这是主语从句，分析如下：
这是一句感叹句，其中省略了it is that， 完整的句子应该是：What a shame it is that you can't come.
而其陈述句形式是：It's a shame (that) you can't come.
在陈述句中，it实际上是形式主语，真正的主语是that you can't come, 正常的语序应该是：That you can't come is a shame. 谓语（系动词）是is，a shame是表语。这里的That you can't come是主语从句。在It's a shame (that) you can't come.中that可以省略。
因此，What a shame you can't come中，you can't come是真正的主语（从句），a shame是表语，形式主语it和系动词is都省略了，而what只是感叹句的标志，起感叹词的作用。