (Figure, A–C). Somatosensory-evoked potential displayed slightly increased time in cortical responses. At the last cognitive evaluation in 2017, the Mini-Mental Status Exam score and the score at the Brief Test of Cognition (IQ at the lower range of the normal values) were normal. At the Brief Neuropsychological Examination test, the patient presented a mild intellectual disability with abnormalities in attentive/executive functions, unchanged compared with the cognitive evaluation in 2010. The abnormalities in executive/praxic functions are likely due to a deficit in planning strategies. EMG, EEG, and ECG findings and audiometry and ophthalmologic examination findings were normal. Polysomnography revealed the presence of moderate sleep apnea syndrome. The patient is overweight (weight: 125 kg). Initially investigated for mitochondrial disease, lactic acid was normal, whereas 3 cytochrome c oxidase (COX)-negative fibers were noted at muscle biopsy (Figure, D and E). A complete sequencing of mitochondrial DNA (mtDNA) extracted from skeletal muscle did not show any pathogenic variant (haplogroup U2e2a1c) and pathologic accumulation of macrodeletions. Finally, the mtDNA copy number assessment was normal. The only noticeable result was a relative increase of 7S DNA. Assessment of coenzyme Q in muscle biopsy was also normal.

Figure

Clinical, Histologic, and Genetic Findings of the Patient

(A–C) Brain MRI shows severe cerebellar atrophy more evident at vermis. (D and E) Muscle biopsy (cytochrome c oxidase/succinic dehydrogenase staining) of the patient performed at the age of 39 years showed scattered cox-negative fibers (red arrows). (F) Chromatogram showing KCND3 c.1121T>C segregation within the family in available members. Ages represent age at death (for those marked as deceased) or current age. Moreover, major clinical features are also indicated. MI = myocardial infarction.

Genetic investigation was then expanded to exome sequencing, and an in silico panel analysis of genes associated with spinocerebellar ataxia (SCA) revealed the presence of a heterozygous missense variant, c.1121T>C [p.V374A], in KCND3 (NM_004980.5). This variant has not been reported in the gnomAD database and was predicted to be damaging with a 24.4 CADD-PHRED score. According to the American College of Medical Genetics classification, the c.1121T>C was classified as likely pathogenic with the PM1, PM2, PP2, and PP3 criteria. Segregation analysis was consistent with a possible de novo origin of the V374A variant in the patient because available relatives tested were negative and neurologic disturbances were never reported in the parents and siblings (Figure, F).

Data Availability

Anonymized data not published here will be made available by request from any qualified investigator.

Discussion

We reported an independent case of SCA associated with the V374A variant in KCND3 gene. The cases originally described were a mother and a son (index case) diagnosed with adult-onset slowly progressive cerebellar ataxia, bradyphrenia, and normal general intellectual ability despite low results in cognitive tests.[4] Both presented cerebellar atrophy, more severe in the index case, with moderate-to-severe cerebellar hypometabolism (Table 1). Notably, the index case experienced paroxysmal ataxia exacerbations responsive to acetazolamide when exposed to accelerations/decelerations. The V374A pathogenicity was confirmed in vitro: electrophysiology studies showed that the V374A variant was nonfunctional and caused a conductance reduction predicted to generate an increased Purkinje neuron firing frequency.[4] This family presented an additional A671V variant in the KCNC3 gene (SCA13), for which a potential synergistic effect was excluded in vitro.

Table 1

Clinical Features of Patients With KCND3 V374A Mutation

Our patient, differently from those described by Paucar et al., was affected by early-onset cerebellar ataxia, which progressively worsened, apparently without paroxysmal exacerbations. Notably, mild abnormalities in cognitive testing were also observed. The finding of rare COX-negative fibers and increased 7S DNA may be envisaged as secondary reflection on mitochondrial metabolism due to dysfunctional energy-consuming ion channeling. To date, approximately 20 mutations SCA19/22 have been described in patients with heterogeneous clinical presentations, mainly including cerebellar ataxia, cognitive dysfunction, and movement disorders such as parkinsonism (Table 2).

Table 2

Clinical Features and Inheritance of Patients With KCND3 Mutations

In conclusion, our case consolidates the pathogenicity of this mutation, with a substantially overlapping phenotype except for the paroxysmal exacerbations, for which a synergistic effect of the A671V in KCNC3 gene cannot be completely excluded, and the onset of the disease.