The following explanation is directly from a section of the Genetics page on CHOP's website. I've tweaked the specific chromosome, but the explanation is the same. I think it better explains what is going specifically with Henry's chromosome defect:
The chromosome 4q deletion is a chromosomal difference, which may or may not run in the family. Nothing parents do — or don't do — causes it. In fact, most children who are born with a chromosome 4q deletion didn't have a parent with the disorder, meaning it's a "new mutation."
To understand how the chromosome 4q deletion occurs, you should first have a basic understanding of what chromosomes are. Chromosomes, which are in every cell in our bodies, are made up of smaller structures — called genes — which are in turn made up of deoxyribonucleic acid (DNA). Most people have 23 pairs of chromosomes (46 total), with one of each pair coming from their mother and the other from their father. Chromosomes are numbered 1 through 22; the 23rd pair are called sex chromosomes (X and Y) because they determine a person's gender — male (XY) or female (XX). Chromosomes are also divided into two parts called "arms." The top half is the short or "p" arm and the bottom half is called the long or "q" arm.
When a baby is conceived with either too much or too little genetic material, birth problems (defects) can occur. This may include a whole extra chromosome — as in Down syndrome (an extra 21), a whole missing chromosome — as in Turner syndrome (a missing X), a piece of extra or missing material, or a complex rearrangement of genetic material. Since genes are the body's blueprint, when there are lost or extra, the blueprint changes, frequently leading to birth problems and learning differences.
Children with a 4q deletion have a very small piece of chromosome 4 missing; that's why it's called a "deletion." The q31.3 tells everyone who works in genetics that the missing piece is in a very specific spot on the "q" arm — also called the "long" arm — of the chromosome.
If someone has the deletion, he has a 50 percent chance of passing it on to his children. The chance of having more than one affected child when a parent has the deletion is random, like the chance of getting "heads" twice in a row when you flip a coin twice.
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