You need tab separated vcf file with five row

CHROM POS ID REF ALT

1 227920 . G A

1 228404 . G T

ID row can be blank or . than you can run it.

Alternatively if you have limited missense variants are with you to use SniPA tool.  

The next questions might give a hint to the answer.

What are the variant/variants in question?(are these from genome build 37?). Please provide one or more examples.

How did you get the CADD annotations?

Is your gene annotated in Ensembl 75 at http://grch37.ensembl.org/index.html ?

few of my missense variants  - CADD is precomputed results and if your variant position is not matching to precomputed one you will not get keep those NoCADD category or 

try even different version of CADD like 1.1, 1.2 and 1.3, it may fill up but you have to keep note of it.

Thanks a lot. It got sorted out. It was the problem with the build and hence variant position dint match.

But how should I input insertion or deletion in CADD.

I mean if it is an insertion of TGTG..how shd i represent the ref and alt alleles?

Good, all are issues are part of learning and worth sharing!!!