Introduction:
Mutation of the sodium voltage-gated channel alpha subunit 1 (SCN1A) gene is an important cause of genetic epilepsy and familial hemiplegic migraine. However, data related to genetic variations of SCN1A in Indonesia are limited.

Aim:
To identify SCN1A gene variation in idiopathic epilepsy and common migraine patients in Aceh province, Indonesia.

Material and methods:
A case-control study was conducted at Dr. Zainoel Abidin Hospital, Banda Aceh, Indonesia from 1 March to 30 August 2015. Gene variation analysis of exon 26 of the SCN1A gene was conducted in 33 patients with idiopathic epilepsy, 33 patients with common migraine and 30 controls using polymerase chain reaction and direct sequencing.

Results:
SCN1A gene variations were identified in two partial secondary generalized epilepsy patients. In 1 patient, four silent mutations at nucleotide positions A4440T (Leu1480Leu), T4443C (Leu1481Leu), A5046G (Leu1682Leu) and C5121T (Asn1707Asn) were identified. One silent mutation at position G5505A (Glu1835Glu) was found in another patient. No gene variation was identified among controls and common migraine patients.

Discussion:
This study is the first report on genetic variations of the SCN1A gene in adult patients with idiopathic epilepsy and common migraine in Indonesia. However, the association between these genetic variants and epilepsy needs to be clarified.

Conclusions:
Five genetic variations in exon 26 of SCN1A were identified in 2 patients with partial secondary generalized epilepsy in Aceh, Indonesia.