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?
In addition to what has already been suggested there is also <a href="http://cadd.gs.washington.edu/">CADD</a> and <a href="http://genic-intolerance.org/">RVIS</a> that you should check out, CADD is much like SIFT and PolyPhen, RVIS is a statistic calculated that estimates how tolerant/intolerant genes are to mutations, which is probably very important to take into consideration for what you are looking in to.

The other thing to keep in mind is that not all mutations, even rare ones, will necessarily be detrimental to the protein's function. Some will have minor impacts, many will be essentially neutral in effect, and some may even enhance the protein's function. These are all important concepts from molecular evolution that aren't taken into account as often as they should be by many human geneticists.