count missing values groupby
CLASS FEATURE1 FEATURE2 FEATURE3
X A NaN NaN
X NaN A NaN
B A A A
df.drop('CLASS', 1).isna().groupby(df.CLASS, sort=False).sum().reset_index()
CLASS FEATURE1 FEATURE2 FEATURE3
0 X 1.0 1.0 2.0
1 B 0.0 0.0 0.0