Muhammad Anees, Inayat Fawad, Sethi Bilal Ahmad, Kashif Muhammad, Khan Assad Ullah, Ahmad Shahzad, Atlas Amir, Rehman Shoaib Ur, Sarwar Muhammad Tahir
Molecular Biology & Genetics, Institute of Basic Medical Science, Khyber Medical University, Peshawar, Pakistan.
Department of Biochemistry, Abdul Wali Khan University, Mardan, 23200, Pakistan.
Mol Biol Rep. 2025 Sep 26;52(1):952. doi: 10.1007/s11033-025-11087-w.
Among the Pashtun population in Pakistan, familial epilepsy cases remain under-explored at the molecular level. This study aims to find causative variants in genes associated with epilepsy using whole exome sequencing (ES) in consanguineous Pashtun population of Pakistan.
We took a detailed clinical history followed by head-to-toe physical examination, MRI and EEG test. Afterward, we performed whole exome sequencing followed by variant interpretation using current bioinformatic pipelines based on ACMG guidelines. Then, we performed segregation analysis for the validation of variants among family members to identify the pattern of inheritance.
We identified novel homozygous pathogenic variant in two families. In family, an unreported frameshift pathogenic variant (c.379dup, p.Thr127Asnfs11) was identified in the CLN5 gene in two affected siblings presenting with generalized myoclonic epilepsy, vision problems, developmental and motor delay. In family B, a novel homozygous variant (c.136 C > T, p.Gln46) was identified in the ITPA gene in a male child diagnosed with Developmental and Epileptic Encephalopathy 35 (DEE35). Craniosynostosis was observed in association with the ITPA gene, which have not been reported previously. Other common features were early-onset seizures, developmental delays, microcephaly, and autistic features. Seizures were refractory to multiple antiepileptic drugs in both cases.
To the best of our knowledge, this is the first reported case of an ITPA variant in the Pashtun population of Pakistan, with the newly observed association with craniosynostosis providing useful insights for clinicians and researchers. These two novel variants in ITPA and CLN5 cases, expand the genotypic and phenotypic spectrum of epilepsy in consanguineous Pashtun populations of Pakistan. These findings emphasize the importance of ES in the genetic diagnosis of epilepsy in underserved regions and the need for early age genetic testing, and counseling in high-risk communities.
在巴基斯坦的普什图族人群中，家族性癫痫病例在分子水平上仍未得到充分研究。本研究旨在通过全外显子组测序（ES）在巴基斯坦普什图族近亲人群中寻找与癫痫相关基因的致病变异。
我们详细询问了临床病史，随后进行了从头到脚的体格检查、MRI和脑电图检查。之后，我们进行了全外显子组测序，并根据美国医学遗传学与基因组学学会（ACMG）指南，使用当前的生物信息学流程进行变异解读。然后，我们进行了分离分析，以验证家庭成员之间的变异，从而确定遗传模式。
我们在两个家族中鉴定出了新的纯合致病变异。在家族A中，在两个患有全身性肌阵挛性癫痫、视力问题、发育和运动迟缓的患病兄弟姐妹中，CLN5基因中鉴定出一个未报告的移码致病变异（c.379dup，p.Thr127Asnfs11）。在家族B中，在一名被诊断为35型发育性癫痫性脑病（DEE35）的男童的ITPA基因中鉴定出一个新的纯合变异（c.136 C>T，p.Gln46）。观察到颅骨缝早闭与ITPA基因相关，此前未见报道。其他常见特征包括早发性癫痫发作、发育迟缓、小头畸形和自闭症特征。在这两个病例中，癫痫发作对多种抗癫痫药物均耐药。
据我们所知，这是巴基斯坦普什图族人群中首次报道的ITPA变异病例，新观察到的与颅骨缝早闭的关联为临床医生和研究人员提供了有用的见解。ITPA和CLN5病例中的这两个新变异，扩展了巴基斯坦普什图族近亲人群中癫痫的基因型和表型谱。这些发现强调了全外显子组测序在服务不足地区癫痫基因诊断中的重要性，以及在高危社区进行早期基因检测和咨询的必要性。
