mutations causing predicted gene loss of function in healthy individual - WGS

Question

[joneill4x]

Just for interest, I had my whole genome re-seqeunced (BGISEQ-500, 30X coverage). Variants were called with GATK and the variants were annotated with SnpEff and annovar. SnpEff also predicted the functional effects of the variants.

Interestingly, there are hundred of variants that are predicted cause gene loss-of-function (highly deleterious), and are homozygous for the mutant allele. To my knowledge, I am perfectly healthy.

Can anyone help explain this phenomenon? I see three possibilities:

1. I don't need those genes to work in order to be healthy.
2. I don't actually have those mutations. There was an error in the variant-calling.
3. The functional predictions are wrong.

I can provide some examples of the loss-of-function genes.

Also, can anyone recommend some interesting/creative bioinformatic analysis to perform on my genome data?

Thank you. Sorry of this is the wrong place to post this.

Answer 1

[Pierre Lindenbaum]

https://science.sciencemag.org/content/335/6070/823

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

... Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. ...