I need a way to assign a number to genes representing how broken it is depending on how many SNPs with minor alleles appear on the gene. Based on just a handful of SNPs though, not every SNP.

So lets say for example I know a few SNPs for COMT:

```
Rs165599     AA
Rs6269       AA
Rs737865     AA
Rs4633       TT
Rs769224     GG
Rs4680       AA
```

and some SNPs for STAT3:

```
Rs744166      GG
Rs8069645     AG
Rs9891119     CC
Rs6503691     CC
```

and I wanna find out which gene is more defective (as in which has the most diminshed ability to encode the corresponding protein), how can I do that? These genes obviously have way more SNPs than just those ones, and in every gene I will have many minor alleles so I'm guessing its only certain SNPs that cause problems for the gene. So could I find a number that tells me how much a bad allele of a particular SNP breaks the gene and then use that number to get an overall idea of how malfunctioning the gene is?
<p>There is a number of suggestions on <a href="https://www.biostars.org/p/121218/">this</a> thread.</p>
