What genes cause cheek and chin dimples?

Editor’s note (5/20/2021): This article suggests that chin and cheek dimples are caused by one or a few genes. We now know that the reality is more complicated: both traits are likely caused by many genes interacting in complex ways.

Wow, you're really interested in clefts and dimples! As with most traits, there hasn't been much research on this topic — money tends to go to study more health related issues.

From what I've read, it seems that there are separate cheek and chin dimple genes. One site even placed them on certain chromosomes — cheek dimples on chromosome 5 and cleft chin on chromosome 16! I couldn't find any corroborating evidence for this anywhere, though.

You are right in that it is easy to see how two Dd parents could have a dd child; each parent needs to contribute a d gene. The d form of the gene is probably recessive because of a mutation. Often in these dominant-recessive gene pairs, the recessive copy of the gene is mutated so it doesn't work anymore which is why the dominant version wins out.

Sometimes, though, you can get a working copy of a gene that doesn't work in you for some reason but does work in your children or grandchildren. This concept is called "variable penetrance" and cleft chin is a classic example.

How does penetrance work? Two well-characterized ways that penetrance can work are: environment and modifier genes.

Environment

Sometimes the environment can influence whether a gene gets expressed or not. Let's look at the cleft chin as an example of how this might work.

For some developmental features, a gene may only be on for a short while to cause that feature. Maybe the cleft chin gene only needs to be on for a short period while the fetus is growing. If something in the environment affects the gene during this short period, it will look like the gene isn't there. If there is no change in the gene's sequence, then the children of this person can have a cleft chin.

Modifier Genes

Another way variable penetrance can come about is modifier genes. Modifier genes are simply genes that affect the expression of other genes.

What this means is that now the appearance of a feature like a cleft chin is dependent on two genes, the modifier gene and the cleft gene itself. If both copies of the modifier gene lead to no cleft chin, then the cleft chin gene won't matter — it will be silenced. If the modifier gene lets you have a cleft chin, then you still need to have a working copy of the cleft chin gene.

Clear as mud, huh? Let's try an analogy to hopefully make it a little simpler. Let's compare the situation to the electricity in your house. We can think of the breaker switch, which controls all of the electricity in your house, as the modifier gene.

We'll compare the cleft chin gene to a lamp in your house. Now, if the breaker switch is off, it doesn't matter whether the lamp is on or not, there's no electricity so it won't work. This is the same situation as with the modifier and cleft chin gene. If the modifier gene is "off", then it doesn't matter whether the cleft gene works or not — the "lamp" won't work because there is no juice.

So what we need to propose in your case is that both parents have lamps that work but their breaker switches are off. In the kids, the breaker switch and the lamps are on so you get light (a cleft chin).

What might this look like with "real" genetics? Let's suppose that there is a modifier or silencer gene (M) that, when dominant, doesn't allow the cleft chin gene to work (the breaker switch in the off position is dominant). Now, for the example you gave, we need to propose that both parents are Mm (they have one working copy of this modifier gene each) and that at least one of them has a working copy of the cleft chin gene (C).

Let's say both parents are MmCc; they have a working cleft chin gene but the M masks its presence. There would be a 3 in 16 chance of having either an mmCC or an mmCc child that would have a cleft chin. A Punnett Square (with the three possible children with cleft chin are shown in yellow) of this is shown below:

Since cleft gene is known to have variable penetrance, it is more likely to happen by the modifier gene mechanism.

We haven't even got into the dimple gene that might be masked by a similar penetrance mechanism or may appear in the children by some other mechanism.

As you can see, genetics can get pretty complicated. Of course there are easier explanations like the parents had dimples when they were young but grew out of them (which has been known to happen). Hope this helped.