CACNA1A encodes the α1A subunit (pore-forming subunit) of a neuronal P/Q type calcium channel. Mutations within this gene lead to clinically significant neurological abnormalities with multiple phenotypic presentations, including Familial Hemiplegic Migraine (FHM), episodic ataxia type 2 (EA2), spinocerebellar ataxia type 6 (SCA6), and Developmental and Epileptic Encephalopathy 42 (DEE42). DEE42 is a disorder characterized by the developmental delay with cognitive impairment and multiple types of seizures in the neonatal period.

A karyotype was performed using peripheral blood lymphocytes. A Microarray-based Comparative Genomic Hybridization (aCGH) using CytoScan 750K Array (Affymetrix, Santa Clara, CA, USA) and whole exome sequencing (WES).

Our patient is a female born to non-consanguineous parents with a family history of speech and psychomotor developmental delay in her mother. She was born at term with uneventful antenatal and perinatal history. At 12 months, she presented to the Neurology and Genetics department with macrocephaly, frontal bossing, severe hypotonia, psychomotor delay, and repeated episodes of seizures requiring therapy with valproic acid and levetiracetam. EEG evidenced generalized spike waves. Her course was complicated by a traumatic brain injury that precipitated repeated episodes of status epilepticus. At 28 months old, she had cognitive and communication deficits with severe speech delay. The aCGH showed a 4q21.21 deletion. The final result was given as 46, XX arr[GRCh37/hg19] chr4:79766081-80327420. In this study, we describe a patient with DEE42 due to a novel mutation in CACNA1A identified using WES. WES revealed a novel heterozygous variant in the CACNA1A gene: c.4174G>A (p.Val1392Met). Parent analysis was negative for the mutation.  This novel variant was predicted as a disease-causing mutation.

These findings widen the mutation and phenotypic spectrum of CACNA1A-associated disease. The potential genotype-phenotype correlation would facilitate early identification and help guide future pharmacologic treatment research.