What Is a Microdeletion and What Does It Cause?

A microdeletion is a small missing segment of a chromosome, typically too tiny to see under a standard microscope but large enough to remove one or more genes. These losses range from about a thousand to several million DNA base pairs and can disrupt development in ways that range from barely noticeable to profoundly life-altering. Because each deleted region takes out a different set of genes, microdeletions produce a wide spectrum of conditions affecting the heart, brain, immune system, and other organs. The story of what a microdeletion actually does depends almost entirely on which genes are lost, how many cells carry the deletion, and even which parent the affected chromosome came from.

How a Piece of Chromosome Goes Missing

Most microdeletions arise from errors during the formation of eggs or sperm. The most common mechanism is a process in which two stretches of DNA that look alike but sit in different locations on the chromosome mistakenly line up and swap material during cell division. Geneticists call these look-alike stretches low-copy repeats. When the cell’s recombination machinery treats them as matching partners, the segment of DNA between them can be lost entirely. Research has shown that the likelihood of this event increases when the flanking repeats are longer and decreases when the distance between them is greater.¹ In some well-studied cases, specific hotspots for these swaps have been conserved across millions of years of primate evolution, meaning the same chromosomal architecture that makes humans vulnerable to a particular microdeletion has been present since before our lineage split from other primates.²

Not every microdeletion follows that pattern. Some arise through different repair mistakes in which tiny stretches of shared sequence, sometimes just a few matching base pairs, guide the DNA-repair machinery to stitch together the wrong ends. These mechanisms tend to produce deletions that vary in size from person to person, even when they involve the same gene region.³ A third route involves a more blunt form of DNA repair that simply joins two broken chromosome ends together without relying on any sequence similarity at all.⁴ These different routes explain why some microdeletion syndromes are strikingly uniform in size across patients while others are highly variable.

The Most Recognized Microdeletion Syndromes

A handful of microdeletion syndromes are well-characterized enough to have names, clinical guidelines, and dedicated research communities. They illustrate just how different the consequences of a small chromosomal loss can be depending on the region involved.

22q11.2 Deletion Syndrome

Formerly known as DiGeorge syndrome or velocardiofacial syndrome, 22q11.2 deletion syndrome is one of the most common microdeletion disorders. It results from the loss of a small segment on chromosome 22 and affects multiple organ systems. Heart defects are present in roughly three-quarters of affected individuals, most often involving the outflow tracts of the heart.⁵ Beyond the heart, features can include palate abnormalities, immune deficiency from an underdeveloped thymus, low calcium levels, feeding difficulties, and speech delays. The presentation changes with age: children tend to show the congenital and developmental features, while adolescents and adults are at elevated risk for psychiatric illness, including anxiety, depression, and psychotic disorders.⁶ The range of possible symptoms has expanded considerably since the syndrome was first described, now encompassing autoimmune disease, kidney abnormalities, and gastrointestinal problems.⁷

Williams Syndrome

Williams syndrome involves a deletion on chromosome 7 that removes about 25 to 27 genes. It occurs in roughly one in every 7,500 people. The hallmark medical problem is cardiovascular disease, particularly a narrowing of the large arteries and most commonly the aorta just above the heart valve. People with Williams syndrome also have distinctive facial features, intellectual disability of varying degree, and a remarkably social personality often described as hypersociability.⁸ Because the deleted region is nearly the same size in most affected individuals, the condition illustrates how a deletion mediated by flanking repeat sequences can produce a relatively consistent set of features across patients.

1p36 Deletion Syndrome

When the tip of the short arm of chromosome 1 is lost, the result is 1p36 deletion syndrome, one of the most common terminal deletion syndromes. Typical features include intellectual disability, seizures, vision and hearing problems, short stature, distinctive facial features, and heart defects including structural malformations and cardiomyopathy.⁹ Detailed clinical studies have found that a large anterior fontanelle, low muscle tone, and growth delay are among the most frequently observed signs, alongside behavioral challenges.¹⁰

Prader-Willi and Angelman Syndromes

These two conditions share the same deleted region on chromosome 15 but produce completely different disorders depending on which parent’s chromosome carries the deletion. When the paternal copy is deleted, the result is Prader-Willi syndrome, characterized by insatiable appetite, obesity risk, and intellectual disability. When the maternal copy is deleted, the result is Angelman syndrome, marked by severe developmental delay, seizures, and a characteristically happy demeanor with frequent laughter.¹¹ The difference comes down to genomic imprinting: certain genes in this region are silenced on one parental copy and active only on the other. Microdeletions within a smaller control region, called the imprinting center, can also disrupt this silencing pattern and produce either syndrome without removing the genes themselves.¹²

Why the Same Deletion Can Affect People So Differently

One of the most unsettling aspects of microdeletions for families is that two people carrying what appears to be the same deletion can have dramatically different outcomes. A deletion at 16p11.2, for example, has been linked to both autism and intellectual disability, but it shows incomplete penetrance and variable expressivity, meaning some carriers are significantly affected and others have only mild or no symptoms. This unpredictability complicates genetic counseling and prognosis.

