Dominant KCNA2 mutation causes episodic ataxia and pharmacoresponsive epilepsy

Abstract

Objective: To identify the genetic basis of a family segregating episodic ataxia, infantile seizures, and heterogeneous epilepsies and to study the phenotypic spectrum of KCNA2 mutations.

Methods: A family with 7 affected individuals over 3 generations underwent detailed phenotyping. Whole genome sequencing was performed on a mildly affected grandmother and her grandson with epileptic encephalopathy (EE). Segregating variants were filtered and prioritized based on functional annotations. The effects of the mutation on channel function were analyzed in vitro by voltage clamp assay and in silico by molecular modeling. KCNA2 was sequenced in 35 probands with heterogeneous phenotypes.

Results: The 7 family members had episodic ataxia (5), self-limited infantile seizures (5), evolving to genetic generalized epilepsy (4), focal seizures (2), and EE (1). They had a segregating novel mutation in the shaker type voltage-gated potassium channel KCNA2 (CCDS_827.1: c.765_773del; p.255_257del). A rare missense SCN2A (rs200884216) variant was also found in 2 affected siblings and their unaffected mother. The p.255_257del mutation caused dominant negative loss of channel function. Molecular modeling predicted repositioning of critical arginine residues in the voltage-sensing domain. KCNA2 sequencing revealed 1 de novo mutation (CCDS_827.1: c.890G>A; p.Arg297Gln) in a girl with EE, ataxia, and tremor.

Conclusions: A KCNA2 mutation caused dominantly inherited episodic ataxia, mild infantile-onset seizures, and later generalized and focal epilepsies in the setting of normal intellect. This observation expands the KCNA2 phenotypic spectrum from EE often associated with chronic ataxia, reflecting the marked variation in severity observed in many ion channel disorders.

Figure 1. Family with an autosomal dominant KCNA2 mutation associated with epilepsy and episodic ataxia

(A) WF family pedigree. The KCNA2 mutation (*) segregates with affected status in all individuals. The SCN2A variant (#) is inherited from the unaffected mother. (B) A 9–base pair heterozygous deletion identified in WF-I-1 and WF-III-6. Alignment of whole genome sequencing reads against hg19 genome as seen in the integrative genome viewer. The translation of the wild-type and mutant alleles is indicated with single letter amino acid codes below the alignment.

Figure 2. KCNA2 p.255_257del mutation results in a dominant negative loss of channel function

(A) Representative current traces from Xenopus laevis oocytes injected with water (gray) or cRNA encoding the wild-type (WT) (black), KCNA2 c.765_773del (dark blue), or a mixture of both (light blue) (B). Current amplitudes plotted over test pulses of −60 mV to 40 mV for oocytes injected with water (dotted line) or cRNA encoding wild-type KCNA2 (black), KCNA2 c.765_773del (dark blue), or a mixture of both (light blue).

Figure 3. Homology and structural analysis of KCNA2

(A) A portion of a CLUSTALW alignment of full-length KCNA2 orthologs from multiple vertebrate species. The 3 amino acids that are deleted from KCNA2 (indicated by the braces) are completely conserved in the mammalian, avian, amphibian, and fish species shown. Sequences were identified using the homologene database. (B) Prediction of secondary structures in the S3 domain of wild-type and mutant KCNA2 shows an increase in the α-helical content (H) compared to coil (C) structures. (C) The predicted carbon α-chain structures of wild-type (left) and mutant (right) KCNA2. The region where the deleted amino acids are located is indicated by (*) and a significant deviation between the mutant and wild-type structures can be observed at this position. Critical basic and acidic residues of the voltage-sensing domain are highlighted in magenta. Arrowheads highlight the predicted repositioning of Arg294 and Arg309.