Preheat oven to 350 degrees F (175 degrees C). Line 8 muffin cups with paper liners.
Mix flour, baking powder, baking soda, cinnamon, nutmeg, and salt together in a bowl. Mash white sugar and butter together in a separate bowl until combined; stir in pumpkin puree, egg white, milk, and 1/2 teaspoon vanilla extract. Mix flour mixture into pumpkin mixture until batter is combined. Fill muffin cups 3/4-full with batter.
Bake in the preheated oven until a toothpick inserted in the center comes out clean, 10 to 15 minutes. Cool to room temperature.
Beat cream cheese, margarine, and confectioners' sugar together in a bowl until smooth. Add yogurt and remaining 1/2 teaspoon vanilla extract and beat until frosting is well combined. Frost cupcakes.