One major factor is mosaicism, a situation where only a fraction of a person’s cells carry the deletion while the rest are normal. In a study of 20 individuals with sporadic neurofibromatosis type 1 microdeletions, an unexpectedly high proportion, about 40%, turned out to be mosaic. None of those mosaic patients showed the intellectual disability and facial differences typically associated with the full deletion.¹³ Mosaicism can also make the deletion harder to detect and can lead to subtle enough symptoms in a parent that the condition goes unrecognized until a more severely affected child is born. In at least one documented family, mothers with a 9q34.3 microdeletion present in only some of their cells had nothing more than mild learning difficulties and subtle facial features, while their children, who carried the deletion in every cell, had a more recognizable syndrome.¹⁴

Mosaicism has also surfaced in unexpected diagnostic situations. Some children with Dravet syndrome, a severe form of epilepsy, were found to carry mosaic microdeletions involving the SCN1A gene that standard sequencing had missed entirely. Testing estimated the deletion was present in about 25 to 40% of their cells.¹⁵ These cases highlight that a negative genetic test does not always rule out a microdeletion when only part of the body’s cells are affected.

How Microdeletions Are Found

Traditional chromosome analysis, which involves staining chromosomes and looking at them under a microscope, can pick up large rearrangements but is blind to most microdeletions. The shift toward chromosomal microarray analysis transformed diagnostics. Microarray testing can detect submicroscopic gains and losses across the entire genome in a single test, and a consensus statement from clinical genetics organizations has recommended it as a first-line test for individuals with unexplained developmental delay, intellectual disability, autism, or multiple congenital anomalies. The diagnostic yield of microarray in these populations is roughly 15 to 20%, compared with about 3% for a standard karyotype.¹⁶ The technology has been validated with high sensitivity and specificity, and in several cases has uncovered additional small deletions or duplications that targeted tests like FISH had missed.¹⁷

In prenatal settings, microarray is increasingly offered alongside or instead of karyotyping, particularly when an ultrasound detects a structural abnormality. In pregnancies where a standard karyotype is normal, microarray picks up a clinically important deletion or duplication in roughly 1% of cases with no ultrasound findings and about 6% of cases where a structural anomaly has been seen.¹⁸

Prenatal Screening and Its Limits

Noninvasive prenatal testing, which analyzes fragments of fetal DNA circulating in a pregnant person’s blood, has expanded beyond screening for common chromosome conditions like Down syndrome to include certain microdeletion syndromes. Panels now screen for deletions associated with conditions like DiGeorge syndrome, Prader-Willi/Angelman, 1p36 deletion, and others.¹⁹ However, the accuracy of these screens for microdeletions remains substantially lower than for whole-chromosome aneuploidies. In one cohort of over 8,000 pregnancies, only about 36% of the positive screening results for microdeletions turned out to be true positives after confirmatory testing.²⁰

One tricky source of false positives is the mother’s own DNA. If the pregnant person carries a small copy-number change in their genome, it can be misinterpreted as a fetal microdeletion. Researchers have developed algorithms designed to account for these maternal signals, but the problem has not been fully solved.²¹ For this reason, a positive screening result for a microdeletion should always be followed by a diagnostic test, usually amniocentesis or chorionic villus sampling with microarray, before any clinical decisions are made.

The Counseling Challenge of Uncertain Findings

One consequence of the power of modern genomic testing is that it regularly turns up deletions and duplications whose clinical meaning is unclear. These are often called variants of uncertain significance. When such a finding appears prenatally, it puts families and clinicians in a genuinely difficult position. The deletion is real, but the medical literature may have too few reported cases to predict what, if anything, it will cause. Genetic counselors have raised concerns about the potential for harm in these situations, including the emotional toll on expectant parents and the risk that an uncertain finding could influence pregnancy decisions in ways that are not well-supported by evidence.²²

Professional opinion on what to disclose is split. In one survey of healthcare professionals, most agreed that variants with truly unknown significance should not be disclosed to patients. But they were divided on variants with uncertain clinical significance, where some evidence of possible harm exists but the picture is incomplete. Some considered disclosure helpful for clinical monitoring and family preparation, while others saw it as a source of anxiety with no clear benefit.²³ There is no universal consensus on this yet, and practices vary between countries and even between hospitals within the same country.

