How to Read a 22q11.2 Deletion Genetic Test Report

When you first receive your or your child’s genetic test report, it can feel like trying to read a foreign language. The string of numbers and letters on a Chromosomal Microarray Analysis (CMA) is simply a highly detailed map showing exactly where a tiny piece of DNA is missing on chromosome 22 ^[1]. (Note: If you had a FISH test, it acts more like a targeted “yes/no” check for the deletion and uses different shorthand ^[2]). Breaking down the microarray’s genetic “zip code” can help you understand the boundaries of the deletion and advocate effectively for care, even though the exact size of the deletion cannot perfectly predict which symptoms will occur ^[3][4].

Breaking Down the Genetic Code

Most microarray reports will list a result that looks something like this: arr[GRCh37] 22q11.21(18,648,855-21,505,417)x1. Here is what each part of that code means ^[5][1]:

• arr: Stands for “microarray,” which is the advanced technology used to scan the DNA for missing or extra pieces.
• [GRCh37]: This is the “map version” or reference genome used by the lab to locate the missing DNA (you might also see hg19 or GRCh38). Different versions will change the exact coordinate numbers, but the physical deletion remains the same.
• 22q11.21: This is the specific address. It means the deletion is on chromosome 22, on the long arm (indicated by “q”), in region 11.21.
• (18,648,855-21,505,417): These are the deletion coordinates. They mark the exact starting and ending points of the missing DNA segment.
• x1: This indicates the copy number. We usually have two copies of every gene (one from each parent). The “x1” (or sometimes “del”) means there is only one copy instead of two—confirming a deletion.

Deletion Size: 3 Megabases vs. 1.5 Megabases

By subtracting the starting coordinate from the ending coordinate, specialists calculate the deletion size. For example, in the coordinates above, subtracting 18,648,855 from 21,505,417 equals 2,856,562—or roughly 2.85 million base pairs.

About 85% to 90% of individuals with this syndrome have this “typical” deletion that is roughly 3 Megabases (Mb) long, meaning they are missing about 3 million DNA letters ^[6][7].

Some individuals have smaller “nested” or atypical deletions, often around 1.5 Megabases ^[6][7]. However, because the most critical genes are located in the region shared by both the 3 Mb and 1.5 Mb deletions, the overall size of the deletion does not strictly dictate how severe the syndrome will be ^[6][3]. Two people with the exact same deletion size can have very different medical needs ^[8][4].

Missing Genes You Should Know

Within that deleted segment of DNA are dozens of genes. Knowing the boundaries of the deletion helps geneticists know which specific genes are missing ^[1]. Important genes often discussed include:

• TBX1: This is the major gene responsible for many of the physical features of the syndrome. It plays a critical role in how the heart, aorta, palate (roof of the mouth), and throat structures form during early pregnancy ^[9][10][11].
• Other critical genes: The typically deleted region also contains genes like COMT and PRODH, which researchers study for their links to neurodevelopmental delays, learning challenges, and psychiatric risks (such as an increased risk for schizophrenia) ^[4][10].

If the deletion is “typical” and includes TBX1, it can also impact the development of the thymus gland, leading to lower levels of T-cells (white blood cells that fight infection) ^[12]. This means there may be a higher risk for infections. Research notes that rare, atypical deletions that sit further down the chromosome (distal deletions) and exclude TBX1 tend to have better T-cell counts ^[12][13].

Ultimately, because this is a complex multisystem condition, the care team will rely on thorough, multidisciplinary medical evaluations—checking the heart, calcium levels, immune system, and development—not just the genetic report to guide personalized treatment ^[8][14].