No single genetic test can find every cause of intellectual disability. Each test is designed to see certain types of DNA changes and misses others. The right test depends on your child’s features, history and family background.

The main tests for intellectual disability,
Karyotype. This looks at whole chromosomes under a microscope. It finds conditions such as Down syndrome but misses small deletions and single-gene changes.

Chromosomal microarray. This finds small missing or extra pieces of chromosomes. It cannot see changes inside a single gene.

Exome sequencing. This reads the protein-coding parts of about 20,000 genes. It finds many single-gene causes of intellectual disability. It usually cannot detect fragile X syndrome, some deletions or imprinting conditions.

Trio exome sequencing. This tests the child and both parents together. It makes it easier to tell whether a change is new in the child or inherited.

Genome sequencing. This reads almost all of the DNA, including many regions outside genes. Some repeat and imprinting conditions still need separate tests.

Fragile X test. This measures one specific repeated stretch of DNA in the FMR1 gene. Fragile X syndrome is the most common inherited cause of intellectual disability.

Metabolic tests. These look for chemical signs of metabolic conditions in blood or urine. Some of these conditions are treatable causes of intellectual disability.

Why exome sequencing cannot see fragile X

Fragile X syndrome is caused by a short stretch of DNA that repeats too many times. Exome sequencing reads DNA in small pieces, so it cannot accurately measure a long repeat. A child with intellectual disability and features of fragile X therefore needs the dedicated fragile X test, even after a normal exome result.

What the guidelines say

In 2021, the American College of Medical Genetics and Genomics recommended exome or genome sequencing as a first- or second-tier test for children with developmental delay or intellectual disability. In 2025, the American Academy of Pediatrics recommended exome or genome sequencing as a first-tier test for most children with unexplained intellectual disability. Across studies, exome or genome sequencing finds a cause in about 28% to 43% of children with intellectual disability. Chromosomal microarray alone finds a cause in about 15% to 20%.

How Genetidoc chooses a test

Team Genetidoc chooses the test after a detailed history and examination, not before:

When the features clearly point to one condition, a targeted test is chosen. Examples are a fragile X test, or methylation testing for Angelman syndrome.
When several causes of intellectual disability are possible, exome sequencing is usually chosen, often together with chromosomal microarray.
Genome sequencing is kept as an escalation step, when a genetic cause is strongly suspected but earlier tests have not found the answer.