De Novo Versus Inherited Microdeletions

Most of the well-known microdeletion syndromes arise de novo, meaning the deletion occurs for the first time in the affected individual and was not inherited from either parent. A large genome-wide study identified 66 de novo copy-number changes by comparing parents to offspring in nearly 10,000 parent-child transmissions, and several of the recurrent deletions it found were significantly associated with schizophrenia risk.²⁴ Because severe psychiatric and developmental disorders reduce the likelihood of reproduction, there is ongoing selection pressure against these deletions in the population. They persist because they keep arising anew in each generation.

That said, not all microdeletions appear from nowhere. Some are inherited from a parent who carries the deletion in all their cells but is mildly affected or even apparently unaffected, a pattern seen with several 16p11.2 deletions linked to autism.²⁵ And as discussed in the context of mosaicism, some parents carry a deletion in only a fraction of their cells, which can lead to recurrence in multiple children even though the parent appears healthy. When a microdeletion is found in a child, genetic testing of both parents is standard practice to assess recurrence risk for future pregnancies.

Microdeletions in Cancer

The term microdeletion usually comes up in the context of inherited or congenital genetic conditions, but small deletions also play a significant role in cancer biology. Tumor cells frequently acquire deletions that knock out tumor suppressor genes, the genes whose job is to keep cell growth in check. A large-scale analysis of homozygous deletions across many cancer types identified 16 established tumor suppressors, along with 32 additional regions showing signs that the deletion was actively favored by the cancer’s evolution, and the researchers proposed candidate suppressor genes in 26 of those regions.²⁶ In pediatric kidney tumors known as Wilms tumors, focal deletions have pointed researchers toward previously unknown candidate tumor suppressor genes on chromosomes 1, 7, 11, and 16.²⁷ These somatic deletions, acquired during a person’s lifetime in specific tissues, are fundamentally different from the germline microdeletions present from conception, but the underlying biology of gene loss driving disease is the same principle.

Living With a Microdeletion Syndrome

There is currently no way to replace a missing chromosomal segment, so management of microdeletion syndromes focuses on treating or monitoring each affected organ system. Guidelines tend to recommend a coordinated, multidisciplinary approach led by a primary care provider working alongside specialists. For 15q24 deletion syndrome, for instance, recommended baseline evaluations at the time of diagnosis include a heart ultrasound, hearing and vision tests, and developmental assessments, with ongoing monitoring of growth and feeding. Depending on the individual’s specific needs, specialists in immunology, endocrinology, orthopedics, neurology, and urology may be involved.²⁸ A similar framework applies to 16p11.2 deletion syndrome, where published health supervision guidelines emphasize early developmental support, assistive technology for learning challenges, and advocacy within the educational system.²⁹

For families, one of the most valuable steps after a diagnosis is connecting with condition-specific registries and support organizations. These groups can provide not only emotional support but also practical guidance on navigating educational services, medical surveillance schedules, and transition planning as a child approaches adulthood.

Research Using Lab-Grown Brain Models

Understanding exactly how a missing gene or set of genes alters brain development has been difficult, because researchers obviously cannot study the process directly in a developing human brain. Recent work using brain organoids, three-dimensional clusters of cells grown from patient-derived stem cells that mimic early brain tissue, has started to fill in some of those gaps. For neurofibromatosis type 1 microdeletions, organoids grown from patient cells revealed problems with neuron survival, differentiation, and maturation. The researchers traced these defects to a single gene called CRLF3 and a specific signaling pathway.³⁰

A similar approach has been applied to 22q11.2 deletion syndrome. Researchers generated thalamic organoids, modeling the brain structure that relays sensory information to the cortex, and found that neurons from deletion carriers showed excessive axon growth. They linked this to elevated levels of a gene called FOXP2, which in turn suppressed a guidance receptor called ROBO2 that normally helps keep axon growth in check.³¹ These kinds of studies do not translate immediately into treatments, but they are beginning to identify specific molecular targets that could eventually become the basis for therapies aimed at the downstream consequences of a deletion, even if the missing DNA itself cannot be restored.

Copy-Number Variation as Part of Normal Human Diversity

It is worth noting that not all deletions are harmful. The human genome is full of copy-number variation, stretches of DNA that are present in different numbers of copies from person to person. Some of these differences are entirely benign, functioning as normal polymorphic variation with no health consequences. Others have played a role in driving evolution, contributing to the birth of new genes and the reshuffling of existing ones over millions of years.³² The same architectural features of the genome that make disease-causing microdeletions possible, the repetitive sequences flanking important genes, also make the genome flexible enough to adapt. The line between a pathogenic microdeletion and a harmless variant is often drawn by which genes happen to fall within the deleted region and how sensitive those genes are to having only one working copy instead of two.