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?
1. You're looking for [VEP][1] and/or [Clinvar][2]
2) Be careful with your terminology. Evolutionary Biologists might argue SNPs do not break genes - they create them. But more importantly, people who carry variants (with or without a deleterious phenotype) don't like being called "broken", "bad", "defective", "diminished", "problematic" or "malfunctioning" ;-) But before you blush, don't sweat it - we're taught to think this way in school and with good intentions, but it lands you in awkward situations like a presentation I once sat through re. how "defective individuals" carry the Sickle Cell gene, and a girl in the class had to leave because her mother suffers (she was therefor a carrier) and the whole thing was, rightly, upsetting.

 [1]: http://www.ensembl.org/Tools/VEP
 [2]: http://www.ncbi.nlm.nih.gov/clinvar/