Mohammad Alias Wahdat, provincial governor, said today the incident happened last night in the Yusof Khail district.
Wahdat said the gunman entered the house and shot the cleric and his wife. Two of their children who were in the house survived.
Police investigating say it's not clear who was behind the attack and no one immediately claimed responsibility.
Meanwhile, Gul Agha Roohani, chief of police in eastern Nangarhar province, said Islamic State group militants stormed the security posts in the district of Kot early Friday, killing at least one police officer.
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