Concepts reg Zygosity, copy number variant and variation

Question

[its.roops]

Hi...I have a doubt regarding some definitions related to genomic variation.

1. In case of humans, suppose in chromosome 1, when we define a variant at a particular locus say 435334, and the reference allele is A and the alternate allele is G, is this alternate allele G the dominant allele from one of its parent? What if both the alleles at that locus are recessive?

2. We know that the somatic variants for humans are homozygous, does that mean that the copy number is 2.

[Mark]

1. Dominant/recessive concept is related to genes or phenotypes not to variants. A variant can have an effect, and this effect can be related to inheritance but this is different.
2. Variants can be both homo or hetero, even in somatic cells. Copy number is probably referring copy number of genes.

I think you're confusing concepts related to genes with variants/mutations.

[its.roops]

Yes, you are right..I am confusing the concepts of genes with variants. Thanks for the explanation. May I ask what do we mean by copy number of genes?

[Mark]

In some organisms, multiple copies of the same gene exist in the genome. In bacteria, copy number is sometimes related to antibiotic resistance. In humans I think it's related to disease or lackthereof.